Bugfix for initializeCpp to work with *geMatrix objects.
 

 Fix issue #654 (#655)

* fix issue #654

* update bioc version in gha workflow

* update rspm

---------

Co-authored-by: Kevin Rue <kevinrue@users.noreply.github.com> 

 Merge branch 'RELEASE_3_19' into devel 

 fix standard selector for skyline
 

 Merge pull request #91 from Vitek-Lab/devel

merge bug fix into release 

 Made geneCoexSpace() return a matrix

instead of a dgeMatrix object

Bioconductor bugfix attempt
 

 update docs
 

 1.33.15
 

 update
 

 1.33.12
 

 update version
 

 update version
 

 update results of 10-fold cross-validation
 

 clean up
 

 update figure
 

 update cutoff
 

 1.1.22
 

 1.1.19
 

 focring up-to-date version of GenomicFeatures (1.57.0 in devel, will be 1.56.0 in current 3.19 release)
 

 Date formatted to yyyy-mm-dd
 

 removed unused external_data_store text file from top level
 

 fixing the import statements
 

 shortening up line in Rd file by splitting into two
 

 Add Ensembl release 112
 

 more underscore fixes
 

 Bump version
 

 Change mechanism for automatic design_matrix insertion
 

 Un-deprecate longestConsecutive()
 

 Merge pull request #12 from wkumler/manual_shiny

Implementing a Shiny app for labelFeatsManual 

 Bugfix from CMD CHECK
 

 Updating vignette to reflect new suggestions

rendering plot metrics, new labelFeatsManual, echo=FALSE, other notes from https://github.com/Bioconductor/Contributions/issues/3387
 

 Implementing shiny app for manual labels

Replaces prior graphics device-based one
 

 Adding manual labeler screenshot to vignette
 

 Attempt to solve issues with BioConductor
 

 Merge branch 'devel' of git.bioconductor.org:packages/MSstatsShiny into devel
 

 fix skyline selector bug
 

 feature name for TMT profile plots
 

 fix param 

 plotly fix for design expt
 

 update GOterms_heatmap
 

 fix getDB bug on EPICv2 KYCG
 

 update library
 

 Update scvelo to 0.3.2 (#71)

* bump x.y.z version to even y prior to creation of RELEASE_3_19 branch

* bump x.y.z version to odd y following creation of RELEASE_3_19 branch

* https://github.com/kevinrue/velociraptor/issues/63#issuecomment-2124873730

* success!

* update comment

* exact match

* pin all package versions

* Revert "pin all package versions"

This reverts commit 75035b2f29cf0a32de81f8ad16d6fb369195454a.

* update scvelo to 0.2.5

* propose dynamic selection of scvelo dependencies

* add dependencies required for the same reason as M1

* add linux environment

* fix man page

* add Linux environment

* bump bioc-devel version

* update scvelo to 0.3.2 on M1

* update scvelo to 0.3.2 on linux

* pin environment for windows

* support Linux, not LinuxAarch64

* remove outdated comment

* docs, version bump and news

* use old value of 30 neighbors

* add news

---------

Co-authored-by: J Wokaty <jwokaty@users.noreply.github.com>
Co-authored-by: Kevin Rue-Albrecht <kevinrue@users.noreply.github.com> 

 Merge branch 'devel' of git.bioconductor.org:packages/MoleculeExperiment into devel
 

 used black and white gradient for geom_raster_img
 

 add subset description file
 

 Merge pull request #11 from SydneyBioX/feature-plot-raster

Plot DAPI image as raster underneath ggplot_me 

 Merge branch 'devel' into feature-plot-raster
 

 enlarged legends
 

 added author
 

 initial subset.R
 

 hotfix
 

 replaced reshape2::melt with base R and dplyr
 

 improved image input validation
 

 convert image array to data.frame
 

 create geom_raster_me function
 

 fix remove background
 

 retain original label for geom_df
 

 changed bds_colours
 

 fixed typo
 

 Updated workflows.
 

