May 3, 2019

Bioconductors:

We are pleased to announce Bioconductor 3.9, consisting of 1741 software packages, 371 experiment data packages, 948 annotation packages, and 27 workflows.

There are 105 new software packages, 13 new data experiment packages, 4 new workflows, and many updates and improvements to existing packages; Bioconductor 3.9 is compatible with R 3.6.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release will include an updated Bioconductor Amazon Machine Image and Docker containers.

Visit https://bioconductor.org for details and downloads.

Contents

Getting Started with Bioconductor 3.9

To update to or install Bioconductor 3.9:

  1. Install R >=3.6.0. Bioconductor 3.9 has been designed expressly for this version of R.

  2. Follow the instructions at http://bioconductor.org/install/.

New Software Packages

There are 105 new software packages in this release of Bioconductor.

New Data Experiment Packages

There are 13 new data experiment packages in this release of Bioconductor.

New Workflows

There are 4 new workflow packages in this release of Bioconductor.

NEWS from new and existing Software Packages

ACE

             Changes in version 1.1.2 (2019-04-23)                  

ADAM

            Changes in version 0.99.66 (2018-11-15)                 

AffiXcan

                    Changes in version 1.1.3                        

BUG FIXES

alevinQC

                   Changes in version 0.99.0                        

amplican

                    Changes in version 1.5.8                        

AneuFinder

                   Changes in version 1.11.1                        

BUG FIXES

AnnotationHub

                   Changes in version 2.15.0                        

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

USER-VISIBLE MODIFICATIONS

BUG FIXES

AnnotationHubData

                   Changes in version 1.13.0                        

NEW FEATURES

anota2seq

                    Changes in version 1.5.0                        

apeglm

                    Changes in version 1.5.4                        

ASICS

                     Changes in version 2.0                         

New features

Improvements

AssessORF

             Changes in version 1.1.7 (2019-04-29)                  

ATACseqQC

                    Changes in version 1.7.8                        

atSNP

             Changes in version 0.99.0 (2018-12-29)                 

AUCell

                     Changes in version 1.5                         

BANDITS

                    Changes in version 1.0.0                        

BASiCS

             Changes in version 1.5.34 (2019-04-20)                 

bayNorm

                    Changes in version 1.1.6                        

bcSeq

                   Changes in version 1.5.11                        

beachmat

                    Changes in version 2.0.0                        

BEclear

             Changes in version 2.0.0 (2019-04-30)                  

bigPint

             Changes in version 0.99.7 (2019-01-28)                 

BigPint accepted to Bioconductor (Open source software for bioinformatics)

             Changes in version 0.99.0 (2018-09-30)                 

Vignette for bigPint was released on github.io

bioCancer

                   Changes in version 1.11.00                       

BiocCheck

                    Changes in version 1.19                         

NEW FEATURES

USER SIGNIFICANT CHANGES

BUG FIXES

BiocFileCache

                     Changes in version 1.7                         

BUG FIX

BiocNeighbors

                    Changes in version 1.2.0                        

BiocParallel

                    Changes in version 1.18                         

USER VISIBLE CHANGES

BUG FIXES

biocViews

                   Changes in version 1.51.11                       

NEW FEATURES

BioMM

                   Changes in version 0.99.13                       

biosigner

                   Changes in version 1.11.26                       

NEW FEATURE

MINOR MODIFICATION

MINOR MODIFICATION

MINOR MODIFICATION

MINOR MODIFICATION

MINOR MODIFICATION

MINOR MODIFICATION

MINOR MODIFICATION

MINOR MODIFICATION

MINOR MODIFICATION

MINOR MODIFICATION

BUG FIXED

NEW FEATURES

breakpointR

                    Changes in version 1.1.2                        

BUMHMM

                    Changes in version 1.6.2                        

CAGEfightR

                     Changes in version 1.5                         

CAGEr

                   Changes in version 1.26.0                        

DOCUMENTATION

CAMERA

                   Changes in version 1.39.2                        

BUG FIXES

canceR

                   Changes in version 1.17.6                        

Cardinal

                   Changes in version 2.1.30                        

BUG FIXES

BUG FIXES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

BUG FIXES

BUG FIXES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

cbaf

             Changes in version 1.6.0 (2019-04-28)                  

