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GIT Logs

This is a list of recent commits to git.bioconductor.org, the devel(development) branch of the Bioconductor GIT repository.

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Package: msqrob2
Commit: 7b2399da99e81c40ec74e1b9b5a78b55f2e6c5ab
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 10:02:41 +0200
Commit message:

 Merge pull request #57 from StijnVandenbulcke/master

Updating News and Description files

Package: msqrob2
Commit: ebcf2e326b8fde40fe1df636b19a74f14afecb5c
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 10:01:54 +0200
Commit message:

 Update DESCRIPTION

Package: msqrob2
Commit: 2484c917edd8d03baaa6a041a858474841bf60ff
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 10:01:44 +0200
Commit message:

 Update NEWS.md

Package: msqrob2
Commit: adb3d405e420372b29f47c6e4ef019fec6bb00cb
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 09:59:25 +0200
Commit message:

 Update msqrob.R

Added a drop = FALSE argument, preventing possible issues

Package: msqrob2
Commit: a367242aa4e2df85e6799bfe7a7177c950907bb2
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 00:15:03 +0200
Commit message:

 Merge pull request #56 from StijnVandenbulcke/master

Fixed Issues

Package: msqrob2
Commit: eba0dacdbd57285e6e1b96ad6cba5384a18cf51f
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 00:11:31 +0200
Commit message:

 Update msqrob.R

Fixed issue where model matrix was subsetted incorrectly

Package: msqrob2
Commit: f8cbcc614626d455916d1815d04369117f2cb0bc
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-24 23:08:57 +0200
Commit message:

 Update msqrob.R

Fixed bug related to ordering of levels when using ridge regression

Package: fenr
Commit: 65bdf0dec710a63e6c897b47ee97beec8ed38d7a
Author: Marek Gierlinski <Marek.Gierlinski@gmail.com>
Date: 2024-04-25 10:59:00 +0100
Commit message:

 Version 1.0.9

Package: fenr
Commit: 1800e36dc4b37c32b416827b8b0d1d93b5546416
Author: Marek Gierlinski <Marek.Gierlinski@gmail.com>
Date: 2024-04-25 10:38:57 +0100
Commit message:

 Increased default timeout

Package: fenr
Commit: 6c8200475f68415a5fa6f5538d9a570026827410
Author: Marek Gierlinski <Marek.Gierlinski@gmail.com>
Date: 2024-04-25 10:27:28 +0100
Commit message:

 Increased default timeout

Package: msa
Commit: 84c8ed5da8a54629d13a0318e4a5b9dec6f7e428
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-25 01:04:18 -0700
Commit message:

 fix link to BLOSUM62

Package: msa
Commit: 0e98500b59f80e7bb1429f601ec07235be7252b7
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-25 00:50:13 -0700
Commit message:

 one more tweak

Package: rawDiag
Commit: 5e50e8651ae024b4e2525cdab6504fa6f30746af
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:46:45 +0200
Commit message:

 doc: reran roxygen2::roxygenize()

Package: rawDiag
Commit: b787c763f9d9e4fc7e7fb9391bb2e3eedf982263
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:46:18 +0200
Commit message:

 build: add shiny

Package: rawDiag
Commit: 880250c2d90a9c8d6b362a70ecaf9a8fb211b9b7
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:44:50 +0200
Commit message:

 doc: bump version 0.99.34

Package: rawDiag
Commit: 5873904b12bd8c22abebc371e0d1c6da23357d17
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:41:37 +0200
Commit message:

 fix: handle case having no 'Ms' scans

E.g., caused by using an SRM method

as a result there is no TIC and BPC available
(at least acc. to our def. of BCP and TIC).

Package: rawDiag
Commit: 70a1e6598dcb4aa32304b305f8e81b8744097102
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:18:54 +0200
Commit message:

 doc: add install notes for installing missing pkgs

Package: msa
Commit: 06c35ab3d6ce5d1991fc0dfbd2b82f02fd1f0e28
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:40:57 +0200
Commit message:

 Fixes to account for move of matrices to the 'pwalign' package

Package: msa
Commit: 2b74e88cb76c88d51c1ce8e4e91ac34770573756
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:38:50 +0200
Commit message:

 Fix of help page for msaConservationScore() to account for move of matrices to the 'pwalign' package

Package: MAGAR
Commit: 3c3e5ae93afdd9e7972e80cc8b5e806193eefab2
Author: Michael Scherer <s9mlscer@gmail.com>
Date: 2024-04-25 09:33:33 +0200
Commit message:

 Updated DESCRIPTION

Package: msa
Commit: 6fa77c8d54acbebc9232156a4b881fd0c8fc718a
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:32:44 +0200
Commit message:

 Merge remote-tracking branch 'refs/remotes/origin/master'

Package: msa
Commit: bf997e3b91ca667baad6cff24ebb0fc91604df8a
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:30:37 +0200
Commit message:

 Fix of typo in vignette source

Package: msa
Commit: b5bbad83331efbd1ae975c0bb76b884c8375770c
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:30:37 +0200
Commit message:

 Fix of typo in vignette source

Package: msa
Commit: c480f764f7dc9cdb498586c1b33b1a94409b691f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-25 00:23:53 -0700
Commit message:

 The BLOSUM matrices have moved from Biostrings to pwalign

Package: MatrixQCvis
Commit: 9b2c8c52aba722ed156b644d7e3456f7c16e640f
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2024-04-25 09:10:57 +0200
Commit message:

 bump version to 1.11.7

Package: MatrixQCvis
Commit: 4c5ff15c25b0aa999bc474b5b6ae3d228fb6d96f
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2024-04-23 16:06:44 +0200
Commit message:

 add dplyr:: in front of pull in vignette

Package: iPAC
Commit: c24b078859fba09c37df812505d03cde00ca5607
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 23:34:27 -0700
Commit message:

 Small tweak to NAMESPACE

Import selectively from Biostrings to avoid the following load-time
warning:
  replacing previous import ‘Biostrings::pairwiseAlignment’
  by ‘pwalign::pairwiseAlignment’ when loading ‘iPAC’

Package: scanMiRApp
Commit: 9e75eafa09eed5986877b705a45f852593c8030b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 23:08:02 -0700
Commit message:

 makeTxDbFromGRanges() has moved from GenomicFeatures to txdbmaker

Package: sangeranalyseR
Commit: 204e6de7e1175ea8daf09a61b39b89074ff8f803
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 22:51:33 -0700
Commit message:

 compareStrings() has moved from Biostrings to pwalign

Package: crisprShiny
Commit: f27faf49fa866d24de50ad99ef5a497564b7b098
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 22:39:11 -0700
Commit message:

 compareStrings() has moved from Biostrings to pwalign

Package: ClustIRR
Commit: 533da03929c24996ff75a48a6c1469090e3459c5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 22:27:12 -0700
Commit message:

 stringDist() and the BLOSUM matrices have moved from Biostrings to pwalign

Package: openPrimeR
Commit: 4217da8ccf83fa00012b3de3527b77dd30ca100c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 22:10:17 -0700
Commit message:

 pairwiseAlignment() and related have moved from Biostrings to pwalign

IMPORTANT NOTE to the maintainer of openPrimeR:
Running roxygen2::roxygenize() on the package generates 300+ man pages
that are not in git. Please roxygenize() the package and don't forget
to add the new man pages to git (with 'git add man/*') before you commit
and push. Thanks!

Package: hiReadsProcessor
Commit: 5ee9d977981b151228ea1b8a23fdf3137f178062
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 21:39:29 -0700
Commit message:

 pairwiseAlignment() has moved from Biostrings to pwalign

- Make necessary adjustments to DESCRIPTION and imports to account for
  pairwiseAlignment() being now in pwalign instead of Biostrings.

- Also remove Tutorial.R, Tutorial.html, and Tutorial.md from the
  vignettes/ folder. Only Tutorial.Rmd belongs to git. The other files
  get automatically generated and added to the resulting package source
  tarball by 'R CMD build', and so should not be added to git.

Package: scanMiR
Commit: f2b3ece1a58789acea1341059b2592acf7d81d19
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 21:09:06 -0700
Commit message:

 pairwiseAlignment() and related have moved from Biostrings to pwalign

Package: kmcut
Commit: d777f9a6564f24f110ba4c02e90c377cdd6f404b
Author: unknown <ikuznetsov@albany.edu>
Date: 2024-04-24 23:51:19 -0400
Commit message:

 This is completely updated version of the package that addresses all the changes. Detail responses are below.
COMMENT:
The vignette contains the following line:
Introduction to the KMCUT package
*  but the name of the package is kmcut (all lower-case). R in general, and package names in particular, are case-sensitive.

RESPONSE:
The package name was changed to lower-case letters.

COMMENT:
*  Man pages have very long titles, each of them made of several sentences that repeat exactly the content of the Description section. Good man page titles should be short (a few words only).

RESPONSE:
Titles of man pages were shortened.

COMMENT:
*  You seem to misunderstand the purpose of importing other packages in your package. The examples in most man pages start with many library() calls e.g. in kmoptpermcut:
library(survival)
library(stringr)
library(data.table)
library(tools)
library(pracma)
library(foreach)
library(doParallel)
library(parallel)
library(kmcut)
*  Please note that packages that are imported are automatically available to the code inside your package so there's no need to put the extra burden to manually load each of them on the user. For loading the kmcut package itself, a widely accepted convention is to not pollute the examples in the man pages of a given package (say foo) with explicit calls to library(foo). The reason for this convention is that it is considered reasonable to assume that the package is already loaded when the user is looking at its man pages.

RESPONSE:
All library() calls in examples were removed.

COMMENT:
*  Please minimize the dependencies of your package and only import what you actually need to import. For example, the package does not seem to use anything from the stringr package so that dependency is not needed. Please re-evaluate all the other dependencies and make sure to drop those that you don't need.

RESPONSE:
The dependencies on  and other unnecessary packages were removed.

COMMENT:
*  Also please re-evaluate the need for all the library() calls at the beginning of the vignette (although keeping library(kmcut) is fine there and is actually needed).

RESPONSE:
All library() calls at the beginning of the vignette were removed, except for library(kmcut)

 COMMENT:
*  Bioconductor recommend against the use of flatcase style for your function names (e.g. kmoptpermcut, transposetable, kmqcut, kmucut, etc...), as it makes the names hard to read and/or remember. Please use snake_case or camelCase instead.

RESPONSE:
All function names were changed to include underscores (as in  snake_case )

COMMENT:
*  About the file with gene expression-like features. The vignette says: "The first column must contain sample identifiers and and the first row must contain gene identifiers." Isn't it the otherway around?

RESPONSE:
You are correct. This error was fixed.

COMMENT:
*  The kmoptpermcut() function is extremely slow, to a point that seems to make it almost unsuitable for real-world data. For example, calling it on the example_genes_295.txt file provided in the package takes 89 sec on my laptop when n_iter is set to 1000. However, the file only contains 2 rows (i.e. 2 genes) and the man page for kmoptpermcut() recommends to set n_iter to 10,000. This means that using the recommended n_iter on a file with 100 genes will take more than 10 hours!

RESPONSE:
Unfortunately, km_opt_pcut() cannot be made much faster. It estimates the unknown sampling distribution of the test statistics by applying the permutation test, which is very slow. It is recommended that kmoptpermcut be run on at least 16 CPUs (this can be achieved on a low/midrange desktop or high-end laptop). This function is meant to be applied to a relatively small subset of candidate genes identified by the km_opt_scut function. The recommendation regarding application of km_opt_pcut() to a relatively small subset of genes identified by km_opt_scut() was added to the vignette. The size of the package's built-in example dataset was reduced to better reflect the number of samples in a real life dataset.

COMMENT:
*  How useful is the kmoptpermcut() function when called with wpdf=FALSE? In this case, the function will display a series of plot, one after the other, the next one replacing the previous one at a possibly fast pace, with barely enough time for the user to look at them!

RESPONSE:
When  km_opt_pcut()  is used with wpdf=FALSE from RStudio or R GUI, after the execution is over, the user can go back and forth through the plots by clicking  left  and  right  arrows. The main reason why this option was added is to provide a functionality to embed the graphs during the vignette compilation.

COMMENT:
*  If the goal is to make it as simple as possible for clinical oncologists or other scientists without strong programming skills to use the package, then some improvements on how errors are handled would be welcome. For example, I doubt that the targeted audience will be able to make sense of an error message like this one:
> kmoptscut(fname="survival_data_295.txt", sfname="example_genes_295b.txt")
Error in order(sdat$sample_id) : argument 1 is not a vector

RESPONSE:
The check of file existence and other argument checks were added to all functions.

COMMENT:
Documenting a function argument like this:
fname: character vector that specifies the name of the file etc...
*  without specifying that the character vector must be of length 1 suggests that the character vector could be of arbitrary length. Note that many functions in R that work on character data are vectorized and can handle a character vector of arbitrary length (e.g. tolower() or grepl()) but that doesn't seem to be the case here. Please disambiguate.

RESPONSE:
This was clarified in the updated version, all man pages now state that file name must be a character vector of length one.

COMMENT:
*  Finally note that coordinating right-censored survival data and gene expression-like features, and keeping them aligned when subsetting the data, is exactly what the SummarizedExperiment container is for. In your case, the SummarizedExperiment object would have the feature ids as rownames and the sample ids as colnames, and the right-censored survival time data would be stored in the colData component of the object. All you would need to do is implement a function that loads the input data in a SummarizedExperiment object e.g. load_kmcut_input(). The function would essentially do something like this:
load_kmcut_input <- function(epath, spath)
{
    edat <- read.delim(epath, header = TRUE, stringsAsFactors = FALSE)
    sdat <- read.delim(spath, header = TRUE, row.names = 1)
    ...
    ... some sanity checks about 'edat' and 'sdat'
    ...
    assay <- as.matrix(edat[ , -1])
    rownames(assay) <- edat[ , 1]
    coldata <- DataFrame(sdat)
    SummarizedExperiment(list(expr=assay), colData=coldata)
}
Typical use:
epath <- system.file("extdata", "example_genes_295.txt", package = "kmcut")
spath <- system.file("extdata", "survival_data_295.txt", package = "kmcut")
kmcut_se <- load_kmcut_input(epath, spath)
kmcut_se
12. Then all functions in the package would take such object as input instead of fname and sfname, making them slightly easier to use and avoiding the need to load the same data from disk again and again.
Furthermore, the user can now subset the data at will by doing things like kmcut_se["MYH2", c("SEQC_NB002", "SEQC_NB003")] with the guarantee that the right-censored survival data and the gene expression-like data remain aligned at all time, hence avoiding the need of utility functions like extractrows() or extractcolumns(). Every Bioconductor user knows how to perform such basic subsetting operation. This is the true Bioconductor way and it has proven to be a very valuable approach to software design.