 Added KEGG info to vignette.
 

 Added support for KEGG enrichment
 

 pathwayPlots now supports the output from fgsea.
 

 Merge pull request #14 from hancockinformatics/devel

Merge Devel 1.1.6 

 Updated package doc to get rid of warning.
 

 Fixed warnings from pathnetGGraph test.
 

 Fixed typo, updated README and NEWS.
 

 fix trajectory chapter
 

 version bump 1.17.4
 

 minor fix to literal {}
 

 use .gcloud_access_token for TDR
 

 Map delayed type conversions to their corresponding native operations.
 

 Tighten up class checks to consider the package of origin.
 

 Update documentation of `find_de_neighborhoods`
 

 Change cntrst argument back in test_de unit test
 

 Extend unit test for `test_de` with compute_lfc_se
 

 Always include `lfc_se` if compute_lfc_se == TRUE
 

 Merge branch 'ridge_in_prediction' into devel
 

 Fix copy-paste error
 

 Add compute_lfc_se option to test_de
 

 update NEWS.md
 

 Merge branch 'master' into devel
 

 Bump version: 3.11.16 → 3.11.17
 

 Bump version: 3.11.15 → 3.11.16
 

 restored version after merge from bioc
 

 removed cosmos related stray imports from namespace
 

 `.nse_ensure_str`: strip backticks
 

 docs rebuild
 

 bugfix: escape url
 

 fix: sync bioc and github versions
 

 fix: sync bioc and github versions
 

 ci: trigger build
 

 refactor: reoxygenate
 

 refactor: remove gDRimport leftovers:
 

 doc: fix typo in description
 

 refactor: reoxygenate
 

 refactor: move prism testdata to gDRimport
 

 Merge pull request #83 from gdrplatform/GDR-2501

[GDR-2501] Correct typo reponse -> response 

 Merge pull request #151 from gdrplatform/GDR-2535

Gdr 2535 

 Merge pull request #150 from gdrplatform/GDR-2497

[GDR-2497] Move `define_matrix_grid_positions` function to `gDRutils` package 

 chore: restore package site
 

 Merge pull request #149 from gdrplatform/GDR-2516

Gdr 2516 

 chore: move  function to  package
 

 refactor: update logic to support GDS identifiers
 

 refactor: update logic
 

 refactor: update namespacing (II)
 

 refactor: replace custom annotation by reannotation logic
 

 refactor: appease lintr
 

 chore: bump version and update NEWS.md
 

 test: add unit tests
 

 Merge pull request #148 from gdrplatform/GDR-2501

[GDR-2501] Correct typo reponse -> response 

 Merge pull request #119 from gdrplatform/GDR-2535

Gdr 2535 

 fix: sync bioc and github versions
 

 chore: resolve conflict
 

 chore: update desc
 

 chore: update desc
 

 chore: update desc
 

 chore: update depenedecies
 

 chore: update desc
 

 chore: resolve conflict
 

 Merge pull request #116 from gdrplatform/GDR-2349

Gdr 2349 

 fix: fix check notes
 

 chore: update NEWS
 

 refactor: simplify logic of supported experiments
 

 doc: restore package site
 

 doc: update desc
 

 tests: add tests for define_matrix_grid_positions and round_concentration
 

 chore: shorten functions
 

 chore: add example to define_matrix_grid_positions
 

 doc: add missing return field
 

 chore: move  function from  package
 

 chore: update dependencies
 

 Merge pull request #114 from gdrplatform/GDR-2501

[GDR-2501] Correct typo reponse -> response 

 Merge pull request #113 from gdrplatform/GDR-2494

Gdr 2494 

 refactor: update as per review
 

 refactor: restore experiment_validators
 

 refactor: reoxygenate
 

 refactor: move validate functions from gDRcomponents to gDRutils
 

 fix versio coflict
 

 Update news file
 

 Bump Version number 

 Removed duplicated gene_id column from vignette
 

 Merge pull request #113 from rformassspectrometry/jomain

Don't keep an active network connection 

 refactor: support storing database name instead of active connection

- Add support to store the database file name in the object instead of the
  active connection to the database. This allows to serialize/deserialize
  `CompDb` and `IonDb` classes (and would even support parallel processing). For
  SQLite databases this is now the default. Issue #112.
- Add brackets `()` for all functions in the documentation.
 