New Features

celaref

                   Changes in version 1.1.10                        

UPDATES

BUG FIXES

UPDATES

UPDATES

UPDATES

UPDATES

BUG FIXES

UPDATES

UPDATES

UPDATES

celda

            Changes in version 0.99.34 (2019-04-23)                 

CellBench

                   Changes in version 0.99.10                       

New Features

Modifications

Modifications

New Features

New Features

Breaking Changes

New Features

New Features

Bug Fixes

Modifications

CellMixS

                   Changes in version 0.99.9                        

ChAMP

                   Changes in version 2.13.2                        

CHETAH

             Changes in version 0.99.0 (2019-02-28)                 

ChIPanalyser

                    Changes in version 1.4.1                        

Package Updates

ChIPpeakAnno

                   Changes in version 3.17.2                        

ChIPseeker

                   Changes in version 1.19.1                        

chromstaR

                    Changes in version 1.9.2                        

BUGFIXES

CHRONOS

                   Changes in version 1.11.1                        

cleaver

             Changes in version 1.21.4 (2018-12-26)                 

CluMSID

                   Changes in version 0.99.13                       

clusterProfiler

                   Changes in version 3.11.1                        

CNVPanelizer

                   Changes in version 1.15.1                        

CNVRanger

                    Changes in version 1.0.0                        

cola

                   Changes in version 0.99.15                       

coMET

             Changes in version 1.15.2 (2018-12-24)                 

ComplexHeatmap

                   Changes in version 1.99.8                        

This a major update of the package. The main changes are

consensusDE

             Changes in version 1.0.7 (2019-03-01)                  

coRdon

                    Changes in version 1.1.3                        

CoRegFlux

             Changes in version 0.99.0 (2019-01-15)                 

csaw

                   Changes in version 1.18.0                        

cTRAP

                    Changes in version 1.0.3                        

cydar

                    Changes in version 1.8.0                        

cytofast

                   Changes in version 0.99.0                        
                   Changes in version 1.21.4                        

dcanr

             Changes in version 0.99.0 (2019-03-25)                 

debrowser

                   Changes in version 1.10.7                        

deco

                   Changes in version 0.99.53                       

decompTumor2Sig

             Changes in version 1.99.1 (2019-04-07)                 

deepSNV

             Changes in version 1.99.3 (2013-07-25)                 

Updates

Bugfixes

Updates

Bugfixes

Updates

Bugfixes

Updates

DEGreport

                   Changes in version 1.19.2                        

DelayedArray

                   Changes in version 0.10.0                        

NEW FEATURES

DelayedMatrixStats

                    Changes in version 1.5.1                        

DeMixT

                   Changes in version 0.99.0                        

derfinder

                   Changes in version 1.17.3                        

NEW FEATURES

BUG FIXES

derfinderHelper

                   Changes in version 1.17.3                        

NEW FEATURES

BUG FIXES

derfinderPlot

                   Changes in version 1.17.2                        

NEW FEATURES

DEsubs

                    Changes in version 1.9.1                        

diffcyt

                   Changes in version 1.3.17                        

diffuStats

                    Changes in version 1.3.1                        

DiscoRhythm

             Changes in version 0.99.8 (2019-04-29)                 

dmrseq

             Changes in version 1.3.1 (2018-11-02)                  

DNABarcodeCompatibility

             Changes in version 0.99.8 (2018-11-25)                 

