done: remove CVXR dependencies
 

 done: remove CVXR dependencies
 

 Switch trend constraint solver to quadprog (removes CVXR dep)
 

 streamline the sensitivity analysis
 

 bug fix for the data sanity check in the devel branch
 

 Merge pull request #292 from FarnazFouladi/bugfix

Regularization of covariance matrix by winsorizing the eigenvalues 

 new features
 

 update example to latest catalog build
 

 Added the proteomics vignette and updated the NEWS file
 

 fix(ptm-tests): Fix unit tests for PTM differential analysis (#204) 

 Final commit for 3.23
 

 minor doc update
 

 bump HCA API ref version 16.1
 

 add MaxQuant TMT multi-run example
 

 A couple of fixes. Updated NEWS file
 

 fix(src): use SET_STRING_ELT in sortcpp instead of const_cast

const_cast on STRING_PTR_RO pointer is UB for ALTREP objects —
the backing store may be read-only memory. Copy through a temporary
vector and write back via SET_STRING_ELT (official write-barrier API).
 

 revert metadata for fixed data
 

 Switch to Authors@R format in DESCRIPTION

- Update author and maintainer info to use Authors@R.
- Update email to seandavi@gmail.com.
- Bump version to 2.67.4.
 

 Fix compilation errors and safety in windowChisq.c

- Use (DL_FUNC) cast for windowChisq to fix -Wincompatible-pointer-types error.
- Replace bitwise & with logical && in window search loops.
- Reorder loop conditions to perform bounds check before array access.
- Remove unused variable 'xa'.
- Bump version to 2.67.1.
 

 Updated NEWS file
 

 Changes FEA test to be less stringent (#165)

* Fix of FEA unit test with tolerance for permutation-based scores

* Updated dataFEA_fgsea dataset

* Updated DESCRIPTION and NEWS.md with new versioning

* Update of FEA() to include seed as new parameter for unit test consistency

* Added new seed parameter to the FEA() function

* changed test for FEA to be less strict

---------

Co-authored-by: Alessia Campo <acampo@kb-bioinfo01.cancer.dk> 

 update for bioc
 

 update for bioc
 

 Update check-bioc.yml 

 Fix CITATION + resolve rlang dependency issue
 

 Remove failing example from vignette due to dependency change.
 

 final changes for check
 

 Add files via upload 

 rm bh version control and bump
 

 remove code formatting in titles
 

 fix duplicated code chunk name
 

 add updated vignette
 

 Replace HiCBricks with rhdf5 in getChrCGFromCools

The vignette build was segfaulting in H5close() called from
HiCBricks::Create_many_Bricks_from_mcool. Reading mcool files
directly via rhdf5 (already a dependency) avoids the crash and
removes HiCBricks as a dependency entirely.

Verified output matches cgEx exactly (all.equal: TRUE).
 

 fix partial arg
 

 Pathway data update
 

 further HDR improvements, allow for donor_mismatch in is_hdr_strict, automatic sizing for variant plots
 

 add Sanchit Saini as contributor
 

 update DESC and bump version
 

 add news.md file
 

 Update survival score
 

 limpa 1.3.13
- Update NEWS.Rd for Bioc 3.23 release.
- Argument `precursor.column` of readDIANN() changed to `feature.column`.
- readDIANN() and readSpectronaut() now check for deprecated arguments.
- Update limpa-Tests.Rout.save to R 4.6.0.
- Go back to nanoparquet::read_parquet from arrow::read_parquet.
 

 restore top_prenv() and top_prenv_dots() as wrappers and use them internally to ensure test coverage
 

 Fix run_benchmark_once: message() escapes tryCatch under testthat

The tryCatch handlers in run_benchmark_once() called `message(e)` where
`e` is the caught condition. R's `message()` re-signals any condition
passed to it. Under testthat's calling handlers, signaling an error
condition is treated as a test error — which escapes the tryCatch
even though tryCatch *did* catch it.

This caused test-run_benchmark to fail on GitHub Actions whenever the
g:Profiler API returned malformed JSON (e.g. for fruit fly → human).
The all_genes() and convert_orthologs() calls were supposed to record
NA and continue, but the test errored at line 9 instead.

Fix: pass `conditionMessage(e)` (a plain string) to `message()` so it
prints the message text without re-signaling the condition.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 </pre>
    </div>
  
    

      Package: orthogene

      Commit: f977afdb58c8cfcba45b264b44bb32be5cce9f5c

      Author:  bschilder <brian_schilder@alumni.brown.edu> 

      Date: 2026-04-25 15:46:28 -0400

      Commit message:


	  
		
 Fix Bioc 3.23 R CMD check: use offline ortholog method in examples/tests

The g:Profiler API has been intermittently returning JSON with literal
`NaN` tokens, which `jsonlite` cannot parse. This caused examples and
several tests in the Bioconductor 3.23 build to fail with
`lexical error: invalid char in json text`.