RESPONSE:
All core function were changed to take a SummarizedExperiment object as input. A function that creates SummarizedExperiment objects from two input files, create_se_object(), was also added.
 </pre>
    </div>
  
    
      Package: CardinalWorkflows

      Commit: b1bfb8147012177dcb3013c82c3b6b30f63c09d7

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 23:48:45 -0400

      Commit message:


	  
		 v1.35.5
 
    
  
    
      Package: CardinalWorkflows

      Commit: 9592e29305454c76bb2ead990cc1905fda0a1875

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 12:19:16 -0400

      Commit message:


	  
		 add startup message
 
    
  
    
      Package: svaNUMT

      Commit: 03c48947a951f4e594b991eb78bdf46d09e82dcb

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-24 20:48:02 -0700

      Commit message:


	  
		 pairwiseAlignment() and related have moved from Biostrings to pwalign
 
    
  
    
      Package: GenomicFeatures

      Commit: 755b3dfc8347b279be5986a14a9aed8e0b83da1f

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-24 20:34:48 -0700

      Commit message:


	  
		 minor cosmetic
 
    
  
    
      Package: BSgenome

      Commit: a1925b59a6ddb038c2e0e9fb101ab1ef6506c48d

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-24 20:33:23 -0700

      Commit message:


	  
		 minor cosmetic
 
    
  
    
      Package: Biostrings

      Commit: d9cc6dbe7b5d69998fb9ef404f781bae23942bfa

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-24 20:31:05 -0700

      Commit message:


	  
		 minor cosmetic
 
    
  
    
      Package: Cardinal

      Commit: 6a2edd3b33fdec8212c59ce9bc5d886a8d54cb91

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 23:26:35 -0400

      Commit message:


	  
		 v3.5.4
 
    
  
    
      Package: Cardinal

      Commit: 897a331f948583e196f348a8727943dde3fc647a

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 22:27:04 -0400

      Commit message:


	  
		 add image3D back again
 
    
  
    
      Package: Cardinal

      Commit: f764446047b2b4b707d0bef2035c6fd2d2cc9e0d

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 18:11:04 -0400

      Commit message:


	  
		 add check arg to readMSIData(), add is3D method again
 
    
  
    
      Package: Cardinal

      Commit: 016548d5552e447f8e42d63f5df485b91fada283

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 14:33:23 -0400

      Commit message:


	  
		 fix removing position columns with coord()<-
 
    
  
    
      Package: Cardinal

      Commit: c65c45fb518ffc1e7c085d24f89b90a28a87542c

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 14:08:18 -0400

      Commit message:


	  
		 fix deprecated functionality for iData()
 
    
  
    
      Package: Cardinal

      Commit: cda4f817b69f240d259c1c1b822a8aa5ffae9ea7

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 13:59:45 -0400

      Commit message:


	  
		 export vizi_style() + vizi_engine(); rearrange some docs
 
    
  
    
      Package: Cardinal

      Commit: 0e732ecac6bbcb6bc2261d11e157da85c156297a

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-23 20:59:43 -0400

      Commit message:


	  
		 fix pls coef plotting; update gitignore
 
    
  
    
      Package: LinTInd

      Commit: c6348376cdd8db9c0147c29c82ef8db90758768d

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-24 20:22:08 -0700

      Commit message:


	  
		 pairwiseAlignment() and related have moved from Biostrings to pwalign
 
    
  
    
      Package: matter

      Commit: e56f72cc327446ce750bfa43910284577c7be61e

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 23:00:15 -0400

      Commit message:


	  
		 v2.5.18
 
    
  
    
      Package: matter

      Commit: faab5e97b9ce2a7d71c8be911aa03e7322f4e6a8

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 22:26:33 -0400

      Commit message:


	  
		 fix plotly error on non-gridded voxels
 
    
  
    
      Package: matter

      Commit: be1e2dc4db28c825c9471df3eef2ca7995097360

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 20:47:20 -0400

      Commit message:


	  
		 update NEWS w/ plot_image 3d support
 
    
  
    
      Package: matter

      Commit: 5347ef8429f5290e508dfa043d3526153de4d14e

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 20:42:00 -0400

      Commit message:


	  
		 add 3d support to plot_image()
 
    
  
    
      Package: matter

      Commit: e5f8fb00e30f5fe10e060ef28690d86501155bd2

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 18:34:06 -0400

      Commit message:


	  
		 change parse_formula eval default
 
    
  
    
      Package: matter

      Commit: 842476fb74ef07f956b9cedd7b80ef6e3f70852c

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 18:24:34 -0400

      Commit message:


	  
		 update NEWS re: parse_formula()
 
    
  
    
      Package: matter

      Commit: 55dcb6a99bdc192779b66118e99c11c12dbd2ed0

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 18:22:45 -0400

      Commit message:


	  
		 export parse_formula()
 
    
  
    
      Package: matter

      Commit: aaf2cb7d77d9bd80f8997742bd5bf41069c9846c

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 12:51:41 -0400

      Commit message:


	  
		 add vizi_engine()
 
    
  
    
      Package: matter

      Commit: 8bec4ea2bdd2853d0b651df5b62ba23e2f00d089

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-23 23:33:17 -0400

      Commit message:


	  
		 cleanup aspect ratio
 
    
  
    
      Package: matter

      Commit: 9869773e4d2a682104319be799980471ae257919

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-23 23:08:54 -0400

      Commit message:


	  
		 cleanup plot_init and friends; fix free facet axes for plotly
 
    
  
    
      Package: matter

      Commit: 81597937e13be62f95ad8c1c07b1d793a82fe6dc

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-23 22:36:22 -0400

      Commit message:


	  
		 fix aspect ratio for plotly
 
    
  
    
      Package: matter

      Commit: 41180b91ca64995e69d9bc17876a6aedc115eac4

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-23 22:13:42 -0400

      Commit message:


	  
		 fix facet plot initialization for plotly
 
    
  
    
      Package: matter

      Commit: 20c71cc6f40f63c05942f6db6f66f20fc2180132

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-23 21:49:38 -0400

      Commit message:


	  
		 fix reversed axes for plotly
 
    
  
    
      Package: matter

      Commit: b1056cd19130802fe9690664294b5d89305778b7

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-23 21:23:43 -0400

      Commit message:


	  
		 fix bug in flooring x-axis for mark=peak
 
    
  
    
      Package: matter

      Commit: 7fa4599b09cb84f81e875cd81802dd567d862c63

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-23 20:51:35 -0400

      Commit message:


	  
		 fix bugs in pixels channels
 
    
  
    
      Package: matter

      Commit: 3210959700cc66cdf819511251df694abc558497

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-23 20:37:39 -0400

      Commit message:


	  
		 cleanup NAMESPACE
 
    
  
    
      Package: matter

      Commit: ac8343d7c579348fe5e1ed727b2ac1ab2caeccee

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-23 20:34:39 -0400

      Commit message:


	  
		 finish up 1st draft plotly support
 
    
  
    
      Package: matter

      Commit: 8f87381e3cb1d14234defd949327abc4ec6aa3d7

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-23 17:32:13 -0400

      Commit message:


	  
		 update plotly support for legends
 
    
  
    
      Package: matter

      Commit: bdca4767e1dd6aaea46197e87273aca810d22dc5

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-22 17:43:15 -0400

      Commit message:


	  
		 added mark vizi_bars
 
    
  
    
      Package: matter

      Commit: ca2e8eeae2f5502ffc1a91aff9cd26e6637eb994

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-21 16:53:08 -0400

      Commit message:


	  
		 add vizi engine=plotly support
 
    
  
    
      Package: IsoformSwitchAnalyzeR

      Commit: bd680e93c87f1778af432ac250d8c4b7e16860b9

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-24 19:22:58 -0700

      Commit message:


	  
		 Add 2 missing symbols to NAMESPACE

Many many more are missing as reported by 'R CMD check' under "Undefined
global functions or variables".
See for example CHECK result on Bioconductor daily report:
https://bioconductor.org/checkResults/3.19/bioc-LATEST/IsoformSwitchAnalyzeR
Note that this is unrelated to the move of pairwiseAlignment() to the
new pwalign package (previous commit).
 
    
  
    
      Package: SCArray.sat

      Commit: e3c68e5ff4ccd85d5fcb786b22924ea8c5ace72e

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2024-04-24 21:27:47 -0500

      Commit message:


	  
		 update for Seurat v5
 
    
  
    
      Package: IsoformSwitchAnalyzeR

      Commit: 4c35fe8431c65942402f6494d60a0ca8493c3319

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-24 19:11:45 -0700

      Commit message:


	  
		 pairwiseAlignment() has moved from Biostrings to pwalign
 
    
  
    
      Package: SPLINTER

      Commit: 2aade96cb831ce64901e9d6bc1a9a79602fc6c3c

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-24 16:05:00 -0700

      Commit message:


	  
		 pairwiseAlignment() and related have moved from Biostrings to pwalign
 
    
  
    
      Package: RTCGAToolbox

      Commit: 4420e7ae0852afd3b3722730c11c54f1293e3152

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 19:05:47 -0400

      Commit message:


	  
		 version bump 2.33.3
 
    
  
    
      Package: RTCGAToolbox

      Commit: 185354d884067ec75aaa004b17e93ddea8e254ec

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 19:05:45 -0400

      Commit message:


	  
		 update NEWS file
 
    
  
    
      Package: BiocHubsShiny

      Commit: a2353e2b2139bd2ba223422c5e57c851f8dbc1e2

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 17:56:10 -0400

      Commit message:


	  
		 version bump 1.3.1
 
    
  
    
      Package: BiocHubsShiny

      Commit: e788b358db99ec4015200ce8afd900f8eec876e4

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 17:56:03 -0400

      Commit message:


	  
		 update NEWS file
 
    
  
    
      Package: TENxIO

      Commit: 30b79e52886101801e12939ae2261654a9509276

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 17:51:10 -0400

      Commit message:


	  
		 version bump 1.5.4
 
    
  
    
      Package: TENxIO

      Commit: feb03d484960a651d71de8ddce7d327bc5256552

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 17:51:09 -0400

      Commit message:


	  
		 update NEWS file
 
    
  
    
      Package: pwalign

      Commit: b6da850610afe7c8201131a3738fabbd0b8277d2

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-22 22:22:07 -0700

      Commit message:


	  
		 small tweaks
 
    
  
    
      Package: BiocBaseUtils

      Commit: c5278d3d8b6ea63e96ce86b9fcf5588b46fc9b80

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 17:38:39 -0400

      Commit message:


	  
		 version bump 1.5.2
 
    
  
    
      Package: BiocBaseUtils

      Commit: 75e7a008dad940354493f6bc37d4043c1002c1e9

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 17:38:31 -0400

      Commit message:


	  
		 update NEWS
 
    
  
    
      Package: BiocBaseUtils

      Commit: 9d877ee6e7cde9d8c612f83c1651a4bfd62e0ada

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 17:28:26 -0400

      Commit message:


	  
		 add checkInstalled function
 
    
  
    
      Package: CardinalIO

      Commit: 6f5fbb25ec9513600a9d8bc0f150aa8caea545f9

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 17:25:31 -0400

      Commit message:


	  
		 v1.1.6 fix error if extraArrays not found
 
    
  
    
      Package: OmnipathR

      Commit: 442b9cf43368e72c6915878654bd9b80be2f0141

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-24 23:18:30 +0200

      Commit message:


	  
		 Bump version: 3.11.13 → 3.11.14
 
    
  
    
      Package: OmnipathR

      Commit: 6e8f2ce899b9ed5767af40580896f0e7f36a57b8

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-24 23:18:25 +0200

      Commit message:


	  
		 namespace update
 
    
  
    
      Package: OmnipathR

      Commit: e05841c293e7b12956757b52f97605ffcf29dc85

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-01-16 13:34:04 +0100

      Commit message:


	  
		 `misc`: some more operator and formatting routines
 
    
  
    
      Package: OmnipathR

      Commit: 38893e92422297e74395e0afc27214d4b6a92afc

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-01-24 02:12:11 +0100

      Commit message:


	  
		 `for_organism`: fixed: custom mapping erased the result
 
    
  
    
      Package: OmnipathR

      Commit: b25bd513fbf8c98d35d3a6908432f0b35729a745

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-01-19 12:53:53 +0100

      Commit message:


	  
		 `misc`: `maybe_call`, `maybe_get`: clean wrappers around `get` optionally calling a func
 
    
  
    
      Package: OmnipathR

      Commit: 8efe882a3bcc58444ad9b6611fcdc172fd36ef7b

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-01-19 12:52:43 +0100

      Commit message:


	  
		 read built-in organism support data into pkg env on load
 
    
  
    
      Package: OmnipathR

      Commit: 22dafedc289105917a65a1f8f636daa939ca963d

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-01-18 01:19:19 +0100

      Commit message:


	  
		 use `read_yaml` instead of `yaml.load_file`
 
    
  
    
      Package: OmnipathR

      Commit: e35ff45eab2ef61e4d248ad9e8f4efac776c523e

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-24 23:15:32 +0200

      Commit message:


	  
		 namespace update with `organism_for`
 
    
  
    
      Package: OmnipathR

      Commit: 53ef0c5f024b4f7a1149db1792183d74d5529e8c

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-01-18 01:18:31 +0100

      Commit message:


	  
		 `taxonomy`: `organism_for` - access organism support of resources
 
    
  
    
      Package: OmnipathR

      Commit: 6d0a0ced5356b17c8924da652f2a54b1d9cfc3f5

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-24 23:08:36 +0200

      Commit message:


	  
		 `oma`: URL encode ID types for query string
 
    
  
    
      Package: OmnipathR

      Commit: 444b78d5f1bc8dcc7c9fd5d8f5ba5696dc20755f

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-24 23:08:16 +0200

      Commit message:


	  
		 `oma`: error handling for incorrect ID types in query string (that results less columns than expected)
 
    
  
    
      Package: OmnipathR

      Commit: 83f2cf1ab1c1f418ab2df911f6bf023c0b8e2541

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-24 23:07:11 +0200

      Commit message:


	  
		 `oma`: updated reader parameters for new TSV layout
 
    
  
    
      Package: OmnipathR

      Commit: 76b66ab93810b1e1a5b262804631f56bcedb5f42

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-24 23:06:22 +0200

      Commit message:


	  
		 `oma`: `oma_pairwise_translated`: generic function for all ID types that OMA does not provide
 
    
  
    
      Package: OmnipathR

      Commit: 59358703ab6e8308adbe095f1e7cea589f9a428a

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-24 23:04:03 +0200

      Commit message:


	  
		 `oma`: use `organism_for`
 
    
  
    
      Package: OmnipathR

      Commit: 78faa6ba2ebcacb7b6ef8b15b39ab9d74af8d98e

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-24 23:02:00 +0200

      Commit message:


	  
		 `oma`: organism config
 
    
  
    
      Package: OmnipathR

      Commit: d2d8874aae758294b146f4697f5745534c52b867

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-24 23:00:09 +0200

      Commit message:


	  
		 `oma`: updated API URL
 
    
  
    
      Package: OmnipathR

      Commit: 29f02990a335082f6e1841a4c8a5e15c26e7f983

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-24 22:47:05 +0200

      Commit message:


	  
		 `oma`: fixed ID type codes
 
    
  
    
      Package: OmnipathR

      Commit: ba8fab39f56c1a6c72c9f295b9a8e1b3e9dc79a7

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-24 22:39:34 +0200

      Commit message:


	  
		 `oma`: function to list all the OMA organism codes
 
    
  
    
      Package: OmnipathR

      Commit: 83cb658b2b7cc120a7933c0b18b406c732b8b728

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-13 11:44:04 +0200

      Commit message:


	  
		 docs update
 
    
  
    
      Package: OmnipathR

      Commit: c379027ed9f494a24e6b3d28b653f1b4b919d4ce

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-13 11:39:12 +0200

      Commit message:


	  
		 pkgdown site rebuild
 
    
  
    
      Package: OmnipathR

      Commit: 440e99037a97bafbd2562e17b586010acebd82aa

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-12 03:49:06 +0200

      Commit message:


	  
		 Bump version: 3.11.12 → 3.11.13
 
    
  
    
      Package: OmnipathR

      Commit: b75ed2297e70bbe9a465337470b7a8e10c80a305

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-12 03:48:59 +0200

      Commit message:


	  
		 docs rebuild
 
    
  
    
      Package: OmnipathR

      Commit: de31b50f3dc8741a60c40d27881ade6f2b51a973

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-12 03:48:05 +0200

      Commit message:


	  
		 function for resource name matching (primary, secondary)
 
    
  
    
      Package: OmnipathR

      Commit: e1dbcee625ca0ae4690a0b2bd65e3d4468e8b398

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-12 03:47:32 +0200

      Commit message:


	  
		 `only_from`: fixed: do not insert resource prefix in case of zero references
 
    
  
    
      Package: OmnipathR

      Commit: 94a40e6b619757d0c6e388ff7f286424a3f1a678

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-12 03:46:45 +0200

      Commit message:


	  
		 `from_evidences`: function for resource name construction
 
    
  
    
      Package: OmnipathR

      Commit: b9a3402285343c1f67f3170fbcc38a0fd126521f

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-12 01:21:11 +0200

      Commit message:


	  
		 `only_from`: remove records that remained without any evidence after filtering (no idea how this happened before bc I have not encountered such records until now)
 
    
  
    
      Package: OmnipathR

      Commit: c61403ac5408fa92715b007374fcfd6d77dd39c8

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-12 01:18:04 +0200

      Commit message:


	  
		 `exclude` and `.keep` parameters for `only_from` (`filter_evidences`): exclude certain resources; keep and update the "evidences" columns
 
    
  
    
      Package: OmnipathR

      Commit: 6ffb09fd26b4631b1598dafa9718e7c99eb35522

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-12 01:14:31 +0200

      Commit message:


	  
		 `evidences_from`: updating "evidences" column in `only_for`
 
    
  
    
      Package: OmnipathR

      Commit: f802029810dbd0268be57b44155e2b00fe11cb16

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-12 01:12:32 +0200

      Commit message:


	  
		 `match_evidence`: moved evidence matching into function (for evidence filtering)
 
    
  
    
      Package: OmnipathR

      Commit: bec3d0b930056fbcc6f231e26af03954217dc99b

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-10 13:53:03 +0200

      Commit message:


	  
		 Bump version: 3.11.11 → 3.11.12
 
    
  
    
      Package: OmnipathR

      Commit: 308e9e9e9519fec433ffb108a56b09a6decd2227

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-10 13:52:55 +0200

      Commit message:


	  
		 docs+pkgdown rebuild
 
    
  