DominoEffect

                    Changes in version 1.3.1                        

UDPATE

NEW FEATURES

DOSE

                    Changes in version 3.9.4                        

doseR

                   Changes in version 0.99.5                        

DropletUtils

                    Changes in version 1.4.0                        

easyRNASeq

                   Changes in version 2.19.6                        

edgeR

                   Changes in version 3.26.0                        

ENCODExplorer

                    Changes in version 2.9.0                        

NEW FEATURES

EnhancedVolcano

                    Changes in version 1.1.4                        

EnrichedHeatmap

                   Changes in version 1.13.1                        

enrichplot

                    Changes in version 1.3.2                        

enrichTF

             Changes in version 1.0.0 (2019-04-30)                  

ensembldb

                   Changes in version 2.7.10                        

ensemblVEP

                   Changes in version 1.26.0                        

EpiDISH

                    Changes in version 2.0.0                        

epihet

                   Changes in version 0.99.0                        

IMPROVEMENTS AND BUG FIXES

epivizrServer

                   Changes in version 999.999                       

evaluomeR

            Changes in version 0.99.81 (2019-02-26)                 

ExperimentHub

                    Changes in version 1.9.0                        

SIGNIFICANT USER-VISIBLE CHANGES

ExperimentHubData

                    Changes in version 1.9.0                        

NEW FEATURES

FamAgg

                   Changes in version 1.11.5                        

FELLA

                    Changes in version 1.3.1                        

fgsea

                    Changes in version 1.9.6                        

fishpond

                   Changes in version 0.99.30                       

flowAI

                   Changes in version 1.12.5                        

flowCL

                   Changes in version 1.21.1                        

flowClust

                   Changes in version 3.21.2                        

FoldGO

             Changes in version 1.1.2 (2019-04-12)                  

GAPGOM

             Changes in version 1.0.0 (2018-02-13)                  

Added

Changed

Removed

Fixed

Added

Changed

Removed

Fixed

Added

Changed

Removed

Fixed

Added

Changed

Removed

Fixed

Added

GateFinder

                    Changes in version 1.3.2                        

gdsfmt

                   Changes in version 1.20.0                        

UTILITIES

NEW FEATURES

BUG FIXES

BUG FIXES

GeneNetworkBuilder

                   Changes in version 1.25.1                        

GENESIS

                   Changes in version 2.13.7                        

GENIE3

                    Changes in version 1.5.2                        

GenomeInfoDb

                   Changes in version 1.20.0                        

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

GenomicDataCommons

                    Changes in version 1.7.4                        

GenomicFeatures

                   Changes in version 1.36.0                        

NEW FEATURES

BUG FIXES

GenomicRanges

                   Changes in version 1.36.0                        

NEW FEATURES

DEPRECATED AND DEFUNCT

GenomicScores

                    Changes in version 1.8.0                        

USER VISIBLE CHANGES

BUG FIXES

GEOquery

                   Changes in version 2.51.1                        

Improvements

ggtree

                   Changes in version 1.15.6                        

GladiaTOX

                   Changes in version 0.99.0                        

GNET2

                   Changes in version 0.99.13                       

GOfuncR

                    Changes in version 1.3.4                        

USER-LEVEL CHANGES

USER-LEVEL CHANGES

gpuMagic

             Changes in version 0.99.6 (2019-04-19)                 

graper

             Changes in version 0.99.0 (2018-11-07)                 

graphite

             Changes in version 1.29.3 (2019-04-17)                 

gtrellis

                   Changes in version 1.15.2                        

Guitar

             Changes in version 1.99.0 (2019-04-24)                 

Gviz

                   Changes in version 1.28.0                        

BUG FIXES

HCABrowser

                    Changes in version 1.0.0                        

HDF5Array

                   Changes in version 1.12.0                        

NEW FEATURES

HiCBricks

                    Changes in version 1.1.5                        

HilbertCurve

                   Changes in version 1.13.3                        

hipathia

             Changes in version 1.5.1 (2019-02-21)                  

HIREewas

             Changes in version 1.0.1 (2018-11-18)                  

HPAanalyze

                     Changes in version 1.1                         

hpar

                    Changes in version 1.25                         

Changes in version 1.25.1

Changes in version 1.25.0

HTSFilter

                   Changes in version 1.23.1                        

ideal

                    Changes in version 1.8.0                        

New features

Other notes

infercnv

             Changes in version 0.99.8 (2019-04-20)                 