* `convert_orthologs()`, `map_orthologs()`, `all_genes()` examples now
  pass `method = "homologene"` so they run offline.
* Tests that incidentally hit the default g:Profiler path
  (`test-aggregate_mapped_genes`, `test-convert_orthologs`,
  `test-infer_species`) now request `method = "homologene"` explicitly.
* Tests that intentionally cover g:Profiler
  (`test-all_genes_gprofiler`, `method = "gprofiler"` in
  `test-convert_orthologs`) skip gracefully when the API is unavailable.
* `test-run_benchmark`: `mean()` aggregates use `na.rm = TRUE` so a
  transient g:Profiler failure doesn't NA-poison benchmark assertions.
* `test-infer_species`: tolerate ties in `top_match` (human/monkey via
  babelgene tie at 94%) so the test passes as long as the expected
  species is among the top matches.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: orthogene

      Commit: 266f4aadf6ac28921e338e6d1d3f5fa1506bc9b0

      Author:  bschilder <brian_schilder@alumni.brown.edu> 

      Date: 2026-01-25 12:29:43 -0500

      Commit message:


	  
		
 Fix rbuildignore
 
    
  
    

      Package: orthogene

      Commit: 5d8286058c24a52d9f85719970f7ff88db7d0b15

      Author:  bschilder <brian_schilder@alumni.brown.edu> 

      Date: 2026-01-25 12:17:01 -0500

      Commit message:


	  
		
 update citation. [skipci]
 
    
  
    

      Package: orthogene

      Commit: c2728ce33bc072c6a9efa137bd63fd8c077f421b

      Author:  bschilder <brian_schilder@alumni.brown.edu> 

      Date: 2026-01-25 12:11:45 -0500

      Commit message:


	  
		
 update citation. [skipci]
 
    
  
    

      Package: phylobar

      Commit: 696f211cdbc7ab69786df3cc4ba619f57b2ed8d7

      Author:  Kris Sankaran <sankaran.kris@gmail.com> 

      Date: 2026-04-25 11:12:06 -0500

      Commit message:


	  
		
 checkSupportReg failure appears transient
 
    
  
    

      Package: phylobar

      Commit: 46a1b41dfe145319ad0d6674751e34236a765638

      Author:  Kris Sankaran <sankaran.kris@gmail.com> 

      Date: 2026-04-25 10:44:06 -0500

      Commit message:


	  
		
 try after support site login
 
    
  
    

      Package: MSstatsPTM

      Commit: 0054027f48a0343aaa57b86a54e737d16d35ad96

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

      Date: 2026-04-25 11:30:33 -0400

      Commit message:


	  
		
 Update package version to 2.13.4

Bump version number from 2.13.3 to 2.13.4. 
    
  
    

      Package: MSstatsPTM

      Commit: 34354a273fe2a8f79deeabd9744eea5c73c13804

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

      Date: 2026-04-25 11:30:04 -0400

      Commit message:


	  
		
 fix(dataProcessPlots): Change default of ylimDown to minimum of log2 intensity - 3 
    
  
    

      Package: motifTestR

      Commit: 36e92936e1ee7cb6e8999165a130aacb2fa32fa1

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

      Date: 2026-04-25 16:23:38 +0930

      Commit message:


	  
		
 Changed min_score default
 
    
  
    

      Package: GOaGO

      Commit: aae6d14c01abe8bbf69fd5d5226dc2a561cadab7

      Author:  Aleksander Jankowski <aleksander.jankowski@uw.edu.pl> 

      Date: 2026-04-25 08:00:31 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: scider

      Commit: 68e327dcdfda28aaf65cd8561f37713dfa5df3ea

      Author:  Yunshun Chen <yuchen@wehi.edu.au> 

      Date: 2026-04-25 16:04:21 +1000

      Commit message:


	  
		
 * scider v1.9.1:

- Update help pages
- New function getHVG() to find top HVGs
- New function plotLISAscatter() to generate a LISA scatter plot
- New functions readVisium(), readVisiumHD(), readXenium(), readProseg() for reading in data of different types
- Use Matrix package for matrix operations
- Update gridDensity() to handle different types of input
- Speed up hexDensity computation
 
    
  
    

      Package: SeqArray

      Commit: f77e3ddd9e0fc3b2115cf98dc0448aa8d484a783

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2026-04-24 22:51:55 -0500

      Commit message:


	  
		
 fix seqApply(,margin=by.sample)
 
    
  
    

      Package: metabinR

      Commit: c50d2b55ffcab1fc8c2a5ae81b0626594dd03e45

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 06:24:42 +0300

      Commit message:


	  
		
 Fix formatting and improve clarity in README.md
 
    
  
    

      Package: metabinR

      Commit: 167ac56936f79b9dca16da286e82ce44e51c6158

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 05:36:36 +0300

      Commit message:


	  
		
 Merge branch 'devel' of https://github.com/gkanogiannis/metabinR into devel
 
    
  
    

      Package: metabinR

      Commit: 00dd1b870d1732068b0ad1e08e2fe519200c68bf

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 05:33:33 +0300

      Commit message:


	  
		
 Merge branch 'devel' of https://github.com/gkanogiannis/metabinR into devel
 
    
  
    

      Package: metabinR

      Commit: 02684afbb3a9262340598b2b7044c337085e2b80

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 05:33:33 +0300

      Commit message:


	  
		
 Merge branch 'devel' of https://github.com/gkanogiannis/metabinR into devel
 
    
  
    

      Package: metabinR

      Commit: 776ed35505f64494307cc78f8fc49e5d8f3b2b89

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 05:19:17 +0300

      Commit message:


	  
		
 Clean
 
    
  
    

      Package: metabinR

      Commit: 56a665b011ab7b40a123ef14619d8466adbf0a79

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 05:16:53 +0300

      Commit message:


	  
		
 Bump version 1.99.0
 
    
  
    

      Package: metabinR

      Commit: ca9cd8606226f392ae38101b4c738e945f8dfcad

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 05:16:53 +0300

      Commit message:


	  
		
 Bump version 1.99.0
 
    
  
    

      Package: metabinR

      Commit: 64d3d0b300fe4dc5f0c27d26ad04fb0c08902419

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 05:16:53 +0300

      Commit message:


	  
		
 Bump version 1.99.0
 
    
  
    

      Package: metabinR

      Commit: 9d62a7f94718e94f558a0532ba4ba364e1066d02

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 05:12:57 +0300

      Commit message:


	  
		
 Remove build-jar workflow
 
    
  
    

      Package: metabinR

      Commit: 6b5622b5063cd8e152695079f2912f038cc681d1

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 04:52:42 +0300

      Commit message:


	  
		
 Update check-bioc workflow
 
    
  
    

      Package: metabinR

      Commit: da0cc4b26b168cbbd0d0e0fc63368d758e82f527

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 04:31:19 +0300

      Commit message:


	  
		
 Update build configuration
 
    
  
    

      Package: metabinR

      Commit: 29265e055c26ee44a12963f1ec05e07d40e9d3e0

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 02:18:27 +0300

      Commit message:


	  
		
 Update Java version to 11 in workflows and documentation
 
    
  
    

      Package: metabinR

      Commit: 9e59b240452ab997c8269891e16fe83f2f7dd14c

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 02:03:44 +0300

      Commit message:


	  
		
 - Introduced pom.xml for Maven build configuration.
- Added S4 class MetabinResult with accessors for results.
- Updated documentation for abundance_based_binning, composition_based_binning, and hierarchical_binning functions to reflect new S4 object return type.
- Implemented as.data.frame method for MetabinResult for backwards compatibility.
- Enhanced vignettes to include usage examples and JVM configuration.
- Created build-jar.sh script for building the Java JAR.
- Updated tests to validate return types and results of binning functions.
 
    
  
    

      Package: edgeR

      Commit: 38d82261798dbfce78889c37bff3de0ce144ed16

      Author:  Yunshun Chen <yuchen@wehi.edu.au> 

      Date: 2026-04-25 12:31:06 +1000

      Commit message:


	  
		
 Update NEWS.Rd, test files, and user's guide.
 
    
  
    

      Package: MetaboDynamics

      Commit: 0681e4e5eef46723ce3e3dfbc58cf498958b7c10

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-04-25 04:00:14 +0200

      Commit message:


	  
		
 logo added and typo in plot_cluster
 
    
  
    

      Package: MetaboDynamics

      Commit: aea0b6eb60c6c36006a20ad5fb0c8f6d0f95f292

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-04-24 11:56:15 +0200

      Commit message:


	  
		
 logo
 
    
  
    

      Package: MetaboDynamics

      Commit: c52cb3f0cf75506b61bd4954ece482aa98414326

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-04-24 11:51:49 +0200

      Commit message:


	  
		
 logo
 
    
  
    

      Package: Aerith

      Commit: d8dbb4c1cc6d868be9b9a0adb01db230d2a64ea2

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2026-04-24 17:52:49 -0500

      Commit message:


	  
		
 fix macos warning
 
    
  
    

      Package: fastreeR

      Commit: 366bd2e9d80b02206b16cc557e7fd6e0073e3bc1

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 01:26:14 +0300

      Commit message:


	  
		
 Remove redundant API call for backend JAR retrieval in update-backend workflow
 
    
  
    

      Package: fastreeR

      Commit: f1842d2635e96f8a7822cadeb1dd39ed50981220

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 01:08:46 +0300

      Commit message:


	  
		
 Update backend API URLs and increment version to 2.1.6
 
    
  
    

      Package: bedbaser

      Commit: c06e7267e962e1da7f9c45c37a0c05272b7cdac4

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-04-24 18:05:33 -0400

      Commit message:


	  
		
 Update bedbase api to 0.12.7
 
    
  
    

      Package: bedbaser

      Commit: 055fb7bc8c344b34bc1997cbcfeed87b3bc33fea

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-03-26 16:54:12 -0400

      Commit message:


	  
		
 Add missing fnd entries to Authors@R in DESCRIPTION (#24) 
    
  
    

      Package: ImageArray

      Commit: 7d7df30de6c2ff0a2165ad60f80b1ff610266700

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2026-04-24 23:59:12 +0200

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: ImageArray

      Commit: 678675e7b7b372a525fc210e498e228f30070c64

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2026-04-24 23:58:21 +0200

      Commit message:


	  
		
 fix example code failing with unused argument
 
    
  
    

      Package: methodical

      Commit: f493587725975795fb98f4d83103f6e191967d1a

      Author:  Richard Heery <richardheery@gmail.com> 

      Date: 2026-04-24 22:47:39 +0100

      Commit message:


	  
		
 Fixed vignettes
 
    
  
    

      Package: fastreeR

      Commit: 89b85555cbbfb7a0130b6fdaf088b355b7760068

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-25 00:54:28 +0300

      Commit message:


	  
		
 Minor bug fix in backend VCF2TREE
 
    
  
    

      Package: HIBAG

      Commit: 3ae441d5a317ab484ddfb47cafa80be83febf298

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2026-04-24 16:48:45 -0500

      Commit message:


	  
		
 improve Makevars.win
 
    
  
    

      Package: MSstatsShiny

      Commit: e225219813238a94bd89f3e9fe7742157c8c7119

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-24 17:40:43 -0400

      Commit message:


	  
		
 Bump version to 1.13.6 in DESCRIPTION file 
    
  
    

      Package: MSstatsShiny

      Commit: b0ffb2e8b7f35d73790951325791a92b3187dfb8

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-24 17:32:18 -0400

      Commit message:


	  
		
 fix(network-viz): Make MSstatsPTM results compatible with network visualization (#202) 
    
  
    

      Package: MSstatsShiny

      Commit: 5ba9c2ac7329873a64c3067ba4b7bb2cebe4287e

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-24 17:08:34 -0400

      Commit message:


	  
		
 Update package version to 1.13.5

Bump package version from 1.13.4 to 1.13.5. 
    
  
    

      Package: MSstatsShiny

      Commit: 700d5dd5139dac4b1f46b98533525316c86c80e7

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-24 17:06:35 -0400

      Commit message:


	  
		
 fix(volcano plot): Upgrade PTM volcano plots to be interactive via plotly (#200) 
    
  
    

      Package: MSstatsShiny

      Commit: 062daf459234d0c7f39d9877f06debb4effd69fa

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-24 17:03:52 -0400

      Commit message:


	  
		
 fix(network-viz): Fix deletion logic with protein complex edges (#201) 
    
  
    

      Package: MSstatsShiny

      Commit: ccd22d3639a7f67494a0673fc383e75eb7f56793

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-24 16:20:33 -0400

      Commit message:


	  
		
 fix(PTMs): Fix bugs related to PTM E2E processing (#199) 
    
  
    

      Package: MSstatsShiny

      Commit: 83156fff27b0336a712d047cad458bf43662e297

      Author:  Swaraj Patil <patil.swaraj@northeastern.edu> 

      Date: 2026-04-24 14:43:15 -0400

      Commit message:


	  
		
 Merge some bugfixes for DIANN dataset into Development (#193) 
    
  
    

      Package: MSstatsShiny

      Commit: 9beff49dfde55a89f5b6a4af5bc2c561eadb7e4c

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-24 13:14:10 -0400

      Commit message:


	  
		
 Fix(TMT): Bug fixes for TMT processing (#198) 
    
  
    

      Package: MSstatsShiny

      Commit: 60cf68c904c6cbd1868363a7cc3453d6d4c7606a

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-24 10:19:31 -0400

      Commit message:


	  
		
 feat(MSstats+): Add quality metric temporal plots (#197) 
    
  
    

      Package: MSstatsShiny

      Commit: c218b5b61f705b5eb6de76d194543210044c2457

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-23 13:54:44 -0400

      Commit message:


	  
		
 fix(loadpage): wrap top 6 rows of preview table in horizontal scrollbar (#196) 
    
  
    

      Package: MSstatsShiny

      Commit: d7e7355250868d52bfb97dabcd5466fe055dd3fd

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-23 12:54:58 -0400

      Commit message:


	  
		
 fix(DIANN): Adjust converter to pass NULL labeled amino acid for protein (#195) 
    
  
    

      Package: MSstatsShiny

      Commit: 5915a28b30fa35f9b10232bcf2646424913cb267

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-23 08:53:26 -0400

      Commit message:


	  
		
 Add NEWS file (#194) 
    
  
    

      Package: MSstatsShiny

      Commit: 6a5ae5be68f86317624f82c6970b2745ebc57378

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-22 21:59:03 -0400

      Commit message:


	  
		
 fix(turnover): Order group by numerical time value for QC plot (#192) 
    
  
    

      Package: MSstatsShiny

      Commit: 177f2ee2e2c93a217f34cb06196ab5b442139285

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-22 15:46:03 -0400

      Commit message:


	  
		
 fix(turnover): Adjust response curve visualization to have a zero heavy ratio for zero timepoint (#191) 
    
  
    

      Package: MSstatsShiny

      Commit: 841d69032d8826fa26f7ef37bfe668aa42f127e3

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-22 15:22:02 -0400

      Commit message:


	  
		
 feat(protein turnover): Add a new template for protein turnover (#189) 
    
  
    

      Package: MSstatsShiny

      Commit: b232c54562a4b00a111af27d8095f162e6c36675

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-21 21:59:03 -0400

      Commit message:


	  
		
 refactor(chemoproteomics): Create a template for chemoproteomics workflows (#188) 
    
  
    

      Package: MSstatsShiny

      Commit: 0c12984f36ee2fac3ca5bdd7d9c6e9836a47ce3a

      Author:  Tony Wu <wu.anthon@northeastern.edu> 

      Date: 2026-04-20 15:34:54 -0400

      Commit message:


	  
		
 Revert "Revert "feat(chemoproteomics): Integrate sample size calculation for dose response experiments (#181)""

This reverts commit b489b1b32a1a2305278d5f4cd66eb58d924a43ba.
 
    
  
    

      Package: MSstatsPTM

      Commit: f7cde3badfd856824877f6ae537c826efa3bcf81

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

      Date: 2026-04-24 17:02:39 -0400

      Commit message:


	  
		
 Update package version to 2.13.3

Bump version number from 2.13.2 to 2.13.3. 
    
  
    

      Package: MSstatsPTM

      Commit: db16d1a193885cedd95ce9682a04bc0f54bafa74

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

      Date: 2026-04-24 17:01:31 -0400

      Commit message:


	  
		
 fix(groupComparisonPlots): fix bug around printing (#130) 
    
  
    

      Package: MSstatsPTM

      Commit: 885d4c16ef52ae5ba2a8f389a05956d462681b6e

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

      Date: 2026-04-24 15:20:20 -0400

      Commit message:


	  
		
 fix(dataProcessPlotsPTM): Fix documentation around originalPlots (#129)

parameter 
    
  
    

      Package: pRolocGUI

      Commit: 844d138242ed5f79329376312791596be448d092

      Author:  Lisa Breckels <lms79@cam.ac.uk> 

      Date: 2026-04-22 11:53:31 +0100

      Commit message:


	  
		
 bump version for bioc
 
    
  
    

      Package: pRolocGUI

      Commit: e413058a44ed8a6a89de9bae92d20ffd3c628f23

      Author:  Lisa Breckels <lms79@cam.ac.uk> 

      Date: 2025-11-05 15:39:25 +0000

      Commit message:


	  
		
 push upstream from bioc and fix bug
 
    
  
    

      Package: pRolocGUI

      Commit: 4d7a95febc4b498d9720eccd2fcf449237e6ced0

      Author:  Lisa Breckels <lms79@cam.ac.uk> 

      Date: 2025-11-05 15:28:44 +0000

      Commit message:


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

      Package: pRolocGUI

      Commit: d6c0621671b57f326dade6b7f1549d591de824d5

      Author:  Lisa Breckels <lms79@cam.ac.uk> 

      Date: 2025-06-05 16:55:24 +0100

      Commit message:


	  
		
 Merge pull request #121 from lgatto/devel

Devel 
    
  
    

      Package: pRolocGUI

      Commit: 56c2609790a14f377c70acd1ce8bab85276e2fb5

      Author:  Lisa Breckels <lms79@cam.ac.uk> 

      Date: 2025-02-13 15:59:49 +0000

      Commit message:


	  
		
 update news following devel release
 
    
  
    