    
      Package: OmnipathR

      Commit: 7189357b363345e36153267b34464551da8c2670

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-10 13:52:17 +0200

      Commit message:


	  
		 missing import
 
    
  
    
      Package: OmnipathR

      Commit: dd31d1a714e2dfad3dcb78034d496d5325487ff3

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-10 13:51:53 +0200

      Commit message:


	  
		 `resources_in`: collect resources from a data frame column
 
    
  
    
      Package: OmnipathR

      Commit: c7d361426fea6de02c9b48a4d7225f8b6607d899

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-10 13:48:36 +0200

      Commit message:


	  
		 `misc`: new helper function to unlist, unique and sort anything
 
    
  
    
      Package: OmnipathR

      Commit: 6305befd5585771a594c11e8b6f333cd606a2cca

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-09 18:14:16 +0200

      Commit message:


	  
		 Bump version: 3.11.10 → 3.11.11
 
    
  
    
      Package: OmnipathR

      Commit: 9437af175889ecefdd0ad093917aca664e08e4d9

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-09 18:08:28 +0200

      Commit message:


	  
		 `omnipath`: added `keep_evidences` to known parameters
 
    
  
    
      Package: OmnipathR

      Commit: 0b864ba3b1a603adb84243fd104b9d69de1b8d37

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-09 17:51:40 +0200

      Commit message:


	  
		 `evidences`: new arg `.keep` for `unnest_evidences` & `only_from`: keep the "evidences" column
 
    
  
    
      Package: OmnipathR

      Commit: 27c39acf65f8ae79ceb605b513a9a29d0d801cbe

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-09 17:49:20 +0200

      Commit message:


	  
		 little style corrections
 
    
  
    
      Package: OmnipathR

      Commit: 1b222ae2eb5ccced71a6e76f66fe26f5659397c3

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-09 17:48:57 +0200

      Commit message:


	  
		 `check_param/post_download`: `keep_evidences` if the evidences field was requested in the call
 
    
  
    
      Package: OmnipathR

      Commit: 71a0e9dac75aef2da17bc60a2e25a58109e4de49

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-09 15:57:03 +0200

      Commit message:


	  
		 pkgdown site: missing fonts
 
    
  
    
      Package: OmnipathR

      Commit: b95b7f9f7fdcf8fea5c97343a713dd05a1cd7469

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-09 15:54:30 +0200

      Commit message:


	  
		 pkgdown site: missing `font.css`
 
    
  
    
      Package: OmnipathR

      Commit: d1302c6913045b2b045abbb04e59a21477e146c0

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-09 15:48:53 +0200

      Commit message:


	  
		 pkgdown site bootstrap version update
 
    
  
    
      Package: OmnipathR

      Commit: 5a8e99657c0ff8ab85ff5b213fac960a28728bc0

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2024-04-07 18:00:44 +0200

      Commit message:


	  
		 pkgdown site rebuild
 
    
  
    
      Package: SingleCellMultiModal

      Commit: 3156f1ec6757c2e72cb7b8c25b05367acd1799fd

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 16:31:48 -0400

      Commit message:


	  
		 version bump 1.15.1
 
    
  
    
      Package: SingleCellMultiModal

      Commit: 47da2f18039f78125d35618885a9eb37542121dd

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 16:31:44 -0400

      Commit message:


	  
		 update NEWS
 
    
  
    
      Package: TCGAutils

      Commit: 3c6f903569c91a1231394b863bcdd10185091a8a

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 16:28:59 -0400

      Commit message:


	  
		 version bump 1.23.5
 
    
  
    
      Package: TCGAutils

      Commit: d40070f096a3607944fe39461231fd25ae99903e

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 16:28:56 -0400

      Commit message:


	  
		 update NEWS
 
    
  
    
      Package: RaggedExperiment

      Commit: 33a664778997a89406ebd260d3c43503394fe0b4

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 16:08:42 -0400

      Commit message:


	  
		 version bump 1.27.2
 
    
  
    
      Package: RaggedExperiment

      Commit: 32cc4590a3555cc026c371b3e0bbcb34984bec2d

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 16:08:37 -0400

      Commit message:


	  
		 update NEWS file
 
    
  
    
      Package: PureCN

      Commit: e2de63642828324c6261b798de89e813e91f2e08

      Author:  Markus Riester <markus.riester@novartis.com> 

      Date: 2024-04-24 15:17:15 -0400

      Commit message:


	  
		 Version bump.
 
    
  
    
      Package: PureCN

      Commit: 0edcd4dda56a384400e656a33e7916ee792d0e2a

      Author:  Markus Riester <markus.riester@novartis.com> 

      Date: 2024-04-24 15:15:01 -0400

      Commit message:


	  
		 Merge pull request #366 from lima1/issue_40

Issue 40 
    
  
    
      Package: PureCN

      Commit: 354413cc04eac7854b4ad4e8da0682203f6ce9aa

      Author:  Markus Riester <markus.riester@novartis.com> 

      Date: 2024-04-24 15:13:23 -0400

      Commit message:


	  
		 Merge pull request #365 from lima1/issue_363

Issue 363 
    
  
    
      Package: PureCN

      Commit: 37f0097a34030cd46a9c98d484a9700d57ce4a24

      Author:  Markus Riester <markus.riester@novartis.com> 

      Date: 2024-04-24 14:47:05 -0400

      Commit message:


	  
		 Attempt in fixing #363.
 
    
  
    
      Package: PureCN

      Commit: 822e4df325df61cf5bdd67478e660455ab385fa1

      Author:  Markus Riester <markus.riester@novartis.com> 

      Date: 2024-04-24 14:43:56 -0400

      Commit message:


	  
		 Attempt in fixing #363.
 
    
  
    
      Package: PureCN

      Commit: 5ec2226363f7e29b5886a87a5a32deb2a51fba88

      Author:  Markus Riester <markus.riester@novartis.com> 

      Date: 2024-04-01 11:39:12 -0400

      Commit message:


	  
		 Changed default of min.ratio to cleaner -8.
 
    
  
    
      Package: PureCN

      Commit: daf175bf1f3df9f06274d98a9e8c9e7b627826be

      Author:  Markus Riester <markus.riester@novartis.com> 

      Date: 2024-03-31 17:02:36 -0400

      Commit message:


	  
		 Fix broken test.
 
    
  
    
      Package: PureCN

      Commit: 5169999d03b10c9715039bd842b42bea73cef526

      Author:  Markus Riester <markus.riester@novartis.com> 

      Date: 2024-03-31 16:38:37 -0400

      Commit message:


	  
		 Attempt in a resolution for #40.
 
    
  
    
      Package: cBioPortalData

      Commit: 5838dd37d0dbd87f933ff2d5254aa4a9718a92ae

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 15:58:07 -0400

      Commit message:


	  
		 version bump 2.15.5
 
    
  
    
      Package: cBioPortalData

      Commit: 18136ee61e72096a277215df73325addbcac712b

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 15:58:02 -0400

      Commit message:


	  
		 update NEWS file
 
    
  
    
      Package: MSstatsPTM

      Commit: 804a856c6b5acac4db6842beb7826462704ee0fc

      Author:  devonjkohler <devonjkohler@gmail.com> 

      Date: 2024-04-24 15:57:43 -0400

      Commit message:


	  
		 version bump
 
    
  
    
      Package: MSstatsPTM

      Commit: 03c79cc7c829366fea418a672a47dd59b2ba9c37

      Author:  tonywu1999 <ant.wu@northeastern.edu> 

      Date: 2024-04-17 16:05:52 -0400

      Commit message:


	  
		 version bump 
    
  
    
      Package: MSstatsPTM

      Commit: 529334959fb0e8f7039c322f9d7d4bac7480a248

      Author:  tonywu1999 <ant.wu@northeastern.edu> 

      Date: 2024-04-17 16:04:14 -0400

      Commit message:


	  
		 feat(metamorpheus): Add global profiling feature to Metamorpheus PTM converter (#87)

* feat(metamorpheus): Add global profiling feature to Metamorpheus PTM converter

* add news on metamorpheus converter

* added more unit tests 
    
  
    
      Package: MSstatsPTM

      Commit: ad8cc8095d4702df3b844f983e171d44402a60a2

      Author:  tonywu1999 <ant.wu@northeastern.edu> 

      Date: 2024-03-04 09:58:50 -0500

      Commit message:


	  
		 version bump 
    
  
    
      Package: MSstatsPTM

      Commit: 7ff61cd341c98863345a84babd7f7cc6ca00c5c6

      Author:  tonywu1999 <ant.wu@northeastern.edu> 

      Date: 2024-03-04 09:58:20 -0500

      Commit message:


	  
		 feat(metamorpheus-converter): Create converter for Metamorpheus to MSstatsPTM format (#86)

* feat(metamorpheus-converter): Create converter for Metamorpheus to MSstatsPTM format

* fix: For ptm_input, filter out rows without targeted ptm 
    
  
    
      Package: MSstatsPTM

      Commit: fc90cfadb4170f7433a6297ea7867862154efdc1

      Author:  Devon Kohler <35807256+devonjkohler@users.noreply.github.com> 

      Date: 2024-02-14 15:00:51 -0500

      Commit message:


	  
		 Merge pull request #85 from Vitek-Lab/devel

bug fix 
    
  
    
      Package: MSstatsPTM

      Commit: 81da1b02f773a3b2b471c874bb53c81c80ea0ba7

      Author:  devonjkohler <devonjkohler@gmail.com> 

      Date: 2024-02-14 14:59:13 -0500

      Commit message:


	  
		 bug fix
 
    
  
    
      Package: MSstatsPTM

      Commit: 1c871e05ea28a844358775c3caca1428ccd48868

      Author:  Devon Kohler <35807256+devonjkohler@users.noreply.github.com> 

      Date: 2024-02-13 09:05:17 -0500

      Commit message:


	  
		 Merge branch 'RELEASE_3_18' into master 
    
  
    
      Package: MSstatsPTM

      Commit: 8378cced13cbb48c9e24d2535dbbb580c0984cc6

      Author:  Devon Kohler <35807256+devonjkohler@users.noreply.github.com> 

      Date: 2024-02-13 09:04:41 -0500

      Commit message:


	  
		 Merge pull request #83 from Vitek-Lab/devel

Devel 
    
  
    
      Package: MSstatsPTM

      Commit: 3e423f0dec1439aa86cd25b12e911d1eecac1653

      Author:  Devon Kohler <35807256+devonjkohler@users.noreply.github.com> 

      Date: 2024-02-04 11:26:17 +0200

      Commit message:


	  
		 version bump 
    
  
    
      Package: MSstatsPTM

      Commit: d6277b3dd9a233620169602bc97b118812faaeed

      Author:  Devon Kohler <35807256+devonjkohler@users.noreply.github.com> 

      Date: 2024-02-04 11:26:00 +0200

      Commit message:


	  
		 version bump 
    
  
    
      Package: MSstatsPTM

      Commit: a89750191ab0d44904be3170d8207dfddfcfc1ed

      Author:  Devon Kohler <35807256+devonjkohler@users.noreply.github.com> 

      Date: 2024-02-04 04:25:01 -0500

      Commit message:


	  
		 Merge pull request #82 from Vitek-Lab/master

PD bug fix 
    
  
    
      Package: MSstatsPTM

      Commit: f65db0aaf3cf59587a5105fa66fab2733b63a7e2

      Author:  devonjkohler <devonjkohler@gmail.com> 

      Date: 2024-01-31 14:43:13 -0500

      Commit message:


	  
		 remove model file
 
    
  
    
      Package: MSstatsPTM

      Commit: 9678ad1b046ea04b305dbe06e0182f63e0deece6

      Author:  Devon Kohler <35807256+devonjkohler@users.noreply.github.com> 

      Date: 2024-01-31 14:40:58 -0500

      Commit message:


	  
		 version bump 
    
  
    
      Package: MSstatsPTM

      Commit: b16eea1632d4ad0966b09894d6c937c15da67d11

      Author:  Devon Kohler <35807256+devonjkohler@users.noreply.github.com> 

      Date: 2024-01-31 14:40:34 -0500

      Commit message:


	  
		 Merge pull request #80 from Vitek-Lab/master

skyline bug 
    
  
    
      Package: cBioPortalData

      Commit: a6fba305b31b5c86b8ed728672a37ec762ce37e2

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 15:56:28 -0400

      Commit message:


	  
		 version bump 2.15.4
 
    
  
    
      Package: cBioPortalData

      Commit: 01fe589283a614b1e538e771a7addfa763455732

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 15:56:18 -0400

      Commit message:


	  
		 use package name in CITATION
 
    
  
    
      Package: cBioPortalData

      Commit: 1356109249899cbabdc0c5812bdc92745e3b14cb

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 15:52:32 -0400

      Commit message:


	  
		 update roxygen
 
    
  
    
      Package: cBioPortalData

      Commit: f4b327179a11761637ef5d09fd65c5c20f3ac2cc

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 15:52:22 -0400

      Commit message:


	  
		 avoid partial arg match warning
 
    
  
    
      Package: MultiAssayExperiment

      Commit: 8ed6e47ba6602df656fe8084a45df41f111863eb

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 15:41:54 -0400

      Commit message:


	  
		 version bump 1.29.2
 
    
  
    
      Package: MultiAssayExperiment

      Commit: cbec5787d0d1a52357b1dcde71c80806755b9bf4

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 15:40:17 -0400

      Commit message:


	  
		 update NEWS file
 
    
  
    
      Package: MultiAssayExperiment

      Commit: dbe61a1dcb972be3e4c81b0efa6e16d68785a098

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2024-04-24 15:40:02 -0400

      Commit message:


	  
		 update formatting in inst/REFERENCES.bib
 
    
  
    
      Package: MSstatsTMT

      Commit: 5c8b9e79093e9555a191b34505b4b2e7be390de2

      Author:  devonjkohler <devonjkohler@gmail.com> 

      Date: 2024-04-24 15:32:13 -0400

      Commit message:


	  
		 fix news file
 
    
  
    
      Package: MSstatsTMT

      Commit: cb5070d5b21b1af43301e5b4cf689a8f5344a2ef

      Author:  devonjkohler <devonjkohler@gmail.com> 

      Date: 2024-04-24 15:30:56 -0400

      Commit message:


	  
		 removed dup news file
 
    
  
    
      Package: MSstatsTMT

      Commit: d811d000e740cc472e9473cbfbf0eee9b549af24

      Author:  Devon Kohler <35807256+devonjkohler@users.noreply.github.com> 

      Date: 2024-04-24 15:30:21 -0400

      Commit message:


	  
		 Delete inst/NEWS.rd 
    
  
    
      Package: rtracklayer

      Commit: 843c950c4f6c1ae09d022dbb16e0b488bc8f37c7

      Author:  Michael Lawrence <michafla@gene.com> 

      Date: 2024-04-24 11:45:34 -0700

      Commit message:


	  
		 Merge pull request #118 from hpages/master

Fix linking error on Windows/Rtools44 
    
  
    
      Package: rtracklayer

      Commit: f70856a67e3e77ce2ee5189f76b59b922f58cd6b

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-21 10:45:40 -0700

      Commit message:


	  
		 Fix linking error on Windows/Rtools44
 
    
  
    
      Package: extraChIPs

      Commit: b317aa9500d182d00cf7acca7889e72b0d5049f6

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2024-04-25 02:30:06 +0930

      Commit message:


	  
		 Bugfix in mergeByHMP
 
    
  
    
      Package: epiregulon

      Commit: e8b6e4e55b75c34ee4ca4eca5de9f2bc9f4987b4

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-04-24 09:34:49 -0700

      Commit message:


	  
		 0.99.21
 
    
  
    
      Package: epiregulon.extra

      Commit: 1aa00b24a4c3334fe2bcddfcdb56b40a4179c7f4

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-04-24 08:31:07 -0700

      Commit message:


	  
		 0.99.17
 
    
  
    
      Package: epiregulon.extra

      Commit: c46c43cdfcda64af94305b0d6b41ae0498b27ad6

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-04-24 08:26:01 -0700

      Commit message:


	  
		 0.99.17
 
    
  
    
      Package: epiregulon.extra

      Commit: 049e0d0d2299c7e5d26d459944c635cdae6688e1

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-04-24 08:25:15 -0700

      Commit message:


	  
		 update news
 
    
  
    
      Package: epiregulon.extra

      Commit: 77bedde1dcdc7d9d4bdc81475490c002a43f488e

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-04-24 08:19:05 -0700

      Commit message:


	  
		 0.99.16
 
    
  
    
      Package: epiregulon.extra

      Commit: 556bc30332cf28683570092d4c15ef5598117cfd

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-04-24 08:18:37 -0700

      Commit message:


	  
		 BioC second view update news and NAMESPACE
 
    
  