InPAS

                   Changes in version 1.15.2                        

INSPEcT

                   Changes in version 1.12.1                        

IntEREst

                    Changes in version 1.8.0                        

NEW FEATURES

BUG FIXES

IRanges

                   Changes in version 2.18.0                        

NEW FEATURES

BUG FIXES

DEPRECATED AND DEFUNCT

iSEE

                    Changes in version 1.3.9                        

IsoCorrectoR

                    Changes in version 1.0.3                        

IsoCorrectoRGUI

                    Changes in version 0.0.1                        

IsoformSwitchAnalyzeR

isomiRs

                   Changes in version 1.11.3                        

FEATURES

FIX

FEATURES

karyoploteR

                   Changes in version 1.10.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG-FIXES

KEGGprofile

                   Changes in version 1.25.1                        

KinSwingR

             Changes in version 1.0.4 (2019-04-24)                  

limma

                   Changes in version 3.40.0                        

maftools

                    Changes in version 2.0.0                        

SIGNIFICANT USER-LEVEL IMPROVEMENT

IMPROVEMENTS

BUG FIX

MAGeCKFlute

                    Changes in version 1.2.2                        

matter

                   Changes in version 1.9.11                        

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

BUG FIXES

BUG FIXES

BUG FIXES

mbkmeans

             Changes in version 0.99.0 (2019-03-08)                 

Melissa

                   Changes in version 0.99.0                        

metagene2

             Changes in version 1.1.0 (2019-04-05)                  

metagenomeSeq

                    Changes in version 1.25                         

MetaNeighbor

                    Changes in version 1.3.0                        

MetCirc

             Changes in version 1.13.1 (2019-04-04)                 

methimpute

                    Changes in version 1.5.2                        

BUGFIXES

methylGSA

                    Changes in version 1.1.5                        

methylKit

                    Changes in version 1.9.4                        

NEW FUNCTIONS AND FEATURES

IMPROVEMENTS AND BUG FIXES

IMPROVEMENTS AND BUG FIXES

IMPROVEMENTS AND BUG FIXES

IMPROVEMENTS AND BUG FIXES

methylPipe

                   Changes in version 1.17.1                        

MetNet

             Changes in version 1.1.2 (2019-04-16)                  

MGFR

                    Changes in version 1.9.2                        

microbiome

             Changes in version 1.5.4 (2018-11-20)                  

minfi

                    Changes in version 1.29                         

miRSM

                    Changes in version 1.1.4                        

miRsponge

                    Changes in version 1.9.3                        

Modstrings

             Changes in version 0.99.0 (2019-01-15)                 

MOFA

             Changes in version 0.99.0 (2019-01-25)                 

motifStack

                   Changes in version 1.27.5                        

mpra

                    Changes in version 1.5.3                        

MSnbase

                     Changes in version 2.9                         

Changes in version 2.9.6

Changes in version 2.9.5

Changes in version 2.9.4

Changes in version 2.9.3

Changes in version 2.9.2

Changes in version 2.9.1

Changes in version 2.9.0

MSnID

                   Changes in version 1.17.1                        

msPurity

                   Changes in version 1.9.12                        

mzR

                   Changes in version 2.17.4                        

NADfinder

                    Changes in version 1.7.4                        

NBAMSeq

             Changes in version 0.99.1 (2019-02-13)                 

NBSplice

                    Changes in version 1.1.1                        

netboost

              Changes in version 0.99 (2019-04-02)                  

NetPathMiner

                   Changes in version 1.19.1                        

ngsReports

             Changes in version 0.99.8 (2019-04-03)                 

OmaDB

             Changes in version 1.99.3 (2019-04-15)                 