      Package: pRoloc

      Commit: 8f13f53c53fee97dfc42628525808bffddab037f

      Author:  Lisa Breckels <lms79@cam.ac.uk> 

      Date: 2026-04-22 10:31:48 +0100

      Commit message:


	  
		
 update for Bioc devel
 
    
  
    

      Package: pRoloc

      Commit: 95de37ea49abb8c2cbae72e9d6f946214a2836ef

      Author:  Lisa Breckels <lms79@cam.ac.uk> 

      Date: 2025-11-05 15:43:11 +0000

      Commit message:


	  
		
 update news
 
    
  
    

      Package: pRolocdata

      Commit: f717d11e22beab97deca6b82306b00367cf55fca

      Author:  Lisa Breckels <lms79@cam.ac.uk> 

      Date: 2026-04-22 11:57:58 +0100

      Commit message:


	  
		
 bump for devel
 
    
  
    

      Package: pRolocdata

      Commit: 71d30a0fe9060d5fe9c57b84b8ee0eb477a8195d

      Author:  Lisa Breckels <lms79@cam.ac.uk> 

      Date: 2025-11-05 15:45:18 +0000

      Commit message:


	  
		
 update news
 
    
  
    

      Package: bugsigdbr

      Commit: 5cbe716af835e21a173e016cc0d670720499ae75

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-04-24 16:38:58 -0400

      Commit message:


	  
		
 Bump to 1.17.4
 
    
  
    

      Package: bugsigdbr

      Commit: 3c8f7ad787f8af824f597849806c68aa5fece19a

      Author:  jwokaty <jwokaty@users.noreply.github.com> 

      Date: 2026-04-24 16:37:01 -0400

      Commit message:


	  
		
 Bugsigdbexports 1.3.1 (#78)

* Update BugSigDBExports to 1.3.1
* Update action to Bioconductor 3.23 
    
  
    

      Package: ImageArray

      Commit: 055e73e824128499ac7f75dd21fd9ea4df9c3631

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2026-04-24 22:28:46 +0200

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: ImageArray

      Commit: 3868a0ea4199d5e047b05cd8371c786ec5ef7ea4

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2026-04-24 22:17:59 +0200

      Commit message:


	  
		
 describe the difference between crop and [ based slicing
 
    
  
    

      Package: ImageArray

      Commit: 3a3ed0fc69f2282b1c363283f5b14c94e6be9396

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2026-04-24 21:50:54 +0200

      Commit message:


	  
		
 update GHA and remove zarr group message
 
    
  
    

      Package: ImageArray

      Commit: 603cfb94269fd7fe6afa728debee819c393f5cf3

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2026-04-24 21:37:58 +0200

      Commit message:


	  
		
 update the behaviour of format and output arguments
 
    
  
    

      Package: OAtools

      Commit: 38dd8f40d7d2b2e9bd65733e7cf81d507be56b26

      Author:  Aidan Shea <aidantshea@gmail.com> 

      Date: 2026-04-24 13:09:36 -0700

      Commit message:


	  
		
 feat: add run date to experiment colData
 
    
  
    

      Package: Cardinal

      Commit: 7b0a3e7fa1b45e7fb30aafcd8cb52c20307efb27

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

      Date: 2026-04-24 16:14:29 -0400

      Commit message:


	  
		
 delete old NEWS
 
    
  
    

      Package: Cardinal

      Commit: 76a258c9cc0d0123b1b608e0f97e5e6b2f1f51b2

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

      Date: 2026-04-24 16:09:00 -0400

      Commit message:


	  
		
 v3.13.4 change NEWS to NEWS.md; fix LICENSE errors
 
    
  
    

      Package: enrichViewNet

      Commit: abc5309a15e019cb7979db579235e95d2c8bb6f0

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2026-04-24 15:21:46 -0400

      Commit message:


	  
		
 Version bump in devel
 
    
  
    

      Package: enrichViewNet

      Commit: 6eedf45cc5bb0d14f6b73d02131a714411f5c696

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2026-04-24 15:07:35 -0400

      Commit message:


	  
		
 Update unit tests
 
    
  
    

      Package: AnVILPublish

      Commit: 314e27681caf47f090576106988247d3de701723

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 15:39:02 -0400

      Commit message:


	  
		
 version bump 1.21.2
 
    
  
    

      Package: AnVILPublish

      Commit: 1bbbeaf222332b271be859f96ccbb9a879d01e14

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 15:38:57 -0400

      Commit message:


	  
		
 add positai to .Rbuildignore .gitignore
 
    
  
    

      Package: AnVILPublish

      Commit: 67860fb52cafb404181bb41dffa5465c4d588f90

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 15:38:24 -0400

      Commit message:


	  
		