 Handle no-op wrapper matrix seeds from alabaster.matrix.
 

 Merge branch 'master' into devel
 

 Merge remote-tracking branch 'upstream/devel' into devel
 

 Add section into the vignette about using EPIC_V2
 

 Clean up comments denoting sections I edited
 

 Add .DS_Store to git ignore
 

 Update match statements to use rownames of flat.u rather than cpg column - now accounts for cgNUM_INFO probe names in EPIC_V2
 

 Update DESCRIPTION file with annotation and manifest packages for EPIC_V2
 

 Change naming scheme from EPICv2 to EPIC_V2
 

 Add support for EPICv2 array to goregion.R
 

 Add support for EPICv2 array to plottingFunctions.R
 

 Add support for EPICv2 array to gometh.R
 

 version bump 1.31.2
 

 remove old version limits in DESC
 

 version bump in devel
 

 Bugfix when checking universalmotifs
 

 Version bump after doc-fix
 

 Merge pull request #66 from gdrplatform/GDR-2535

Gdr 2535 

 Merge pull request #65 from gdrplatform/GDR-2501

[GDR-2501] Correct typo reponse -> response 

 Merge pull request #80 from gdrplatform/GDR-2535

Gdr 2535 

 Merge branch 'devel' of git.bioconductor.org:packages/CytoPipeline into devel
 

 re-activated all unit tests
 

 test #5 for solving unit test issue with GHA
 

 3rd test to solve issue with unit tests in github actions
 

 test to solve unit test issue (with readSampleFiles) with github actions
 

 processing step argument marching using `phenoData` : update way of working

- phenoData argument matching using $KEYWORD$
- bumped to version 1.5.1
 

 process time improvements for meta.SON.clustering
 

 minor bug fix in resetCallFilter()
 

 version bump to 1.1.0 for recompilation after beachmat upgrade
 

 Handle non-JSON error responses returned by intermediate parties.

This refers to proxies or firewalls between the client and the gypsum API, the
latter of which should only be returning JSON error bodies with 'reason'.
 

 update new

update README
 

 after release

Reduce dependent packages
Revise the rd file
 

 Bump version
 

 Update Roxygen version
 

 bump to 1.23.4
 

 update to sesame mLiftOver documentation
 

 minor, message omitted
 

 Allow user to decide if y-scale (usually p-value) should be -log10 transformed. Default signif.rel.pos value changed from 0.4 to 0.2.
 

 Use rappdirs to choose the cache directory.
 

 update git actions settings.
 

 update marker selection functions.
 

 Modify suggested import. Update to default arguments.
 

 Version bump to trigger BBS
 

 Fixing image rendering problems in vignette
 

 Removing unnecessary figures now that they're generated during vignette knit
 

 Large scale vignette restructuring to improve new-user experience
 

 Bugfixes
 

 Adding citation file
 

 Adding package-level documentation
 

 Updating documentation
 

 Adding labelSingleFeat function
 

 Adding installation and updating demo
 

 Update citation info for Visium_SPG_AD
 

 try to address issue #11
 

 Merge pull request #51 from gdrplatform/GDR-2525

fix: fix check notes 

 ignore macOS build for now due to upstream issue with SparseArray
 

 Merge branch 'devel' of git.bioconductor.org:packages/ggmanh into devel
 

 Merge pull request #2 from jmacdon/master

Small fix so manhattan_plot works for GRanges objects. 