OmicsLonDA

                   Changes in version 0.99.10                       

OncoSimulR

             Changes in version 2.13.2 (2019-03-18)                 

onlineFDR

                    Changes in version 1.1.3                        

MODIFICATIONS

MODIFICATIONS

MODIFICATIONS

oposSOM

                    Changes in version 2.0.3                        

ORFik

                    Changes in version 1.3.7                        

SIGNIFICANT USER-VISIBLE CHANGES

OVESEG

             Changes in version 0.99.2 (2019-01-14)                 

PAST

            Changes in version 0.99.19 (2019-04-22)                 

PathoStat

                    Changes in version 1.8.1                        

pathview

                   Changes in version 1.23.3                        

pathwayPCA

                   Changes in version 0.99.1                        

2019-02-01

We are submitting to Bioconductor soon, so we are resolving as many of the BiocCheck() ERRORs, WARNINGs, and NOTEs. See https://github.com/gabrielodom/pathwayPCA/issues/64

                   Changes in version 0.98.0                        

2018-12-13

See the issues within the “Bioconductor Submission” and “Vignette Work” milestones for detailed descriptions of these changes, their discussion, and motivation: https://github.com/gabrielodom/pathwayPCA/issues

2018-03-20

pcaExplorer

                   Changes in version 2.10.0                        

New features

Other notes

PCAtools

                    Changes in version 1.0.0                        

PepsNMR

             Changes in version 1.1.3 (2019-03-11)                  

NEW FEATURES

BUG CORRECTION

PGA

                   Changes in version 1.13.3                        

phantasus

                    Changes in version 1.3.5                        

piano

                    Changes in version 2.0.0                        

NEW FEATURES

DOCUMENTATION

Pigengene

             Changes in version 1.9.26 (2019-04-24)                 

Bug Fixes

Changes in existing functions

Changes in existing functions

Changes in existing functions

Changes in existing functions

Changes in existing functions

pipeFrame

             Changes in version 1.0.0 (2019-04-30)                  

polyester

                   Changes in version 1.99.3                        

PoTRA

            Changes in version 0.99.93 (2019-04-16)                 

pqsfinder

                     Changes in version 2.0                         

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

pram

                   Changes in version 0.99.17                       

profileplyr

             Changes in version 0.99.0 (2019-03-29)                 

pRoloc

                    Changes in version 1.23                         

Changes in version 1.23.4

Changes in version 1.23.3

Changes in version 1.23.2

Changes in version 1.23.1

Changes in version 1.23.0

PureCN

                   Changes in version 1.14.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUGFIXES

qckitfastq

                   Changes in version 0.99.12                       

qPLEXanalyzer

                    Changes in version 1.1.4                        

qsmooth

            Changes in version 0.99.11 (2019-04-09)                 

QuasR

                   Changes in version 1.24.0                        

NEW FEATURES

r3Cseq

             Changes in version 1.29.0 (2018-12-08)                 

Rbowtie

                   Changes in version 1.23.2                        

NEW FEATURES

RcisTarget

                     Changes in version 1.3                         

RCM

                    Changes in version 0.3.0                        

Rcpi

             Changes in version 1.19.2 (2019-02-24)                 

Bug Fixes

Bug Fixes

Improvements

RcwlPipelines

            Changes in version 0.99.11 (2019-03-27)                 

RCy3

                    Changes in version 2.4.0                        

recount

                    Changes in version 1.9.7                        

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

regionReport

                   Changes in version 1.17.2                        

NEW FEATURES

RepViz

                   Changes in version 0.99.14                       

RELEASE

rGREAT

                   Changes in version 1.15.1                        

rgsepd

                    Changes in version 1.15                         

rhdf5

                   Changes in version 2.28.0                        

NEW FEATURES

USER VISIBLE CHANGES

BUG FIXES

Rhisat2

                   Changes in version 0.99.0                        

Rhtslib

                   Changes in version 1.16.0                        

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

RMassBank

                   Changes in version 2.11.2                        

rmelting

                   Changes in version 0.99.7                        

RNASeqR

                    Changes in version 1.1.3                        

RnaSeqSampleSize

             Changes in version 1.15.1 (2018-11-12)                 