 Update NEWS.md for upcoming Bioconductor release

- Added entries for versions 1.14.0, 1.16.0, 1.18.0, 1.20.0, and 1.22.0
- Summarized changes from git history since 1.12.0
- Included export of create_workspace() in v. 1.22.0

assisted-by: Gemini 2.0 Flash
 
    
  
    

      Package: AnVILPublish

      Commit: 7745b6ac43641537821d96e330211a7853ae36ee

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 15:37:57 -0400

      Commit message:


	  
		
 minor formatting changes
 
    
  
    

      Package: igblastr

      Commit: 437e924afc94ae504c855360e14600eed404a8ab

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

      Date: 2026-04-24 12:19:44 -0700

      Commit message:


	  
		
 igblastr 1.1.29

Add 'extra_fields' arg to functions extract_intdata_from_ogrdb_json()
and extract_auxdata_from_ogrdb_json().

Some improvements to man/download_OGRDB_germline_json.Rd including
some examples now added for extract_auxdata_from_ogrdb_json().

Fix a minor issues in compute_auxdata() and in internal helper
create_region_db().

Improve unit tests for install_IMGT_germline_db().
 
    
  
    

      Package: AnVILGCP

      Commit: f37363f7ea8d3cab672674535fa563ffdc236fc0

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 15:13:04 -0400

      Commit message:


	  
		
 version bump 1.5.4
 
    
  
    

      Package: AnVILGCP

      Commit: 943a8647ba3b0e6ad4698c39a88016d2862854f9

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 15:12:42 -0400

      Commit message:


	  
		
 add positai to .gitignore and .Rbuildignore
 
    
  
    

      Package: AnVILGCP

      Commit: 319ee5409938c814d8b7eea7974e699a19c86cda

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 15:12:19 -0400

      Commit message:


	  
		
 Update NEWS.md for version 1.4.0 and 1.6.0

- Summarize changes since version 1.2.0 including deprecations, new features, and bug fixes.
- Identify missing entries for version 1.4.0 and draft entries for upcoming version 1.6.0.

Assisted-by: Gemini 2.0 Flash
 
    
  
    

      Package: AnVILBase

      Commit: 2409531d49f0ce8050c6a9c7218c2531968c45e9

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 14:58:25 -0400

      Commit message:


	  
		
 version bump 1.5.2
 
    
  
    

      Package: AnVILBase

      Commit: 1608447da85edaf70b74f0a598542d8f878b414f

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 14:57:52 -0400

      Commit message:


	  
		
 Update NEWS.md for releases 1.2.0, 1.4.0, and 1.6.0

Co-authored-by: Gemini CLI <gemini-cli@google.com>
 
    
  
    

      Package: GSVA

      Commit: dd38e0284eb3717202c5f9c61006abd8d1e2916f

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

      Date: 2026-04-24 20:44:37 +0200

      Commit message:


	  
		
 Updated vignette
 
    
  
    

      Package: SMTrackR

      Commit: 8a7064df57e6d465da17f331677d9215f173cf37

      Author:  satyanarayan-rao <satyanarayan.rao@cuanschutz.edu> 

      Date: 2026-04-24 23:51:59 +0530

      Commit message:


	  
		
 imporved vignette
 
    
  
    

      Package: AnVILAz

      Commit: f55d9fc9b9a2d0d4736e1d50781bb48f9b6231f0

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 14:21:37 -0400

      Commit message:


	  
		
 version bump 1.5.2
 
    
  
    

      Package: AnVILAz

      Commit: 57a56d16dedc9591aa774375f5d8b2de9c8aafa2

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 14:21:28 -0400

      Commit message:


	  
		
 minor updates to .Rbuildignore and .gitignore
 
    
  
    

      Package: AnVILAz

      Commit: 5cfdfe69f853b1ecefefa89b9d6ad7ef05c09859

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 14:21:06 -0400

      Commit message:


	  
		
 update NEWS.md file

assisted-by: gemini-3-flash
 
    
  
    

      Package: imcRtools

      Commit: e34f1717141d12f6b667866662a5f9f9471fc3d3

      Author:  SchulzDan <shooltz@gmx.de> 

      Date: 2026-04-24 19:50:48 +0200

      Commit message:


	  
		
 Merge pull request #147 from BodenmillerGroup/fix_scuttle_deprecation

changes due to deprecation of scuttle aggregateAcrossCells 
    
  
    

      Package: imcRtools

      Commit: d80e11630257d09fda8b0135210438e4467309cc

      Author:  SchulzDan <shooltz@gmx.de> 

      Date: 2026-04-24 15:41:24 +0000

      Commit message:


	  
		
 fixed isses with new aggregateAcrossCells
 
    
  
    