    
      Package: epiregulon.extra

      Commit: bbee48b9bd542cf4a238df3a6e3d30fb4fc201ef

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-24 08:28:14 -0700

      Commit message:


	  
		 v0.99.16
 
    
  
    
      Package: epiregulon.extra

      Commit: de31ff1b88ab37d559a63129ac610275b242c0f5

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-24 07:42:04 -0700

      Commit message:


	  
		 Merge branch 'devel' of git.bioconductor.org:packages/epiregulon.extra into devel
 
    
  
    
      Package: epiregulon.extra

      Commit: fef941f9ce43fd014e29f0c837bf888d940e2bca

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-24 07:41:10 -0700

      Commit message:


	  
		 v0.99.15
 
    
  
    
      Package: epiregulon.extra

      Commit: f74a20256bbb431002f81a489b9d80437533d4ec

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-24 07:40:42 -0700

      Commit message:


	  
		 NEWS update
 
    
  
    
      Package: autonomics

      Commit: 092dbef5a333a39e16aa6457bde4d172d795dd79

      Author:  Aditya Bhagwat <aditya.bhagwat@uni-marburg.de> 

      Date: 2024-04-24 16:40:12 +0200

      Commit message:


	  
		 1.11.108 : create `fix_xlgenes`
 
    
  
    
      Package: ENmix

      Commit: b71062e45764d4bccc297ce7f2a53f4f9762c082

      Author:  Zongli Xu <xuz@niehs.nih.gov> 

      Date: 2024-04-24 10:40:27 -0400

      Commit message:


	  
		 bugfix

Signed-off-by: Zongli Xu <xuz@niehs.nih.gov>
 
    
  
    
      Package: zitools

      Commit: 5f45d497ccbf72259c0d37c386d7035b17000471

      Author:  cmeyring <122982530+cmeyring@users.noreply.github.com> 

      Date: 2024-04-24 16:21:43 +0200

      Commit message:


	  
		 Merge pull request #2 from kreutz-lab/devel

Devel 
    
  
    
      Package: zitools

      Commit: 33975f77ad062af7941c0154dcc9282cad181eb1

      Author:  cmeyring <122982530+cmeyring@users.noreply.github.com> 

      Date: 2024-04-24 16:19:37 +0200

      Commit message:


	  
		 Merge branch 'main' into devel 
    
  
    
      Package: zitools

      Commit: d3dcc636f73541f8a90d527f34be3a832fb358bc

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-24 16:13:37 +0200

      Commit message:


	  
		 Merge branch 'devel' of https://github.com/kreutz-lab/zitools into devel
 
    
  
    
      Package: zitools

      Commit: 0375ab1fb80a57300ceb18b54d6ab9327c9618f3

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-24 16:13:20 +0200

      Commit message:


	  
		 Updated README.md
 
    
  
    
      Package: MungeSumstats

      Commit: 16afb54bd60847003b45235287999200b40a272d

      Author:  Al-Murphy <alanmurph94@hotmail.com> 

      Date: 2024-04-24 15:17:29 +0100

      Commit message:


	  
		 enable local chain files
 
    
  
    
      Package: mia

      Commit: 9c1902ee4c712f6a136ed41ff72bc89687af39a1

      Author:  Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

      Date: 2024-04-24 16:46:20 +0300

      Commit message:


	  
		 importMetaphlan: bugfixes (#530)

 
    
  
    
      Package: mia

      Commit: 88947bba18ceba799589faa3d9870b7675ca952d

      Author:  Théotime Pralas <151254073+thpralas@users.noreply.github.com> 

      Date: 2024-04-24 16:20:40 +0300

      Commit message:


	  
		 Deprecate functions *_join (#515)

 
    
  
    
      Package: mia

      Commit: 1ab099804e92c7a41f8dfabc7c2f2a4c4cbbe2c9

      Author:  Théotime Pralas <151254073+thpralas@users.noreply.github.com> 

      Date: 2024-04-24 15:59:25 +0300

      Commit message:


	  
		 correct typo 'importBiom' to 'importBIOM'  (#525)

Co-authored-by: Leo Lahti <leo.lahti@iki.fi> 
    
  
    
      Package: mia

      Commit: 1b84bc52016b62041c275a24127d78219fc73a30

      Author:  Théotime Pralas <151254073+thpralas@users.noreply.github.com> 

      Date: 2024-04-19 16:36:57 +0300

      Commit message:


	  
		 deprecate subset* functions (#518)

 
    
  
    
      Package: mia

      Commit: 58cc49bd118ff2b75d12b2eca006cfd48c307933

      Author:  Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

      Date: 2024-04-18 10:30:43 +0300

      Commit message:


	  
		 Revert "Issue 334 estimate diversity" (#516)

 
    
  
    
      Package: mia

      Commit: c96a4e5d31362e3aa8abbb359110f7f099cff7dd

      Author:  nmdegunst <74536546+Insaynoah@users.noreply.github.com> 

      Date: 2024-04-17 10:19:22 +0300

      Commit message:


	  
		 Issue 334 estimate diversity (#514)

 
    
  
    
      Package: mia

      Commit: f0d3436b7df37cddd1193967644ede26cdd19f76

      Author:  Théotime Pralas <151254073+thpralas@users.noreply.github.com> 

      Date: 2024-04-16 15:47:51 +0300

      Commit message:


	  
		 Explain difference between phylogenetic and hierarchy trees (#510)

 
    
  
    
      Package: mia

      Commit: b7dd1c27318731d5cc5042695d35ae657816d086

      Author:  Théotime Pralas <151254073+thpralas@users.noreply.github.com> 

      Date: 2024-04-15 15:05:40 +0300

      Commit message:


	  
		 rename importers to standardize "import" terminology (#505)

Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 
    
  
    
      Package: epiregulon

      Commit: be942f92d7e1e446f0f09c56d8aa3faf86d1b637

      Author:  TomVuod <tomwlo@gmail.com> 

      Date: 2024-04-24 06:31:01 -0700

      Commit message:


	  
		 news update
 
    
  
    
      Package: epiregulon

      Commit: bcef194ccc0d242cf4fc9e62aa4d051eca2cc58e

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-04-22 21:25:50 -0700

      Commit message:


	  
		 edit vignette
 
    
  
    
      Package: scaeData

      Commit: 064c3c76baa5da2f4b9843386ea6ec4ab5f43bcf

      Author:  Ahmad Al Ajami <ahmad.alajami@kgu.de> 

      Date: 2024-04-24 15:08:00 +0200

      Commit message:


	  
		 fixed a typo in the lookup table of pbmc 5k dataset; version bump triggered
 
    
  
    
      Package: methodical

      Commit: 5e6d3a23270abdfbb9a725184713e5b39d7dfae7

      Author:  richardheery <richardheery@gmail.com> 

      Date: 2024-04-24 14:44:31 +0200

      Commit message:


	  
		 Bumped version
 
    
  
    
      Package: atena

      Commit: e814a13d541840de228930a6dcdb8cd154cced5e

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2024-04-24 13:54:58 +0200

      Commit message:


	  
		 Reduced execution time in some of the examples
 
    
  
    
      Package: zitools

      Commit: 859a17096bdc3bcecef4ebe296b4a845ae6ffc32

      Author:  cmeyring <122982530+cmeyring@users.noreply.github.com> 

      Date: 2024-04-24 13:25:37 +0200

      Commit message:


	  
		 Update DESCRIPTION 
    
  
    
      Package: zitools

      Commit: 02a2cc453a567b253307b95d25c4014c0cbb0b03

      Author:  cmeyring <122982530+cmeyring@users.noreply.github.com> 

      Date: 2024-04-24 13:21:27 +0200

      Commit message:


	  
		 Merge pull request #1 from kreutz-lab/devel

Devel 
    
  
    
      Package: zitools

      Commit: 0d3ac13d07890743ee28a81a1f6a56e6f68ee675

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-24 12:56:47 +0200

      Commit message:


	  
		 update DESCRIPTION and Version Number
 
    
  
    
      Package: MungeSumstats

      Commit: bf83eaacc908c0913dbb945cfc42055156d11206

      Author:  Al-Murphy <alanmurph94@hotmail.com> 

      Date: 2024-04-24 11:21:11 +0100

      Commit message:


	  
		 drop miss dat select cols
 
    
  
    
      Package: MungeSumstats

      Commit: 588a898fd64cf3e3ae4134c7729667c960038b25

      Author:  Alan Murphy <62257358+Al-Murphy@users.noreply.github.com> 

      Date: 2024-04-24 10:19:49 +0100

      Commit message:


	  
		 Merge pull request #182 from rmgpanw/dev_check_missing_data_cols

add `drop_na_cols` parameter to `format_sumstats()` 
    
  
    
      Package: MungeSumstats

      Commit: b88a70dcf44378c267972c238bf63f1c9012e18e

      Author:  rmgpanw <alasdair.warwick06@gmail.com> 

      Date: 2024-04-22 22:47:32 +0100

      Commit message:


	  
		 add `drop_na_cols` parameter to `format_sumstats()` and `check_miss_data()`
 
    
  
    
      Package: tripr

      Commit: df7ee2395eb83e3ff432372a7f20769adaafb1bc

      Author:  KonstantinosKardamiliotis <k.kardamiliotis@gmail.com> 

      Date: 2024-04-24 11:38:57 +0300

      Commit message:


	  
		 Bioconductor 3.19 release commit
 
    
  
    
      Package: fenr

      Commit: 104b0d4ae30e83255a4be0355b46d1d425e6b26e

      Author:  Marek Gierlinski <Marek.Gierlinski@gmail.com> 

      Date: 2024-04-24 09:15:02 +0100

      Commit message:


	  
		 Version 1.0.8. Improving error handling
 
    
  
    
      Package: cleaver

      Commit: a85947b60d7b846a5ca95f3979908b5439fa7ae6

      Author:  Sebastian Gibb <mail@sebastiangibb.de> 

      Date: 2024-04-24 10:15:30 +0200

      Commit message:


	  
		 ci: upgrade to biocthis::use_bioc_github_action('devel')
 
    
  
    
      Package: cleaver

      Commit: 5f02afa33a2b2aabb0cc1998d11abe861a202021

      Author:  Sebastian Gibb <mail@sebastiangibb.de> 

      Date: 2024-04-24 09:57:59 +0200

      Commit message:


	  
		 chore: bump version
 
    
  
    
      Package: cleaver

      Commit: c5b3b798847bb58b269da49fb7850fe93e3a288c

      Author:  Sebastian Gibb <mail@sebastiangibb.de> 

      Date: 2024-04-24 09:57:48 +0200

      Commit message:


	  
		 fix: use along.with instead of along to avoid partial matching
 
    
  
    
      Package: cleaver

      Commit: c2db5c2776ae4e82b29f049b6b754b0a430979de

      Author:  Sebastian Gibb <mail@sebastiangibb.de> 

      Date: 2024-04-24 09:56:55 +0200

      Commit message:


	  
		 feat: add trypsin-{high,low,simple}
 
    
  
    
      Package: SFEData

      Commit: 63324c09ad8c6393fe382b197013d2c1117782f9

      Author:  Lambda Moses <dlu2@caltech.edu> 

      Date: 2024-04-24 01:07:53 -0700

      Commit message:


	  
		 Added note on raw bytes in XeniumOutput
 
    
  
    
      Package: SFEData

      Commit: cf613beee8aaac7a72a228838be94e3805debd9e

      Author:  Lambda Moses <dlu2@caltech.edu> 

      Date: 2024-04-24 01:04:22 -0700

      Commit message:


	  
		 Made XOA v2 data subset. Cropping the multi file OME-TIFF was the worst pain in the ass.
 
    
  
    
      Package: SFEData

      Commit: 9bf639c9154186bdfc1ad178f805b0f8d31830c9

      Author:  Lambda Moses <dlu2@caltech.edu> 

      Date: 2024-04-23 18:10:25 -0700

      Commit message:


	  
		 Added Seurat test data
 
    
  
    
      Package: zitools

      Commit: eec747685335757efb0281bfc130aa7dff38b81f

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-24 09:44:49 +0200

      Commit message:


	  
		 Update News File
 
    
  
    
      Package: zitools

      Commit: 0e1aa28728d066775c8cc1692d6fe7211c478417

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-24 09:18:59 +0200

      Commit message:


	  
		 Update NEWS File
 
    
  
    
      Package: atena

      Commit: ad226bc0b12ec6b4aa938aa3a59bad03ba2ba614

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2024-04-24 09:12:58 +0200

      Commit message:


	  
		 Updated vignette, added progress reporting messages
 
    
  
    
      Package: dar

      Commit: d86de14543ad38aa8fcbe749ae0fe9a11ab020ef

      Author:  xec-cm <fcatala@irsicaixa.es> 

      Date: 2024-04-24 08:28:11 +0200

      Commit message:


	  
		 bump
 
    
  
    
      Package: dar

      Commit: 29a3d4adc846ef559a3d41aefd3d2053219a3e2a

      Author:  xec-cm <fcatala@irsicaixa.es> 

      Date: 2024-04-24 08:26:53 +0200

      Commit message:


	  
		 Update data_import.Rmd
 
    
  
    
      Package: amplican

      Commit: b6cdef124c10cdb9b1eca5baebcc5fbccdbf14d5

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 22:40:12 -0700

      Commit message:


	  
		 import coverage from IRanges
 
    
  
    
      Package: amplican

      Commit: 1389265bbdd6362fe075efa9ec2358bc73fbb995

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 22:34:34 -0700

      Commit message:


	  
		 pairwiseAlignment() and related have moved from Biostring to pwalign
 
    
  
    
      Package: ClassifyR

      Commit: beae92285cd98ea487eb5337f71356d4b83ad4b2

      Author:  Dario Strbenac <dario@maths.usyd.edu.au> 

      Date: 2024-04-24 15:25:36 +1000

      Commit message:


	  
		 - News file updated in preparation for next Bioconductor release.
 
    
  
    
      Package: Rcpi

      Commit: 6bd4a59c378da46c1e9c6ce59ca3b0ed16b49838

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 21:59:03 -0700

      Commit message:


	  
		 pairwiseAlignment() has moved from Biostrings to pwalign
 
    
  
    
      Package: QuartPAC

      Commit: ab5838bf15eeb726a428c2b89afc07f3587aa2ef

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 21:45:33 -0700

      Commit message:


	  
		 pairwiseAlignment() has moved from Biostrings to pwalign
 
    
  
    
      Package: GUIDEseq

      Commit: 27314e39213fb51ed312f31cb7d26523224bfe4b

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 21:08:55 -0700

      Commit message:


	  
		 pairwiseAlignment() and related have moved from Biostrings to pwalign
 
    
  
    
      Package: girafe

      Commit: 7fd255495078c36e9b6a1a5c8c8fcef491c3fd9a

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 20:46:26 -0700

      Commit message:


	  
		 pairwiseAlignment() has moved from Biostrings to pwalign
 
    
  
    
      Package: IMMAN

      Commit: 298baab116ffae96e3963dd501ceddd68f9a45bf

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 19:51:55 -0700

      Commit message:


	  
		 pairwiseAlignment() has moved from Biostrings to pwalign
 
    
  
    
      Package: QSutils

      Commit: a2ba66be100df1a2dd8a52d422bb1ca1c32d221c

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 19:45:18 -0700

      Commit message:


	  
		 pairwiseAlignment() has moved from Biostrings to pwalign
 
    
  
    
      Package: methylscaper

      Commit: e3b95d38d37d250607520b951734e275b886d344

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 19:34:25 -0700

      Commit message:


	  
		 pairwiseAlignment() and related have moved from Biostrings to pwalign
 
    
  
    
      Package: DMRcate

      Commit: 3bfb7c55412ff594c79f38ab78af7028261bfed1

      Author:  timpet <t.peters@garvan.org.au> 

      Date: 2024-04-24 12:25:00 +1000

      Commit message:


	  
		 DMRcate_2.99.6
 
    
  
    
      Package: sangerseqR

      Commit: a3fbf6b28fdf531b774a2b42dda6c0285d05063c

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 19:22:11 -0700

      Commit message:


	  
		 pairwiseAlignment() has moved from Biostrings to pwalign
 
    
  
    
      Package: BioNAR

      Commit: 14ae53f85bada21668274b55bdb779e45cb10e3a

      Author:  Anatoly Sorokin <lptolik@gmail.com> 

      Date: 2024-04-24 11:12:43 +0900

      Commit message:


	  
		 version bumps up
 
    
  
    
      Package: BioNAR

      Commit: ed15467d3de2d5558769fbd297714cd33a3e2316

      Author:  Anatoly Sorokin <lptolik@gmail.com> 

      Date: 2024-04-24 11:12:31 +0900

      Commit message:


	  
		 add GRPEL1 name to all invocation of annotateGeneName
 
    
  
    
      Package: BioNAR

      Commit: d8c789c47b655fdbf8e77cb4c21920bb8430dbb4

      Author:  Anatoly Sorokin <lptolik@gmail.com> 

      Date: 2024-04-24 11:11:38 +0900

      Commit message:


	  
		 review the plot snapshots
 
    
  
    
      Package: R453Plus1Toolbox

      Commit: aede3c3dde6a95b6adc8cca2ed6deead4464e127

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 19:07:18 -0700

      Commit message:


	  
		 pairwiseAlignment() and related have moved from Biostrings to pwalign
 
    
  
    
      Package: edgeR

      Commit: 992f8dc3e8d8dfb33be933a24c0aa230c4770e9e

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2024-04-24 11:52:05 +1000

      Commit message:


	  
		 edgeR 4.1.26
- Seurat2PB() now checks for Seurat version.
- Allow AveLogCPM to be NULL in .computePriorS2().
- Edit description of `design` argument in roast.DGEGLM().
 