BUG FIXES

RnBeads

                    Changes in version 2.1.2                        

rols

                    Changes in version 2.11                         

CHANGES IN VERSION 2.11.2

CHANGES IN VERSION 2.11.1

CHANGES IN VERSION 2.11.0

ropls

                   Changes in version 1.15.26                       

NEW FEATURE

MINOR MODIFICATION

INTERNAL MODIFICATION

NEW FEATURE

INTERNAL MODIFICATION

INTERNAL MODIFICATION

INTERNAL MODIFICATION

INTERNAL MODIFICATION

INTERNAL MODIFICATION

NEW FEATURE

NEW FEATURE

INTERNAL MODIFICATION

INTERNAL MODIFICATION

INTERNAL MODIFICATION

rpx

                    Changes in version 1.19                         

rpx 1.19.4

rpx 1.19.3

rpx 1.19.2

rpx 1.19.1

rpx 1.19.0

Rsamtools

                     Changes in version 2.0                         

SIGNIFICANT USER-VISIBLE CHANGES

RSeqAn

                    Changes in version 1.3.1                        

Rsubread

                   Changes in version 1.34.0                        

RTCA

                 Changes in version 2009-07-13                      

rWikiPathways

                    Changes in version 1.4.0                        

S4Vectors

                   Changes in version 0.22.0                        

NEW FEATURES

BUG FIXES

scAlign

             Changes in version 0.99.0 (2019-02-05)                 

scater

                   Changes in version 1.12.0                        

scds

             Changes in version 0.99.4 (2019-03-21)                 

scMerge

                    Changes in version 0.99                         

scMerge 0.99.24

scMerge 0.99.23

scMerge 0.99.21

scMerge 0.99.20

scMerge 0.99.19

scMerge 0.99.17

scMerge 0.99.11

scran

                   Changes in version 1.12.0                        

scRecover

             Changes in version 1.0.0 (2019-05-01)                  

scTensor

                   Changes in version 0.99.22                       

seq2pathway

                   Changes in version 1.15.0                        

SeqArray

                   Changes in version 1.24.0                        

NEW FEATURES

BUG FIXES

UTILITIES

NEW FEATURES

BUG FIXES

seqCAT

                    Changes in version 1.6.0                        

FEATURES

seqcombo

                    Changes in version 1.5.1                        

SeqVarTools

                   Changes in version 1.21.5                        

sevenbridges

                   Changes in version 1.13.5                        

Improvements

New Features

Improvements

New Features

Improvements

New Features

Improvements

Bug Fixes

New Features

signeR

                    Changes in version 1.9.3                        

singscore

                    Changes in version 1.3.2                        

sitePath

                   Changes in version 0.99.28                       

SNPRelate

                   Changes in version 1.18.0                        

SpatialCPie

             Changes in version 1.0.0 (2018-08-17)                  

specL

            Changes in version 1.17.22 (2019-01-24)                 

splatter

             Changes in version 1.8.0 (2018-04-18)                  

sRACIPE

             Changes in version 0.99.0 (2019-04-01)                 

ssrch

                   Changes in version 0.99.0                        

statTarget

                     Changes in version 2.0                         

NEW FEATURES

Structstrings

             Changes in version 0.99.0 (2019-03-01)                 

StructuralVariantAnnotation

             Changes in version 0.99.0 (2019-04-05)                 

SWATH2stats

                   Changes in version 1.13.6                        

UPDATE

NEW FEATURES

NEW FEATURES

UPDATE

UPDATE

NEW FEATURES

NEW FEATURES

SynMut

            Changes in version 0.99.12 (2019-04-29)                 