 Release version 2.11.3
 

 Singleton filtering now done by `paraclu` and `distclu` directly

The updated `.ctss_summary_for_clusters` does not remove clusters anymore.

The information on dominant CTSS score and total number of CTSS is now
stored in the dominantCTSS object directly.

Also, reorder computations so that score is the first metadata column in the cluster objects.
 

 Check on R 4.4 and bioc 3.19 on GHA
 

 Update README with some videos + link to blog posts + fix citation info displayed.
 

 push
 

 na.omit function added
 

 Version 1.15.2
 

 version 1.15.2
 

 replacing grep with match
 

 Merge pull request #18 from jonaheaton/master

update example.R 

 Patches for changes to the SVT_SparseMatrix class definition. (#9)

This handles the change in the value/index order as well as the presence
of NULL entries when all values are 1 (e.g., for logical matrices). 

 explicit function calls in tests
 

 bring back gene_info...
 

 sanity checks for sample orders and labeling
 

 enforce ID based ordering to get_dataset_samples, always use get_dataset_samples' processing as authoritative
 

 Use more robust heuristic in internal helper get_current_Ensembl_release()
 

 Updates for the latest version of the tatami library. (#271)

Require the minimum version for the latest beachmat. 

 Added BioC build status badges.
 

 Updated to the latest version of the tatami_hdf5 library. (#2)

Also use the DelayedArray block size as the cache size limits in the C++ constructors. 

 Bumped version to trigger rebuild.
 

 update internal repository names dictionary for clarity
 

 Upgrade vendored libraries to use v3 tatami interface. (#24)

This updates the associate libraries (*_chunked, *_r) and adds the new *_stats library.

We also err on the side of caution and explicitly capture each view's backing 
Rcpp::RObject, rather than relying on the original object; this ensures that any 
implicit allocations (e.g., due to ALTREP realizations) are protected from the GC. 

 Reverse the method name from "gdsfn" back to "gdsfile" per GDSArray change.
 

 bump version to trigger a new build: no change else (error can be reproduced in Bioc_devel docker)
 

 reverse method name of gdsfn back to gdsfile
 

 bump to 1.23.3
 

 Merge remote-tracking branch 'upstream/master'
 

 version Bump
 

 Fixing an issue regarding variable number of genes with data for various cancers
 

 update AlphaFold test case for additional 'amAnnotationUrl' columns

- try to generalize a bit so that test ensures at least those columns
  present today remain present
 

 In response to https://github.com/Bioconductor/Contributions/issues/3381#issuecomment-2103018848
 

 Merge branch 'devel' of gitlab.uni-marburg.de:fb20/ag-graumann/software/autonomics into devel
 

 Fix an attempt to move to non-unique (!?) `Compounds ID`;
 

 Minor formatting fixes;
Comment on uniquifying variable choice;
 

 Merge branch 'devel' of https://gitlab.uni-marburg.de/fb20/ag-graumann/software/autonomics into devel
 

 Implement
- Taudte-lab compatible sample renaming and MS modus determination;
- discarding of compounds without names;
- discarding of QC, blank and standar samples;
 

 Merge pull request #323 from rformassspectrometry/jomain

Add a method to change the data storage base path for on-disk backends 

 fix: use normalzePath for path comparisons
 

 fix: paths for Windows
 

 docs: bump version
 

 feat: add dataStorageBasePath method
 

 new m/z shift correction method
 

 fix a minor bug in estGeno()
 

 fix a bug in setPaarents()
 

 version bump
 

 More work on linear subsetting

Start to work on linear subsetting of a SVT_SparseArray object by a
matrix subscript (M-index).
Fix compilation issue on macOS (Apple clang).
 

 resolved conflicts and merged ratio_statistic branch

Merge branch 'ratio_statistic' into devel

# Conflicts:
#	DESCRIPTION
#	NAMESPACE
#	NEWS.md