    
  
    
      Package: epiregulon.extra

      Commit: aec704abd39f6fe6fdb9fab5ecf233c2fd051618

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2024-04-23 18:51:24 -0700

      Commit message:


	  
		 0.99.15 BioC review
 
    
  
    
      Package: epiregulon.extra

      Commit: 58c84936f9a92e7edfb36b4bc94fcfaef63be464

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-23 14:05:54 -0700

      Commit message:


	  
		 typo
 
    
  
    
      Package: epiregulon.extra

      Commit: 1ccf0570017e32fa9c426132328dcc4aeb9887e0

      Author:  Tomasz Wlodarczyk <tomwlo@gmail.com> 

      Date: 2024-04-23 11:50:25 -0700

      Commit message:


	  
		 Changes after BioC review
 
    
  
    
      Package: MSA2dist

      Commit: e0d3b1e9106bd4d133deeccf70af028dc5ff0216

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 18:50:22 -0700

      Commit message:


	  
		 Substitution matrices BLOSUM* and PAM* have moved from Biostrings to pwalign
 
    
  
    
      Package: MSA2dist

      Commit: dbfa5346e8c60cd5f17906e25fb340de6b55387b

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 18:45:02 -0700

      Commit message:


	  
		 pairwiseAlignment() has moved from Biostrings to pwalign
 
    
  
    
      Package: SeqArray

      Commit: 9c6161626b8744bedf251c8ef8fc79d00a1a8c4c

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2024-04-23 20:17:46 -0500

      Commit message:


	  
		 update seqApply()
 
    
  
    
      Package: StructuralVariantAnnotation

      Commit: ecffeacf00477ca87ee47250f9aa77eba3326ed4

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 18:14:47 -0700

      Commit message:


	  
		 pairwiseAlignment() and related have moved from Biostrings to pwalign
 
    
  
    
      Package: DominoEffect

      Commit: 834c920f724087ab52dc0f43d36863777dd6a1c3

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 17:51:12 -0700

      Commit message:


	  
		 pairwiseAlignment() and pid() have moved from Biostrings to pwalign
 
    
  
    
      Package: HTSeqGenie

      Commit: a5c0bdda1546ce65830aa5ac992fcc305d3bd9b8

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 17:33:48 -0700

      Commit message:


	  
		 pairwiseAlignment() has moved from Biostrings to pwalign
 
    
  
    
      Package: XNAString

      Commit: 638859d4b089458bec9a43dd145cc6d99f80518a

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 17:20:33 -0700

      Commit message:


	  
		 nucleotideSubstitutionMatrix() and pairwiseAlignment() have moved from Biostrings to pwalign
 
    
  
    
      Package: clusterExperiment

      Commit: ff4b21f8ed5b588395a50d5874b74acc1ad1ba04

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2024-04-23 16:54:06 -0700

      Commit message:


	  
		 passes tests
 
    
  
    
      Package: motifbreakR

      Commit: 227e6df5ea6b780c51f9db103ed07d495752cef0

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 16:41:48 -0700

      Commit message:


	  
		 pairwiseAlignment() has moved from Biostrings to pwalign
 
    
  
    
      Package: idpr

      Commit: 3cd821c30b0d66a9723301a1e09c5a6183981b5e

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 16:28:08 -0700

      Commit message:


	  
		 pairwiseAlignment() has moved from Biostrings to pwalign
 
    
  
    
      Package: ShortRead

      Commit: 4699244596409a99845cf573d84af5cf083e8239

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 16:01:33 -0700

      Commit message:


	  
		 Import selectively from Biostrings rather than in bulk

This is to avoid load-time warning:
  replacing previous import ‘Biostrings::pairwiseAlignment’
  by ‘pwalign::pairwiseAlignment’ when loading ‘ShortRead’
 
    
  
    
      Package: gemma.R

      Commit: 9a1b28df08d41ac56e06ce88b4d62ebfeaea8c95

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-04-23 15:59:00 -0700

      Commit message:


	  
		 version bump
 
    
  
    
      Package: gemma.R

      Commit: 465edd3aa0825b710b9623cd724db8ec91ea9810

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-04-23 15:58:37 -0700

      Commit message:


	  
		 fix title
 
    
  
    
      Package: gemma.R

      Commit: 6468a31dd2f6311aad7ba3cb5151abb8f0b727e7

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-04-12 16:45:03 -0700

      Commit message:


	  
		 add news of 3.0
 
    
  
    
      Package: gemma.R

      Commit: 1fca17b04cb1d6a6c0c195d119164e2d8a43a1f3

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-04-12 16:29:46 -0700

      Commit message:


	  
		 few things to ignore
 
    
  
    
      Package: gemma.R

      Commit: b3345a26f8094785439a7599e4bee2e8aa048aa8

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2024-04-12 16:28:50 -0700

      Commit message:


	  
		 delete html
 
    
  
    
      Package: RSVSim

      Commit: edfc0c7ad251f66e1e51623b507dc7cf37f48947

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 15:35:06 -0700

      Commit message:


	  
		 Add pwalign to Suggests

compareSVs() uses nucleotideSubstitutionMatrix() and pairwiseAlignment()
internally which have moved from Biostrings to pwalign.
 
    
  
    
      Package: MSstats

      Commit: 5a5c036ee37decb13298ba428d93d95290a5c428

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2024-04-24 00:26:27 +0200

      Commit message:


	  
		 removed error log
 
    
  
    
      Package: BioCor

      Commit: 8233e6a4579fe99d451faabc9f350b5da3f8be73

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2024-04-23 23:39:15 +0200

      Commit message:


	  
		 Prepare NEWS so that it matches in the release
 
    
  
    
      Package: MSstats

      Commit: 3cecb354760bb869d4dbe0756135f9ce37bb37c4

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2024-04-23 22:53:42 +0200

      Commit message:


	  
		 removed error log
 
    
  
    
      Package: gDRcore

      Commit: 968d74c797c5655a33637485e0be9c70d823acf3

      Author:  gDR team <gdr-support-d@gene.com> 

      Date: 2024-04-23 20:34:40 +0000

      Commit message:


	  
		 Merge branch 'main' into devel
 
    
  
    
      Package: gDRcore

      Commit: b1d4e3adbeef4169dba69c7ee8c9aec8344e7dde

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2024-04-23 22:34:25 +0200

      Commit message:


	  
		 Merge pull request #147 from gdrplatform/GDR-2506

Gdr 2506 
    
  
    
      Package: gDRcore

      Commit: b4dfef4cf61af317187c76847241e86560aca64e

      Author:  czechb3 <bartosz.w.czech@gmail.com> 

      Date: 2024-04-23 20:42:17 +0200

      Commit message:


	  
		 ci: resolve conflict
 
    
  
    
      Package: gDRcore

      Commit: ced2cfd0b1ca4e00ee34182619fdcae9093dfc7b

      Author:  czechb3 <bartosz.w.czech@gmail.com> 

      Date: 2024-04-23 11:13:18 +0200

      Commit message:


	  
		 doc: update as per review (II)
 
    
  
    
      Package: gDRcore

      Commit: 637043f92915cb1decdc7c36bee032e5a9cfa4d7

      Author:  czechb3 <bartosz.w.czech@gmail.com> 

      Date: 2024-04-23 10:41:42 +0200

      Commit message:


	  
		 doc: udpate as per review
 
    
  
    
      Package: gDRcore

      Commit: aa450c6e8cd7d8735e8d9810ce07ecca45bd9504

      Author:  czechb3 <bartosz.w.czech@gmail.com> 

      Date: 2024-04-22 17:16:53 +0200

      Commit message:


	  
		 chore: bump version and update NEWS.md
 
    
  
    
      Package: gDRcore

      Commit: 403afffebaca199aad415b702a7f269151769d1a

      Author:  czechb3 <bartosz.w.czech@gmail.com> 

      Date: 2024-04-22 17:16:08 +0200

      Commit message:


	  
		 doc: add vignette for data annotation
 
    
  
    
      Package: zitools

      Commit: cf2da098373546c4ee561431b769c49870af6221

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-23 15:18:48 +0200

      Commit message:


	  
		 Update Version Number
 
    
  
    
      Package: zitools

      Commit: 2900c7888d3ce7049f04aee7b11c61bb20e19cb9

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-22 10:40:22 +0200

      Commit message:


	  
		 change Vignette Header
 
    
  
    
      Package: zitools

      Commit: 91fef13c2b202e8d947e0b84c50781efc2305fdc

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-08 15:32:05 +0200

      Commit message:


	  
		 Update R Dependency
 
    
  
    
      Package: zitools

      Commit: 82af89d9ebbd644b03d9d59ee0e307f6e5bb1c27

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-08 15:14:13 +0200

      Commit message:


	  
		 address Bioconductor Comments
 
    
  
    
      Package: zitools

      Commit: b71f50f56212e6c83098b4f6e935bbdfd64e4b32

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-06 09:02:24 +0200

      Commit message:


	  
		 Adress Bioconductor comments
 
    
  
    
      Package: zitools

      Commit: 5bfef97c2689fc06244924eff33d46b923884ed8

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-06 08:11:35 +0200

      Commit message:


	  
		 adress Bioconductor comments
 
    
  
    
      Package: zitools

      Commit: 233dc44cb97ce618c8e35bb2a5833e501e7ae90f

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-06 08:10:06 +0200

      Commit message:


	  
		 adress Bioconductor comments
 
    
  
    
      Package: zitools

      Commit: 1e306eaf2b8306c1432ac79c162c252597f3dfc7

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-05 00:28:56 +0200

      Commit message:


	  
		 minor changes
 
    
  
    
      Package: zitools

      Commit: aa81a2e8e8f0abdb7a672a99fabb0fb2483a80ab

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-04 15:20:46 +0200

      Commit message:


	  
		 minor changes
 
    
  
    
      Package: zitools

      Commit: fd12869c8374daa68b5a322fc92314c1a3fe03f2

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-04 12:39:33 +0200

      Commit message:


	  
		 Merge branch 'main' of https://github.com/kreutz-lab/zitools
 
    
  
    
      Package: zitools

      Commit: df5d46079a9c54438c738fa428ce96656192d065

      Author:  cmeyring <carlotta-meyring@web.de> 

      Date: 2024-04-04 12:39:12 +0200

      Commit message:


	  
		 Adress Bioconductor changes
 
    
  
    
      Package: zitools

      Commit: 4eabb857af3ece6cdc8992b51cbc73a4fd4e41a8

      Author:  cmeyring <122982530+cmeyring@users.noreply.github.com> 

      Date: 2024-04-04 12:00:37 +0200

      Commit message:


	  
		 Create NEWS.md 
    
  
    
      Package: zitools

      Commit: 41fb2cf196706ad66993439cb7c2b8e83803200e

      Author:  cmeyring <122982530+cmeyring@users.noreply.github.com> 

      Date: 2024-04-03 07:58:24 +0200

      Commit message:


	  
		 Update README.md 
    
  
    
      Package: BatchQC

      Commit: bbf6cb9a7a8820b3ff4b7d2b47bc015cf68c7d5d

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-04-23 15:38:42 -0400

      Commit message:


	  
		 Update numbering in Intro vignette
 
    
  
    
      Package: iPAC

      Commit: 67a43c7463970e629960086cf4a06727c193536f

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 12:31:23 -0700

      Commit message:


	  
		 pairwiseAlignment() has moved from Biostrings to pwalign
 
    
  
    
      Package: MethTargetedNGS

      Commit: 4b0586630fdbeeebe405ca9da2295742941109bb

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 12:07:27 -0700

      Commit message:


	  
		 pairwiseAlignment() and nucleotideSubstitutionMatrix() have moved from Biostrings to pwalign
 
    
  
    
      Package: enhancerHomologSearch

      Commit: b67050aabe3fbf986ade258dcc7da057c5909d11

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 11:56:07 -0700

      Commit message:


	  
		 unaligned() has moved from Biostrings to pwalign
 
    
  
    
      Package: gDRcore

      Commit: cac1766f14fdbb3bf1291c74e05294246a1e2c00

      Author:  gDR team <gdr-support-d@gene.com> 

      Date: 2024-04-23 18:41:12 +0000

      Commit message:


	  
		 Merge branch 'main' into devel
 
    
  
    
      Package: gDRcore

      Commit: d0caaee2b3e9acf8d092a0d9137d129d24876fca

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2024-04-23 20:40:58 +0200

      Commit message:


	  
		 Merge pull request #146 from gdrplatform/GDR-2505

Gdr 2505 
    
  
    
      Package: gDRcore

      Commit: 24b866523d0422cfb616da4b82c7b635baa1f4f9

      Author:  czechb3 <bartosz.w.czech@gmail.com> 

      Date: 2024-04-23 11:31:21 +0200

      Commit message:


	  
		 refactor: reoxygenate
 
    
  
    
      Package: gDRcore

      Commit: 601885437b85a7565c6d5c41cbf9f0cd21f3d05e

      Author:  czechb3 <bartosz.w.czech@gmail.com> 

      Date: 2024-04-23 11:25:33 +0200

      Commit message:


	  
		 doc: update documentation
 
    
  
    
      Package: gDRcore

      Commit: cdb5220cdbf79194210a879fbbfcdceb27e8ec79

      Author:  czechb3 <bartosz.w.czech@gmail.com> 

      Date: 2024-04-23 11:23:53 +0200

      Commit message:


	  
		 doc: update env vars
 
    
  
    
      Package: gDRcore

      Commit: 4d4b29b2b0fa3036ba6c5dfb34026ed345cc5343

      Author:  czechb3 <bartosz.w.czech@gmail.com> 

      Date: 2024-04-23 08:53:25 +0200

      Commit message:


	  
		 refactor: update as per questions
 
    
  
    
      Package: gDRcore

      Commit: 148ef077ceba5406d91fd553753d7d52cfdd1e27

      Author:  czechb3 <bartosz.w.czech@gmail.com> 

      Date: 2024-04-22 10:25:55 +0200

      Commit message:


	  
		 chore: bump version and update NEWS.md
 
    
  
    
      Package: gDRcore

      Commit: 6d7afb123860a31cd1bf282ff054d9f70b64a5f3

      Author:  czechb3 <bartosz.w.czech@gmail.com> 

      Date: 2024-04-22 10:25:09 +0200

      Commit message:


	  
		 test: update unit tests
 
    
  
    
      Package: gDRcore

      Commit: d770d63909fb4a7bb3afc160fdffac83e2f7d69a

      Author:  czechb3 <bartosz.w.czech@gmail.com> 

      Date: 2024-04-22 10:25:02 +0200

      Commit message:


	  
		 refactor: reoxygenate
 
    
  
    
      Package: gDRcore

      Commit: a50ccd8ce1ee497abd9ba0a4c132eefff79cffcd

      Author:  czechb3 <bartosz.w.czech@gmail.com> 

      Date: 2024-04-22 10:24:41 +0200

      Commit message:


	  
		 feat: add support for external files with annotation
 
    
  
    
      Package: CNEr

      Commit: 11d7b371bc7eff182dd2eea4f006399e946b825d

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 11:40:06 -0700

      Commit message:


	  
		 compareStrings() has moved from Biostrings to pwalign
 
    
  
    
      Package: BatchQC

      Commit: 447afb52263e346edf736048d3ea88905a4db229

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-04-23 14:28:12 -0400

      Commit message:


	  
		 update version number
 
    
  
    
      Package: BatchQC

      Commit: a7aa66b391576069a78f080338fb53f768035352

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-04-23 14:27:45 -0400

      Commit message:


	  
		 update spacing
 
    
  
    
      Package: BatchQC

      Commit: 29f95bbfdcc6f599bf116c0c4b5a838edd53fab9

      Author:  Jessica <102758461+jessmcc22@users.noreply.github.com> 

      Date: 2024-04-23 14:24:40 -0400

      Commit message:


	  
		 Merge pull request #94 from jessmcc22/devel

Update assay name to underscores 
    
  
    
      Package: BatchQC

      Commit: 25a184324e25a00c8b6cd7720de8e7d2b7968ced

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-04-23 14:21:55 -0400

      Commit message:


	  
		 Update assay name to underscores
 
    
  
    
      Package: RnBeads.hg38

      Commit: 0cd6253b6a535c827644d077414dba4163b52fba

      Author:  Fabian Müller <fmueller@mpi-inf.mpg.de> 

      Date: 2024-04-23 20:15:36 +0200

      Commit message:


	  
		 gitignore
 
    
  
    
      Package: RnBeads.hg38

      Commit: 674e1b65afde1a39c2a31ef80ea4285187a3d335

      Author:  Fabian Müller <fmueller@mpi-inf.mpg.de> 

      Date: 2024-04-23 20:13:28 +0200

      Commit message:


	  
		 Major hg38 update including EPICv2 support
 
    
  
    
      Package: ChIPpeakAnno

      Commit: 9e0412d3b6d46acbbbfac7ffd2eb2a5b721f33e3

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 11:14:00 -0700

      Commit message:


	  
		 pairwiseAlignment() has moved from Biostrings to pwalign
 
    
  
    
      Package: TFBSTools

      Commit: f3a764486bb113c81aa15b7b8da0fa239e1a7e24

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 11:11:36 -0700

      Commit message:


	  
		 The PairwiseAlignments class has moved from Biostrings to pwalign
 
    
  
    
      Package: RnBeads.hg38

      Commit: 8ff9c195d5024b11c593d34f5c7e88b24d1e321b

      Author:  Fabian Müller <fmueller@mpi-inf.mpg.de> 

      Date: 2024-04-23 08:29:05 +0200

      Commit message:


	  
		 Description update and commit check
 
    
  
    
      Package: ShortRead

      Commit: d1a4e25f00a7bf9ef3518d777894079b8b18d2db

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 10:46:45 -0700

      Commit message:


	  
		 pairwiseAlignment() has moved from Biostrings to pwalign
 
    
  
    
      Package: DECIPHER

      Commit: 986760602875b50d2b0b8ff727086210d1d3b7da

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-23 10:21:30 -0700

      Commit message:


	  
		 small edit
 
    
  
    
      Package: singleCellTK

      Commit: feb7d1950e5eb27ddf7bdeadf77775d32cb64a8b

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2024-04-23 13:10:37 -0400

      Commit message:


	  
		 Un-deprecate
 
    
  
    
      Package: MSstatsTMT

      Commit: ffcde2e2e81a9f65409fcd4fedf9f920d6d11749

      Author:  devonjkohler <devonjkohler@gmail.com> 

      Date: 2024-04-23 13:04:49 -0400

      Commit message:


	  
		 merge conflict
 
    
  
    
      Package: MSstatsTMT

      Commit: 79fbeb9f515c9222761475de8ef80becacf0bf38

      Author:  devonjkohler <devonjkohler@gmail.com> 

      Date: 2024-04-23 12:54:43 -0400

      Commit message:


	  
		 updated package maintainer
 
    
  
    
      Package: MSstatsTMT

      Commit: a70308cd7d170ce77ed9eb07e5ed7be5ec60a06e

      Author:  Devon Kohler <35807256+devonjkohler@users.noreply.github.com> 

      Date: 2024-04-23 12:45:00 -0400

      Commit message:


	  
		 Update .gitignore 
    
  
    
      Package: MSstatsTMT

      Commit: 6fda14b3be54a965cd7caff9d67136c153dfe532

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2023-02-26 15:49:33 -0800

      Commit message:


	  
		 update description and news
 
    
  
    
      Package: MSstatsTMT

      Commit: 826cf57916f51a717e47f9bee3df03c20b0a7c92

      Author:  Devon Kohler <35807256+devonjkohler@users.noreply.github.com> 

      Date: 2023-02-23 19:54:55 -0500

      Commit message:


	  
		 Merge pull request #68 from Vitek-Lab/dev

Dev 
    
  
    
      Package: MSstatsTMT

      Commit: 86e32af81e4413a7ce47e2b2d706589b2230246e

      Author:  Devon Kohler <35807256+devonjkohler@users.noreply.github.com> 

      Date: 2023-02-23 19:53:51 -0500

      Commit message:


	  
		 Merge pull request #67 from Vitek-Lab/philosopher-input-change

Philosopher input change 
    
  
    
      Package: MSstatsTMT

      Commit: f68283781c78408b3e41b964cb4ed562f0f3f2bb

      Author:  devonjkohler <devonjkohler@gmail.com> 

      Date: 2023-02-23 19:47:16 -0500

      Commit message:


	  
		 philosopher documentation
 
    
  
    
      Package: MSstatsTMT

      Commit: 881f90a3a42aa9f9866dd720d02c91849117d1f6

      Author:  devonjkohler <devonjkohler@gmail.com> 

      Date: 2023-02-21 08:43:17 -0500

      Commit message:


	  
		 minor changes to refactored converter
 
    
  
    
      Package: MSstatsTMT

      Commit: 4701489ee02592bd343c0d5d7100ce2f47331e97

      Author:  devonjkohler <devonjkohler@gmail.com> 

      Date: 2023-02-18 14:30:46 -0500

      Commit message:


	  
		 fixed param defaults
 
    
  
    
      Package: MSstatsTMT

      Commit: 40a0d9b40fd4ce72bc601a29e339a505cd1dd5f0

      Author:  devonjkohler <devonjkohler@gmail.com> 

      Date: 2023-02-18 14:27:40 -0500

      Commit message:


	  
		 updated phil converter
 
    
  
    
      Package: MSstatsTMT

      Commit: 9cbf9bbbf2ec928993816b1755deae4e5206b7ec

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2022-09-12 21:48:16 -0700

      Commit message:


	  
		 Merge pull request #64 from Vitek-Lab/hotifx-normalization

candidate fix for normalization issue 
    
  
    
      Package: MSstatsTMT

      Commit: 09f5a7c138f64ebfe311435d5cd0e7f441510608

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-08-31 19:53:11 +0200

      Commit message:


	  
		 candidate fix for normalization issue 
    
  
    
      Package: MSstatsTMT

      Commit: 05d27934cb37a42218df7d7c7abcfca6d96dc0d6

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2022-02-18 13:39:31 -0500

      Commit message:


	  
		 Merge pull request #60 from Vitek-Lab/refactoring

update version number 
    
  
    
      Package: MSstatsTMT

      Commit: 620275d29e5609e9f782e47e7d380eaf7dd4e76e

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2022-02-18 13:38:58 -0500

      Commit message:


	  
		 update version number
 
    
  
    
      Package: MSstatsTMT

      Commit: 6632fd900c705c3f816337bfc66b473e1d7c7d87

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2022-02-18 13:12:59 -0500

      Commit message:


	  
		 Merge pull request #59 from Vitek-Lab/hotfix-philosopher-paths

Hotfix philosopher paths 
    
  
    
      Package: MSstatsTMT

      Commit: 68a8ea2c858e6e13e888807de0e1034926c67906

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-02-18 18:54:12 +0100

      Commit message:


	  
		 fixed param name
 
    
  
    
      Package: MSstatsTMT

      Commit: 66ea82b699497af366502a9d70fada1218209cd7

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-02-18 18:22:13 +0100

      Commit message:


	  
		 updated Philosopher converter
 
    
  
    
      Package: MSstatsTMT

      Commit: d1df3572ad31ccef0ef5648aa1ebf1a1f1cf755a

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2022-02-18 11:55:52 -0500

      Commit message:


	  
		 Merge pull request #58 from Vitek-Lab/hotfix-philosopher-paths

updated Philosopher inputs 
    
  
    
      Package: MSstatsTMT

      Commit: 408230afaa8c08cc6c1f9a5916682bfab36c35f0

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-02-18 13:46:18 +0100

      Commit message:


	  
		 fixed check in Philpsopher converter 
    
  
    
      Package: MSstatsTMT

      Commit: 98f2c6a2c15f97867d343a3708c0d4622ce127a7

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-02-18 13:45:04 +0100

      Commit message:


	  
		 fixed a typo 
    
  
    
      Package: MSstatsTMT

      Commit: 4684c66deb92e4a82057117cb80fb032fc9e1c90

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-02-18 13:43:13 +0100

      Commit message:


	  
		 fixed a typo 
    
  
    
      Package: MSstatsTMT

      Commit: 0d0576446ac0d0eb0813ecd1219c3ae0ef15bac1

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-02-18 13:14:05 +0100

      Commit message:


	  
		 updated Philosopher inputs 
    
  
    
      Package: MSstatsTMT

      Commit: c3023457bbe3fd19a2d6f1e69203fc0237a9c8af

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2022-02-14 19:02:45 -0500

      Commit message:


	  
		 Merge pull request #56 from Vitek-Lab/refactoring

Update NEWS.rd 
    
  
    
      Package: MSstatsTMT

      Commit: 6a52268594c44791c5b1583409d855e0950c8eeb

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2022-02-14 19:01:57 -0500

      Commit message:


	  
		 Update NEWS.rd
 
    
  
    
      Package: MSstatsTMT

      Commit: 76d3cb85dc4c67fc10cccb2df4b617e52f74721b

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2022-02-14 18:23:08 -0500

      Commit message:


	  
		 Merge pull request #55 from Vitek-Lab/refactoring

Update version number and news 
    
  
    
      Package: MSstatsTMT

      Commit: fe876a7e0f31540c5bed1eef3d47792971d7754b

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2022-02-14 18:21:57 -0500

      Commit message:


	  
		 Update version number and news
 
    
  
    
      Package: MSstatsTMT

      Commit: ee3d2f6532bbcce3f771b20f79880831bcc65be1

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2022-02-14 17:25:07 -0500

      Commit message:


	  
		 Merge pull request #54 from Vitek-Lab/philosopher-converter

Philosopher converter 
    
  
    
      Package: MSstatsTMT

      Commit: 03cf34939a68cddd22f0ffb2e3d15ed7c248c8b4

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-02-08 20:53:40 +0100

      Commit message:


	  
		 updated Philosopher converter
 
    
  
    
      Package: MSstatsTMT

      Commit: 9c9a8ce1e147f8bc36397a321e1aef781ca5327b

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-02-07 23:01:19 +0100

      Commit message:


	  
		 updated Philosopher converter
 
    
  
    
      Package: MSstatsTMT

      Commit: e81ead3af80557d2e43e1a05d435887e3f4cfb58

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-02-07 22:41:56 +0100

      Commit message:


	  
		 fixed logical condition in Philosopher converter 
    
  
    
      Package: MSstatsTMT

      Commit: 31e78d9e1be8cf0e255083688f5eafb8f569b8af

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-02-07 22:34:25 +0100

      Commit message:


	  
		 updated Philosopher converter 
    
  
    
      Package: MSstatsTMT

      Commit: 71eaa3f0832afc21163cc9e1c2ebab7c7496da60

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-02-07 21:43:05 +0100

      Commit message:


	  
		 updated Philosopher converter
 
    
  
    
      Package: MSstatsTMT

      Commit: af457c99ca82697f7b82bd4851c05eb685f40d55

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-02-07 21:42:22 +0100

      Commit message:


	  
		 updated Philosopher converter
 
    
  
    
      Package: MSstatsTMT

      Commit: c6e666151a24f03af928dd74173515d5d0e96c9b

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-02-03 01:22:52 +0100

      Commit message:


	  
		 updated Philosopher converter 
    
  
    
      Package: MSstatsTMT

      Commit: 9aad06bbc70ddffc81c01a5f4090a8d6400f5398

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-02-03 00:42:28 +0100

      Commit message:


	  
		 added Philosopher converter
 
    
  
    
      Package: MSstatsTMT

      Commit: 8c741616bd5d7c12150a4bac45d2c7c05d93754d

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2022-01-31 15:47:46 +0100

      Commit message:


	  
		 added Philosopher converter
 
    
  
    
      Package: MSstatsTMT

      Commit: 7618cdbf77452d3f0569c2a4171936abdd42e39a

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2021-10-26 13:49:49 -0400

      Commit message:


	  
		 Merge pull request #48 from Vitek-Lab/refactoring

update news 
    
  
    
      Package: MSstatsTMT

      Commit: be2a0f73b97789af2c7f4438829ae2ac5ca72c0b

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-10-26 13:47:26 -0400

      Commit message:


	  
		 udpate news
 
    
  
    
      Package: MSstatsTMT

      Commit: 3c945f7cd30eaa9db3e94e9ae80aa8051ff3e6ec

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2021-10-25 19:25:46 -0400

      Commit message:


	  
		 Merge pull request #47 from Vitek-Lab/hotifx-plot-censored-shape

added shape as indicator of imputed values 
    
  
    
      Package: MSstatsTMT

      Commit: 2f9b209d88c2c5aeec091a0c9e5e8d6d6a7a762d

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-10-25 21:10:14 +0200

      Commit message:


	  
		 added shape as indicator of imputed values

per @ekzp6's suggestion 
    
  
    
      Package: MSstatsTMT

      Commit: cbac0cf726a135c4dd56d1008d73ca06bc6fba93

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2021-10-11 02:16:45 -0400

      Commit message:


	  
		 Merge pull request #46 from Vitek-Lab/refactoring

Refactoring 
    
  
    
      Package: MSstatsTMT

      Commit: 692ebdb6d3203b4e344bfe1c3d7160fed2483aca

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-10-11 02:15:59 -0400

      Commit message:


	  
		 Update DESCRIPTION
 
    
  
    
      Package: MSstatsTMT

      Commit: 7c98afef6715b926f01008786ebcde08d2fb9e7c

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-10-11 02:01:36 -0400

      Commit message:


	  
		 update internal data
 
    
  
    
      Package: MSstatsTMT

      Commit: 75adbcc5adb0220ada33e8d4ed2658e209466e3e

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-10-11 00:58:17 -0400

      Commit message:


	  
		 Update utils_group_comparison.R
 
    
  
    
      Package: MSstatsTMT

      Commit: cc2ded5038e30623d91d6113883690d5fb259fd2

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2021-10-11 00:04:53 -0400

      Commit message:


	  
		 Merge pull request #45 from Vitek-Lab/refactoring

Update DESCRIPTION 
    
  
    
      Package: MSstatsTMT

      Commit: 386d9bb4b5de733b674fe3b48bd947ca9223ef98

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-10-11 00:03:32 -0400

      Commit message:


	  
		 Update DESCRIPTION
 
    
  
    
      Package: MSstatsTMT

      Commit: 1f6962d3e8138903393dc52addf47d0488ac098a

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2021-10-06 19:27:40 -0400

      Commit message:


	  
		 Merge pull request #44 from Vitek-Lab/refactoring

Refactoring 
    
  
    
      Package: MSstatsTMT

      Commit: a584ae0467a9af52526aad7aad0fc00dc5828e17

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2021-10-06 19:26:53 -0400

      Commit message:


	  
		 Merge pull request #42 from Vitek-Lab/hotfix-gc-typo

corrected typo 
    
  
    
      Package: MSstatsTMT

      Commit: fb9466e8de07eb93b3cd18ad9cf7006d06dfd8a0

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-10-06 19:24:48 -0400

      Commit message:


	  
		 fix bug for infinite prior df
 
    
  
    
      Package: MSstatsTMT

      Commit: a859851439c56bb68ba888f3cb3d73d832dc5cba

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-10-06 19:08:20 -0400

      Commit message:


	  
		 update version number
 
    
  
    
      Package: MSstatsTMT

      Commit: 358ee404124cf7940e8e82081f0b41b5de366688

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-09-28 00:44:50 +0200

      Commit message:


	  
		 corrected typo 
    
  
    
      Package: MSstatsTMT

      Commit: 3f5b0b05b010df45c2a1ab3b9c72823eafed2778

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2021-09-21 11:19:08 -0400

      Commit message:


	  
		 Merge pull request #40 from Vitek-Lab/hotfix-dpplot-xaxis

Hotfix dpplot xaxis 
    
  
    
      Package: MSstatsTMT

      Commit: 7833c59bd4edec91ca3526b2f6690e2f133e765b

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-09-21 15:07:42 +0200

      Commit message:


	  
		 updated dPPlots - fixed vertical line position
 
    
  
    
      Package: MSstatsTMT

      Commit: dca0b55e5715df14fd50d573d5c57d325649379e

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2021-09-20 17:39:26 -0400

      Commit message:


	  
		 Merge pull request #39 from Vitek-Lab/refactoring

Refactoring 
    
  
    