TargetSearch

                   Changes in version 1.40.0                        

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

                   Changes in version 2.11.2                        

TFEA.ChIP

                    Changes in version 1.3.5                        

New Features

New default database

tofsims

                    Changes in version 099.1                        

SIGNIFICANT USER-VISIBLE CHANGES

INTERNALS

topconfects

             Changes in version 1.1.4 (2018-12-29)                  

topdownr

                     Changes in version 1.5                         

Changes in version 1.5.6

Changes in version 1.5.5

Changes in version 1.5.4

Changes in version 1.5.3

Changes in version 1.5.2

Changes in version 1.5.1

TPP2D

             Changes in version 0.99.0 (2019-03-12)                 

trackViewer

                   Changes in version 1.19.28                       

transcriptogramer

                    Changes in version 1.5.6                        

transite

                    Changes in version 1.0.2                        

treeio

                    Changes in version 1.7.4                        

tRNA

             Changes in version 1.1.2 (2018-03-27)                  

tRNAdbImport

             Changes in version 1.1.1 (2019-01-26)                  

tRNAscanImport

             Changes in version 1.3.2 (2018-02-16)                  

TVTB

             Changes in version 1.9.2 (2019-02-20)                  

Bug fix

tximeta

                   Changes in version 1.1.18                        

tximport

                   Changes in version 1.11.1                        

Ularcirc

                    Changes in version 1.1.3                        

NEW FEATURES

BUG FIXES

Uniquorn

             Changes in version 2.3.5 (2019-02-27)                  

Fixed another windows VCF parse error

Fixed windows VCF parse error

Unzip test vcf file

Remove dependency

universalmotif

                    Changes in version 1.2.0                        

NEW FEATURES

MINOR CHANGES

BUG FIXES

variancePartition

                   Changes in version 1.13.5                        

VennDetail

            Changes in version 0.99.18 (2019-04-25)                 

xcms

                    Changes in version 3.5.5                        

Xeva

                   Changes in version 0.99.7                        

zinbwave

             Changes in version 1.5.3 (2019-04-19)                  

NEWS from new and existing Data Experiment Packages

bodymapRat

             Changes in version 0.99.8 (2019-04-04)                 

CluMSIDdata

                   Changes in version 0.99.5                        

curatedAdipoChIP

             Changes in version 0.99.0 (2019-03-26)                 

curatedAdipoRNA

             Changes in version 0.99.0 (2019-02-06)                 

dsQTL

                    Changes in version 2.17                         

USER VISIBLE CHANGES

FlowSorted.CordBloodCombined.450k

             Changes in version 0.99.0 (2019-01-21)                 

HCAData

                    Changes in version 0.1.0                        

New features

HDCytoData

                    Changes in version 1.3.4                        

mcsurvdata

                    Changes in version 1.0.1                        

MOFAdata

             Changes in version 0.99.0 (2019-01-25)                 

mtbls2

                   Changes in version 1.13.1                        
            Changes in version 0.99.96 (2019-04-24)                 

PtH2O2lipids

                 Changes in version 2016-04-21                      

qPLEXdata

                    Changes in version 1.1.1                        

NEWS from new and existing Workflows

BgeeCall

                    Changes in version 1.0.0                        

recountWorkflow

                    Changes in version 1.7.2                        

BUG FIXES

BUG FIXES

SingscoreAMLMutations

             Changes in version 0.99.0 (2019-03-25)                 

Deprecated and Defunct Packages

Thirteen software packages were removed from this release (after being deprecated in Bioc 3.8): nudge, GeneSelector, BiocInstaller, RamiGO, prot2D, ampliQueso, gaucho, mQTL.NMR, facopy, cytofkit, GoogleGenomics, pbcmc, IrisSpatialFeatures

Thirteen software are deprecated in this release and will be removed in Bioc 3.10: flowQ, rMAT, TSSi, flowQB, rSFFreader, ProCoNA, spliceSites, GOTHiC, DOQTL, NGScopy, SVM2CRM, miRsponge, htSeqTools

Two experimental data packages were removed in this release (after being deprecated in BioC 3.8): iontreeData, MSBdata.

Two experimental data packages are deprecated in this release and will be removed in Bioc 3.10: PGPC, flowQBData