      Package: MSstatsTMT

      Commit: e08dcc9a138f4b3c6d730debeac275545a83fff8

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-09-20 17:38:19 -0400

      Commit message:


	  
		 update news
 
    
  
    
      Package: MSstatsTMT

      Commit: 58938bc584052062c339ed9b0f600eec55e2a7fb

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-09-20 17:38:06 -0400

      Commit message:


	  
		 Add repeated measures design
 
    
  
    
      Package: MSstatsTMT

      Commit: dbe7cb0c4b364bf6ebcc38d5c416383d4e80c3d1

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-09-12 17:25:37 -0400

      Commit message:


	  
		 Merge branch 'refactoring' of https://github.com/Vitek-Lab/MSstatsTMT into refactoring
 
    
  
    
      Package: MSstatsTMT

      Commit: da84c1a470444a94a267701aa939fa87ae5720a9

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2021-09-12 17:24:32 -0400

      Commit message:


	  
		 Merge pull request #37 from Vitek-Lab/dev

Sync updates from dev branch to refactoring branch 
    
  
    
      Package: MSstatsTMT

      Commit: 91cbb2325502f953761ddfc81d991d8c00620f09

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2021-08-30 00:35:28 -0400

      Commit message:


	  
		 Merge pull request #36 from Vitek-Lab/hotfix-dpplots-x-axis

Hotfix dpplots x axis 
    
  
    
      Package: MSstatsTMT

      Commit: 80f9fed0f11934a006b97fc7e6a773ba1dfeef44

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2021-08-30 00:34:53 -0400

      Commit message:


	  
		 Merge pull request #31 from Vitek-Lab/hotfix-gsub-group

updated gsub call 
    
  
    
      Package: MSstatsTMT

      Commit: 25d4002d8e6aa078c7c623bccd885f5886e48915

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-08-16 16:29:44 +0200

      Commit message:


	  
		 Update dataProcessPlotsTMT.R 
    
  
    
      Package: MSstatsTMT

      Commit: cb0e38ec355e770166273d720b117dfff4aad72b

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-06-19 00:11:50 +0200

      Commit message:


	  
		 updated gsub call 
    
  
    
      Package: MSstatsTMT

      Commit: bff897c960b90470f8928cea5942a1c9296964f3

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-06-14 14:51:11 -0400

      Commit message:


	  
		 update description
 
    
  
    
      Package: MSstatsTMT

      Commit: d66cb643490c0636c648ed7fa8f88560bc96e5cb

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-06-11 21:50:16 -0400

      Commit message:


	  
		 Update converters.R
 
    
  
    
      Package: MSstatsTMT

      Commit: e30c56476a86db995fc041833e92b676c79c2c18

      Author:  Ting Huang <thuang0703@gmail.com> 

      Date: 2021-06-11 14:52:19 -0400

      Commit message:


	  
		 Merge pull request #28 from Vitek-Lab/hotfix-no-imputation

updated MSstats output processing 
    
  
    
      Package: MSstatsTMT

      Commit: a8fe3a43d5285ccc8b8fe8e239e556414463ff9e

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-06-11 13:11:14 +0200

      Commit message:


	  
		 updated MSstats output processing 
    
  
    
      Package: MSstatsTMT

      Commit: 72ba010b8002230e0a43742afcee47b57a538140

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-15 00:03:12 -0400

      Commit message:


	  
		 Merge pull request #27 from Vitek-Lab/refactoring

Refactoring 
    
  
    
      Package: MSstatsTMT

      Commit: af62eb6cfaf947ccc0651a971d1b9eb1455f57a1

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-15 00:01:16 -0400

      Commit message:


	  
		 remove doc folder
 
    
  
    
      Package: MSstatsTMT

      Commit: 78568acde4a79e2c3cea5ee02281e4d35ec9444b

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-14 23:59:50 -0400

      Commit message:


	  
		 Merge branch 'master' into refactoring
 
    
  
    
      Package: MSstatsTMT

      Commit: 370779e555087a43a057802bf81098206910e2c8

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-14 23:57:00 -0400

      Commit message:


	  
		 Delete _pkgdown.yml 
    
  
    
      Package: MSstatsTMT

      Commit: bb33b8f63a8069382d6892e43ffb4a1ecbd75243

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-14 23:56:08 -0400

      Commit message:


	  
		 Delete docs directory 
    
  
    
      Package: MSstatsTMT

      Commit: d79861b49f4c70e2491d1f963ab48dbe84565e1f

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-14 22:46:51 -0400

      Commit message:


	  
		 change MSstatsdev to MSstats
 
    
  
    
      Package: MSstatsTMT

      Commit: 5624bf6bda4f793455bae398243bb372fbccb90e

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-14 18:20:03 -0400

      Commit message:


	  
		 Merge pull request #26 from Vitek-Lab/dev

create pacakage site 
    
  
    
      Package: MSstatsTMT

      Commit: 5dd90dbd6fcca783b3e56999a234d6544d622155

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-14 12:16:37 -0400

      Commit message:


	  
		 add examples and fix dependancy issue
 
    
  
    
      Package: MSstatsTMT

      Commit: 0f4531535e4a3a0a2da406f89f68302915c18d58

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-12 21:16:21 -0400

      Commit message:


	  
		 udpate vignettes and function comments
 
    
  
    
      Package: MSstatsTMT

      Commit: 0e76b95f4d59b008bebd11a298b4eda32b553fbd

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-11 23:14:52 -0400

      Commit message:


	  
		 Merge branch 'refactoring' of https://github.com/Vitek-Lab/MSstatsTMT into refactoring
 
    
  
    
      Package: MSstatsTMT

      Commit: 7e91f5b3e5df0ace4cdffb582b75df448011d9e0

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-11 23:14:49 -0400

      Commit message:


	  
		 update functions to new output with FeatureLevelData
 
    
  
    
      Package: MSstatsTMT

      Commit: 5c7a8110ba96720da73b96b475e26d7115a3f93a

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-12 03:06:01 +0200

      Commit message:


	  
		 updated site
 
    
  
    
      Package: MSstatsTMT

      Commit: b316997a633b3eb0c7009091fa4d38c9e43f4eac

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-12 03:04:05 +0200

      Commit message:


	  
		 updated exports and docs
 
    
  
    
      Package: MSstatsTMT

      Commit: f783f2c09fdec4208457d832242968541fa5a5b2

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-05-11 16:39:10 +0200

      Commit message:


	  
		 updated names of MSstatsdev output 
    
  
    
      Package: MSstatsTMT

      Commit: 03650b07e79063ecc1ca0fe632dff3c83e0aabf9

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-05-11 16:34:51 +0200

      Commit message:


	  
		 renamed proteinSummarization output 
    
  
    
      Package: MSstatsTMT

      Commit: 11ac4c435acf6700be4010ded48fcfe3a7c48367

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-05-11 15:05:39 +0200

      Commit message:


	  
		 fixed a typo 
    
  
    
      Package: MSstatsTMT

      Commit: dfe1a2c1fe6b89b0396c83b22978cf0df3ea68c8

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-05-11 15:02:54 +0200

      Commit message:


	  
		 candidate fix for summarization issue 
    
  
    
      Package: MSstatsTMT

      Commit: b99a2c96a86d9ebe793e7792a24b7f68fbcfc6f6

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-05-11 15:01:57 +0200

      Commit message:


	  
		 updated normalization 
    
  
    
      Package: MSstatsTMT

      Commit: 0c7499e468b2d6b06d834a6be6245b38c18f7bca

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-05-11 15:01:36 +0200

      Commit message:


	  
		 candidate fix for problems with summary 
    
  
    
      Package: MSstatsTMT

      Commit: 8c719eed285d2127465ccff8debc661034e620d3

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-05-11 02:10:27 +0200

      Commit message:


	  
		 updated logs 
    
  
    
      Package: MSstatsTMT

      Commit: 03fe6c3d86d804fc231e4e561812ac06e5f88321

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-11 00:23:38 +0200

      Commit message:


	  
		 updated proteinSummarization
 
    
  
    
      Package: MSstatsTMT

      Commit: 5f74eb66fd087b6dec9ede20298de2bf9bf57cda

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-10 21:53:33 +0200

      Commit message:


	  
		 updated groupComparison
 
    
  
    
      Package: MSstatsTMT

      Commit: 05dc81546e1102d1cef5cfd4a4a64353e6cddae9

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-10 21:43:54 +0200

      Commit message:


	  
		 fixed a typo
 
    
  
    
      Package: MSstatsTMT

      Commit: 642f4effe4f95001999bf29adad2140b0a462781

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-10 21:30:09 +0200

      Commit message:


	  
		 fixed contrast matrix
 
    
  
    
      Package: MSstatsTMT

      Commit: dd56e4bc9cead7cdb04dd97cd19bf1d928b03d93

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-10 21:27:11 +0200

      Commit message:


	  
		 updated normalization
 
    
  
    
      Package: MSstatsTMT

      Commit: e39953161a43a23ad5644594cf02f9897d6ef31c

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-05-10 20:57:01 +0200

      Commit message:


	  
		 update groupComparisonTMT

treat some variables as numeric, not matrix 
    
  
    
      Package: MSstatsTMT

      Commit: 8ff778fe6f0cfb070da2227bcb02a1d108584a5f

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-10 03:10:54 +0200

      Commit message:


	  
		 renamed to MSstatsdev
 
    
  
    
      Package: MSstatsTMT

      Commit: 62287d754d45a4b8dfba40c60f9238ba65370cac

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-10 03:06:08 +0200

      Commit message:


	  
		 updated summarization
 
    
  
    
      Package: MSstatsTMT

      Commit: 1cbff94548fb78b29555b99374712e0f9b3087b0

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-09 19:41:14 -0400

      Commit message:


	  
		 update log info for each run
 
    
  
    
      Package: MSstatsTMT

      Commit: b27a235a21f545b99f427fa1aaf34788f67669e5

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-10 01:26:45 +0200

      Commit message:


	  
		 fixed a typo
 
    
  
    
      Package: MSstatsTMT

      Commit: 9eae5814c90f6022b16c5763996f0e320f99ae0f

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-10 01:22:33 +0200

      Commit message:


	  
		 removed parameter from MsstatsSummarizeTMT
 
    
  
    
      Package: MSstatsTMT

      Commit: 64ccc985a94b38e3d5bf425f7c7d9689817317db

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-10 01:16:22 +0200

      Commit message:


	  
		 updated logging
 
    
  
    
      Package: MSstatsTMT

      Commit: 12776ccb2de4edb08a4d7a7482b579ca0a47bd09

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-10 01:10:44 +0200

      Commit message:


	  
		 updated logging
 
    
  
    
      Package: MSstatsTMT

      Commit: ebaedae1d65b6b30f4a8dfdb7e4aa7161bad4aec

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-10 01:10:34 +0200

      Commit message:


	  
		 updated docs
 
    
  
    
      Package: MSstatsTMT

      Commit: 7bcfdc49da09bf09ff2959ab68fd706c7127f9a9

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-10 01:03:36 +0200

      Commit message:


	  
		 updated logging
 
    
  
    
      Package: MSstatsTMT

      Commit: 1644eb6b97bb7f4a33a7d8c57b1225372e47bec9

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-10 01:01:58 +0200

      Commit message:


	  
		 updated logging
 
    
  
    
      Package: MSstatsTMT

      Commit: b84bd7270b4c2ba3f57d29d208eeca2a6ca2db15

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-09 23:49:31 +0200

      Commit message:


	  
		 fixed log settings
 
    
  
    
      Package: MSstatsTMT

      Commit: b3bd9e00ebbc00b2d5a7cbefb99121335a588dc8

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-09 23:46:42 +0200

      Commit message:


	  
		 fixed a typo in log settings
 
    
  
    
      Package: MSstatsTMT

      Commit: 04048892ce004331cf571261afc940a912d2c40c

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-09 11:36:49 -0400

      Commit message:


	  
		 update groupComparisonTMT and summarization functions
 
    
  
    
      Package: MSstatsTMT

      Commit: ce3a37e0bf2ef229f9de65f69064c5b92a6c6f3e

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-09 04:10:21 +0200

      Commit message:


	  
		 added MSstatsContrastsMatrix call
 
    
  
    
      Package: MSstatsTMT

      Commit: 773d11cfa73499e7bacd933c143ce4974a2ea53e

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-07 22:37:45 +0200

      Commit message:


	  
		 updated logging in converters
 
    
  
    
      Package: MSstatsTMT

      Commit: 51ec7b09dcfe8dff521091b3de301a54827819fe

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-07 22:35:49 +0200

      Commit message:


	  
		 updated log
 
    
  
    
      Package: MSstatsTMT

      Commit: 2bf47fbce1ff0026419684126770fa03109c7149

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-07 22:33:32 +0200

      Commit message:


	  
		 updated log in groupComparisonTMT
 
    
  
    
      Package: MSstatsTMT

      Commit: b932a471939646fd0938fe3d371d411845f09649

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-05-07 17:17:54 +0200

      Commit message:


	  
		 Update groupComparisonTMT.R 
    
  
    
      Package: MSstatsTMT

      Commit: 57d1c9602dae4ddf03514a38651a0720984e67e8

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-07 00:15:13 -0400

      Commit message:


	  
		 Update dataProcessPlotsTMT.R

print progress message
 
    
  
    
      Package: MSstatsTMT

      Commit: 3fe5768c7ffa35c17bf309a13120bc9e759d207d

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-07 00:00:03 -0400

      Commit message:


	  
		 update function comments
 
    
  
    
      Package: MSstatsTMT

      Commit: cdf4dc28932515dc7bfb70b31c6127071e0b676c

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-06 23:59:11 -0400

      Commit message:


	  
		 Merge branch 'refactoring' of https://github.com/Vitek-Lab/MSstatsTMT into refactoring
 
    
  
    
      Package: MSstatsTMT

      Commit: 62575ccd5d9d41b197041511bb2631e17790436e

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-05-06 23:46:34 -0400

      Commit message:


	  
		 update dataprocessplots function
 
    
  
    
      Package: MSstatsTMT

      Commit: dfb544d18febb081f570f9221345d05924cda866

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-06 14:17:01 +0200

      Commit message:


	  
		 updated exports and docs
 
    
  
    
      Package: MSstatsTMT

      Commit: cb028416a6a24d4e82efeb74d30a5f2cc1f89de6

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-06 12:44:29 +0200

      Commit message:


	  
		 restored current proteinSummarization version
 
    
  
    
      Package: MSstatsTMT

      Commit: 63fdf97ec2721c274d1f5c2d9ec5a653895e2e81

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-05-05 21:17:22 +0200

      Commit message:


	  
		 Add files via upload 
    
  
    
      Package: MSstatsTMT

      Commit: 0e65c2ac339b38a87b4986891c3ed03e1307b995

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2021-05-05 21:16:38 +0200

      Commit message:


	  
		 Delete dataProcessPlotsTMT.R 
    
  
    
      Package: MSstatsTMT

      Commit: a2cc9b2e77411b6298acb65f325b7670e5594119

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-04 17:46:11 +0200

      Commit message:


	  
		 updated docs
 
    
  
    
      Package: MSstatsTMT

      Commit: 1a6cc95ec5f4b6a9edd544063f139c49721a51b5

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-04 17:46:01 +0200

      Commit message:


	  
		 updated proteinSummarization
 
    
  
    
      Package: MSstatsTMT

      Commit: 4a90f0c463114575c423cc96d532b510ecf73234

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-04 17:44:48 +0200

      Commit message:


	  
		 updated groupComparison
 
    
  
    
      Package: MSstatsTMT

      Commit: d030c0eec6b117564ae871d13b8f0e9cbf8cb230

      Author:  mstaniak <mtst@mstaniak.pl> 

      Date: 2021-05-04 17:43:55 +0200

      Commit message:


	  
		 updated plots
 
    
  
    
      Package: MSstatsTMT

      Commit: 29b18af70aca5edaa21c8cd0aa1d939d519e2bdf

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-04-30 12:44:11 -0400

      Commit message:


	  
		 create pacakage site
 
    
  
    
      Package: MSstatsTMT

      Commit: b34d7a73d19e24256ea46da4e6cb05771f9f124e

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-04-29 00:28:44 -0400

      Commit message:


	  
		 Merge pull request #25 from Vitek-Lab/dev

fix the contrast matrix bug 
    
  
    
      Package: MSstatsTMT

      Commit: c78b7133c957c6af49ca1ead39f5041455159511

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2021-04-29 00:26:32 -0400

      Commit message:


	  
		 fix the contrast matrix bug
 
    
  
    
      Package: MSstatsTMT

      Commit: 7872b439fed3eae23330d8eda25b5a54c4d1254b

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-12-17 23:31:57 -0500

      Commit message:


	  
		 Merge pull request #21 from Vitek-Lab/dev

update groupComparsionTMT() and description file 
    
  
    
      Package: MSstatsTMT

      Commit: 8ed8e947178561a416d49bfab54f52a38e010e51

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-12-17 23:30:45 -0500

      Commit message:


	  
		 update description file
 
    
  
    
      Package: MSstatsTMT

      Commit: 5b10d8ff14e6ce87fe070983ab2748eacadb3060

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-12-17 23:17:06 -0500

      Commit message:


	  
		 udpate groupComparsionTMT()
 
    
  
    
      Package: MSstatsTMT

      Commit: 8851a3c77adad71d7a7ec2ec5d3c1cba95490293

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-12-17 18:25:56 -0500

      Commit message:


	  
		 Merge pull request #20 from Vitek-Lab/minor-update

update progress bar 
    
  
    
      Package: MSstatsTMT

      Commit: 6d189b6109e323803b8988c3f4f40ca20bf264eb

      Author:  Meena Choi <choimeena.ijae@gmail.com> 

      Date: 2020-12-15 14:11:49 -0500

      Commit message:


	  
		 update progress bar
 
    
  
    
      Package: MSstatsTMT

      Commit: 49416ac2eb09a7918c018b9c213dfbd4989d5022

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-12-10 14:42:51 -0500

      Commit message:


	  
		 Merge pull request #19 from Vitek-Lab/dev

Fix typo in function annotation and add citation file 
    
  
    
      Package: MSstatsTMT

      Commit: 96cd7233160d3a5d877c620920f46a372d25fd35

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-12-10 14:41:12 -0500

      Commit message:


	  
		 Fix typo in function annotation and add citation file
 
    
  
    
      Package: MSstatsTMT

      Commit: a8dbd64934477deb01916e69c6e4cbb0facf7829

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-10-26 17:10:42 -0400

      Commit message:


	  
		 Merge pull request #18 from Vitek-Lab/dev

Update linearModel.functions.R 
    
  
    
      Package: MSstatsTMT

      Commit: df689e65304e1adb93bf62670f4ca93fd642807f

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-10-26 17:09:18 -0400

      Commit message:


	  
		 Update linearModel.functions.R
 
    
  
    
      Package: MSstatsTMT

      Commit: f484504185535e76728acf68c07d371d1f24e5c4

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-10-26 15:10:46 -0400

      Commit message:


	  
		 Merge pull request #17 from Vitek-Lab/dev

fix bug in medianpolish summarization 
    
  
    
      Package: MSstatsTMT

      Commit: d80c64494c8455f9a602eeaec245763a5bec2751

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-10-26 15:08:37 -0400

      Commit message:


	  
		 fix bug in medianpolish summarization
 
    
  
    
      Package: MSstatsTMT

      Commit: d9cde1e6d5b5afbaf03c7eee7867668f5dc5cf64

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-20 23:29:42 +0200

      Commit message:


	  
		 restores the .summarizeSimpleStat function

 
    
  
    
      Package: MSstatsTMT

      Commit: 394a0bbf8ebc0253f9365aef92fef3e66bc9b754

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-20 20:42:07 +0200

      Commit message:


	  
		 converts 0 to NA before normalization

 
    
  
    
      Package: MSstatsTMT

      Commit: 7d0ac829cf355d9cbc72e8098658cf02ba9e0e33

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-20 15:32:26 +0200

      Commit message:


	  
		 temporarily splits peptide normalization in two steps

 
    
  
    
      Package: MSstatsTMT

      Commit: 3ec23516fec45d980d919346e5385272b62390f9

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-19 00:20:27 +0200

      Commit message:


	  
		 updates normalization

 
    
  
    
      Package: MSstatsTMT

      Commit: 6b8f4e429e66bd69e16cbfb832368472b4f1b61d

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-18 21:11:18 +0200

      Commit message:


	  
		 updates normalization

 
    
  
    
      Package: MSstatsTMT

      Commit: 024df9e63b4753a5383aadb1db850aa7fb1dc9be

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-18 18:54:07 +0200

      Commit message:


	  
		 updates normalization

 
    
  
    
      Package: MSstatsTMT

      Commit: eea8490ead3e18e86aa31cf494f871d2a36eb360

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-18 00:52:44 +0200

      Commit message:


	  
		 updates normalization

 
    
  
    
      Package: MSstatsTMT

      Commit: d5aafcf36ffbc3b52defa3d92116f33bf31c73e9

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-17 21:07:55 +0200

      Commit message:


	  
		 updates normalization

 
    
  
    
      Package: MSstatsTMT

      Commit: c5358eac0fac0bad76f0323e63f0622136c2a01b

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-17 18:50:58 +0200

      Commit message:


	  
		 updates normalization

 
    
  
    
      Package: MSstatsTMT

      Commit: 69eaaf717f5af61c17efa096012d999dab701bef

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-17 18:47:52 +0200

      Commit message:


	  
		 removes subset from normalization

 
    
  
    
      Package: MSstatsTMT

      Commit: c4c226f72c48650fbb19dbc77483e4b1c0779cb1

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-17 18:38:02 +0200

      Commit message:


	  
		 updates median polish summarization

 
    
  
    
      Package: MSstatsTMT

      Commit: b535bc286e383f1f68325de3dc6e394247e77710

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-17 18:32:59 +0200

      Commit message:


	  
		 updates normalization

 
    
  
    
      Package: MSstatsTMT

      Commit: 605031dc035234562c77514ac8a7208da4636725

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-16 20:46:07 +0200

      Commit message:


	  
		 updates gitignore

 
    
  
    
      Package: MSstatsTMT

      Commit: ee9ccf17c1567faa7c84ade74ab155d0c535ead1

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-16 20:44:28 +0200

      Commit message:


	  
		 adds na.rm to uniqueN for counting runs

 
    
  
    
      Package: MSstatsTMT

      Commit: b16286c5db73745c9e0d155fb37f2f37b9527bd9

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-15 16:49:04 +0200

      Commit message:


	  
		 removes filtering from median polish summarization

 
    
  
    
      Package: MSstatsTMT

      Commit: cc6bf12a536f7557148bef04b37ce448f8f6d484

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-14 19:08:02 +0200

      Commit message:


	  
		 fixes error in MSstats summarization

 
    
  
    
      Package: MSstatsTMT

      Commit: 8b448a533c596db4a93f1a08184280880b26fdb1

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-14 18:46:04 +0200

      Commit message:


	  
		 fixes error for data.frame input

 
    
  
    
      Package: MSstatsTMT

      Commit: abfc1671549a671416f59e2055f8b6a9228d2aab

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-14 16:36:46 +0200

      Commit message:


	  
		 updates summarization with median polish

 
    
  
    
      Package: MSstatsTMT

      Commit: 0ea3abb8dc694df313f0fd6d2941564ac7f2a202

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-14 16:12:09 +0200

      Commit message:


	  
		 typo fix

 
    
  
    
      Package: MSstatsTMT

      Commit: a27734e27b0961ef13acb25332fe28da0586b938

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-14 15:58:15 +0200

      Commit message:


	  
		 fixes summarization

 
    
  
    
      Package: MSstatsTMT

      Commit: d2edae8a1d0e5c66f76bb683b0c698fc74cb5bcb

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-14 15:42:54 +0200

      Commit message:


	  
		 fixes a typo in MSstats summarization

 
    
  
    
      Package: MSstatsTMT

      Commit: f850db73ca35f6c8bb2095684a8c400487165635

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-13 18:59:20 +0200

      Commit message:


	  
		 adds as.data.frame

 
    
  
    
      Package: MSstatsTMT

      Commit: 99db2c19673a1d5d0aac3e8a8a42c30eb991a28a

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-10-13 12:20:40 -0400

      Commit message:


	  
		 Merge pull request #16 from Vitek-Lab/dev

fix a typo in function comments 
    
  
    
      Package: MSstatsTMT

      Commit: 4890c089dc337457f1a935b95f65fdc76ac3e26e

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-10-13 12:18:41 -0400

      Commit message:


	  
		 Delete .DS_Store 
    
  
    
      Package: MSstatsTMT

      Commit: 0c83a2f09422959f11b742d266c6734898e5d682

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-10-13 12:18:29 -0400

      Commit message:


	  
		 Delete .DS_Store 
    
  
    
      Package: MSstatsTMT

      Commit: d1a86bd9587ff7d715a7d10b493e7b1474078078

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-10-13 12:18:00 -0400

      Commit message:


	  
		 Delete .DS_Store 
    
  
    
      Package: MSstatsTMT

      Commit: e511639ef3f3520f09c1f88287d0b943d0aae2c9

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-10-13 12:17:26 -0400

      Commit message:


	  
		 Delete .DS_Store 
    
  
    
      Package: MSstatsTMT

      Commit: 1778e949dd3fb66f52d2666ce0d2abbf212ac91f

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-10-13 12:16:48 -0400

      Commit message:


	  
		 Delete .DS_Store 
    
  
    
      Package: MSstatsTMT

      Commit: 4524deaae91755bced1f1f607afa651120cb5300

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-10-13 12:16:34 -0400

      Commit message:


	  
		 Delete .DS_Store 
    
  
    
      Package: MSstatsTMT

      Commit: aa10d00163bc73c369d4ba82f13ecb3f7d64ed65

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-10-13 12:14:21 -0400

      Commit message:


	  
		 fix a typo in function comments
 
    
  
    
      Package: MSstatsTMT

      Commit: fc67448bd372671b37c5df1a3b8fcb449e057cfe

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-13 02:10:44 +0200

      Commit message:


	  
		 updates calls to dataProcess

 
    
  
    
      Package: MSstatsTMT

      Commit: 870ce1837a2dde5e0c4ad216304406544c8f57fd

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-13 01:55:28 +0200

      Commit message:


	  
		 updates call to dataProcess

 
    
  
    
      Package: MSstatsTMT

      Commit: c696a084571a4821989b92d9543f197fbe8d5e38

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-12 23:10:28 +0200

      Commit message:


	  
		 adds a final message to converters

 
    
  
    
      Package: MSstatsTMT

      Commit: 262f5bdadd49c12bbbc5908c79d316c82cdf1fa0

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-12 23:10:20 +0200

      Commit message:


	  
		 removes make_copy parameter

 
    
  
    
      Package: MSstatsTMT

      Commit: 5d07342be272ced8c8f2b3a4b06f56ab12688d1c

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-12 23:10:11 +0200

      Commit message:


	  
		 re-organizes summarization code

 
    
  
    
      Package: MSstatsTMT

      Commit: cdf2fc26b98951a877be8039477f5254b4733077

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-12 21:23:35 +0200

      Commit message:


	  
		 adds MSstatsdev to Imports

 
    
  
    
      Package: MSstatsTMT

      Commit: d570a97b54e52ee55b7422008c8aa72c1b5c0fd8

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-12 21:18:58 +0200

      Commit message:


	  
		 removes unnecessary parameters

 
    
  
    
      Package: MSstatsTMT

      Commit: d2ab3e9cffd727bedaa350624a9ebd672cb601d6

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-12 21:12:01 +0200

      Commit message:


	  
		 adds saving session info to proteinSummarization

 
    
  
    
      Package: MSstatsTMT

      Commit: 91f1ecbe51f08610f4d5d352148fbc1115593b3d

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-12 21:09:21 +0200

      Commit message:


	  
		 adds make_copy parameter to proteinSummarization

 
    
  
    
      Package: MSstatsTMT

      Commit: 0363135d926bb77945a03811139d0f8150492ded

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-12 20:46:53 +0200

      Commit message:


	  
		 re-organizes proteinSummarization code

 
    
  
    
      Package: MSstatsTMT

      Commit: fa87d6b15864809d2c0fc1583ed17ee3f6bdc4c8

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-10-02 16:39:27 +0200

      Commit message:


	  
		 updates converters

 
    
  
    
      Package: MSstatsTMT

      Commit: b32fe2e74f2d0ad53271c37b7ba190a662fc08f1

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-09-30 00:58:01 +0200

      Commit message:


	  
		 adds MSstatsConvert:: to imported functions

 
    
  
    
      Package: MSstatsTMT

      Commit: c31300ad85a0f86f93832091efee7a07816dc51c

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-09-30 00:07:06 +0200

      Commit message:


	  
		 updates converters

 
    
  
    
      Package: MSstatsTMT

      Commit: 27f766a776c43e30691a16a4cbc48ed25c26c937

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-09-29 23:46:26 +0200

      Commit message:


	  
		 fixes bug in converters

 
    
  
    
      Package: MSstatsTMT

      Commit: 9a5567cbc0bcc0276ccfd438eae0bf4ebdedbe54

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-09-29 22:39:00 +0200

      Commit message:


	  
		 updates logging in converters

 
    
  
    
      Package: MSstatsTMT

      Commit: 4437ae5297a34b71eb1cae875d91e8bbeed53e5b

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-09-29 22:19:16 +0200

      Commit message:


	  
		 adds saving session info

 
    
  
    
      Package: MSstatsTMT

      Commit: c366818ffe1d62486457f38c7209a280ac7ab0e4

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-09-29 22:19:00 +0200

      Commit message:


	  
		 updates docs

 
    
  
    
      Package: MSstatsTMT

      Commit: c02c4ca9350e5a7aa41ac55c1120b80e335b53c1

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-09-29 22:18:20 +0200

      Commit message:


	  
		 updates imports and namespace

temporarily removes function 
    
  
    
      Package: MSstatsTMT

      Commit: 06d241036093364fa7f57387318c8d49a3f18961

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-09-26 13:40:47 +0200

      Commit message:


	  
		 adds codecov

 
    
  
    
      Package: MSstatsTMT

      Commit: 132b7533495b74ea6d699d3a2ec3b27ac0c3126c

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-09-26 13:37:21 +0200

      Commit message:


	  
		 adds Travis

 
    
  
    
      Package: MSstatsTMT

      Commit: 95dcfdd8e9abbaffe4bd6945bbe63a21e81d6ea7

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2020-09-26 13:04:07 +0200

      Commit message:


	  
		 adds converter from MSstatsConvert

 
    
  
    
      Package: MSstatsTMT

      Commit: 805a4cc3ed68a39c3733e077f32899e02594e8dc

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-08-28 19:31:51 -0400

      Commit message:


	  
		 Merge pull request #11 from Vitek-Lab/dev

Fix bugs in converters 
    
  
    
      Package: MSstatsTMT

      Commit: f439620e43183ede4438fa466b0965abfac2102c

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-08-28 19:29:56 -0400

      Commit message:


	  
		 Fix the bug in converters due to fractions with same mean, sum and max values
 
    
  
    
      Package: MSstatsTMT

      Commit: d2e0f9bed4dc591ad944bf1bd898cb641eee3614

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-08-28 17:28:34 -0400

      Commit message:


	  
		 Delete .gitignore 
    
  
    
      Package: MSstatsTMT

      Commit: 6a2af9236e4df919577cc06345b80d17f0efd0bd

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-08-28 17:28:20 -0400

      Commit message:


	  
		 Delete .Rbuildignore 
    
  
    
      Package: MSstatsTMT

      Commit: 4a7da658f2cff218d11604647c1424b0958dd952

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-08-28 17:20:57 -0400

      Commit message:


	  
		 fix the bug in converters

the bug is due to summaryforMultipleRows
 
    
  
    
      Package: MSstatsTMT

      Commit: 604272dafdb3881a95601a37f84d0d89b26a2d15

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-08-24 10:39:00 -0400

      Commit message:


	  
		 fix duplicated row bug in openms converter
 
    
  
    
      Package: MSstatsTMT

      Commit: f4141c31e45f0510d927a35d9bd421ff014ae816

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-06-10 19:02:32 -0400

      Commit message:


	  
		 allow NA in annotation file
 
    
  
    
      Package: MSstatsTMT

      Commit: 0840222442677b61a8172e57428ae272a767b454

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-06-02 23:23:29 -0400

      Commit message:


	  
		 improve groupComparison() to predict for each protein
 
    
  
    
      Package: MSstatsTMT

      Commit: 6b84c3694c0e5edd4a4e8a33a2f47ebc631f34d2

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-04-24 07:06:57 -0400

      Commit message:


	  
		 update version number
 
    
  
    
      Package: MSstatsTMT

      Commit: 4e8b69d1746ede34e622c97148fb3079907d1aa1

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-04-14 08:43:15 -0400

      Commit message:


	  
		 use lmertest for testing
 
    
  
    
      Package: MSstatsTMT

      Commit: 681035fedf038661281923c40faaa77f865b5702

      Author:  Ting Huang <huang.tin@husky.neu.edu> 

      Date: 2020-03-01 16:19:45 -0500

      Commit message:


	  
		 add OpenMStoMSstatsTMTFormat()
 
    
  
  


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