      Package: imcRtools

      Commit: 4bec3f124cf62928ceb23ea079a434c977b39adc

      Author:  SchulzDan <shooltz@gmx.de> 

      Date: 2026-04-24 10:22:37 +0000

      Commit message:


	  
		
 changes due to deprecation of scuttle aggregateAcrossCells
 
    
  
    

      Package: DaMiRseq

      Commit: ed8afbe819ce16bfac531c7c68455f15ca040828

      Author:  BioinfoMonzino <mattia.chiesa@cardiologicomonzino.it> 

      Date: 2026-04-24 19:15:30 +0200

      Commit message:


	  
		
 bugfixed.v.2.23.3_descr
 
    
  
    

      Package: DaMiRseq

      Commit: 8881bb45ea31bb20654aca87d13b165fc13141d5

      Author:  BioinfoMonzino <mattia.chiesa@cardiologicomonzino.it> 

      Date: 2026-04-24 18:55:16 +0200

      Commit message:


	  
		
 bugfixed.v.2.23.3
 
    
  
    

      Package: maaslin3

      Commit: 1423bd774ac5bf3ff44aec2e6c0947995b92f9c5

      Author:  Will Nickols <willnickols@college.harvard.edu> 

      Date: 2026-04-24 08:47:11 -0700

      Commit message:


	  
		
 Update DESCRIPTION
 
    
  
    

      Package: maaslin3

      Commit: e815b6b0e5dc1f5058be66006402f074b5b7929c

      Author:  Will Nickols <78048944+WillNickols@users.noreply.github.com> 

      Date: 2026-04-24 08:08:09 -0700

      Commit message:


	  
		
 Merge pull request #44 from biobakery/devel

Fix scaling on non-numerical data 
    
  
    

      Package: maaslin3

      Commit: fd448c1127d42e80ded7ff0cdf53b4194a491f1b

      Author:  Will Nickols <willnickols@college.harvard.edu> 

      Date: 2026-04-24 07:36:23 -0700

      Commit message:


	  
		
 Fix scaling on non-numerical data

See: https://forum.biobakery.org/t/error-in-maaslin3-nrow-value-must-match-nrow-x/8885
 
    
  
    

      Package: maaslin3

      Commit: 0debe0d5621d6d011b6086c0fe2c2d164626f8aa

      Author:  Will Nickols <78048944+WillNickols@users.noreply.github.com> 

      Date: 2026-03-06 18:14:19 -0800

      Commit message:


	  
		
 Merge pull request #42 from biobakery/andrewghazi-opt

Andrewghazi opt 
    
  
    

      Package: maaslin3

      Commit: 2db787617f2617c96aa98f2f7085325b4ce1c2dd

      Author:  Will Nickols <willnickols@college.harvard.edu> 

      Date: 2026-03-06 16:59:59 -0800

      Commit message:


	  
		
 Update fit.R
 
    
  
    

      Package: maaslin3

      Commit: f2dd45db39199cf6c040c76e054c7069334bae93

      Author:  Will Nickols <78048944+WillNickols@users.noreply.github.com> 

      Date: 2026-03-06 16:55:55 -0800

      Commit message:


	  
		
 Merge branch 'release' into andrewghazi-opt 
    
  
    

      Package: maaslin3

      Commit: 8b0776bf3daa2bbb113c9b0dfccdb45050cdfa05

      Author:  Will Nickols <willnickols@college.harvard.edu> 

      Date: 2026-03-06 15:53:36 -0800

      Commit message:


	  
		
 Fix R CMD check warnings: remove self ::: calls, fix NAMESPACE imports

- Replace all maaslin3::: self-calls with direct calls; pass internal
  functions to mirai daemons via everywhere() instead
- Change library(stats)/library(methods) to requireNamespace()
- Add importFrom("utils", "tail") to NAMESPACE
- Add utils::globalVariables(".progress") to suppress NOTE
- Add dplyr to Suggests (used in vignettes)
- Add tests for all of the above

Made-with: Cursor
 
    
  
    

      Package: maaslin3

      Commit: 13ad88815991fe203a15dc02be25474f3b465bae

      Author:  Will Nickols <willnickols@college.harvard.edu> 

      Date: 2026-02-22 18:25:07 -0800

      Commit message:


	  
		
 Updated tests, fix testthat failures
 
    
  
    

      Package: maaslin3

      Commit: 80b7cf77cfb58a5db532fba4457871f40a2d3d28

      Author:  Will Nickols <78048944+WillNickols@users.noreply.github.com> 

      Date: 2026-02-18 08:52:37 -0800

      Commit message:


	  
		
 Merge pull request #41 from biobakery/devel

Add option to bypass small random effects group warning 
    
  
    

      Package: maaslin3

      Commit: 6705d90a0b447fd03cba634e48d1746783724fd7

      Author:  Will Nickols <willnickols@college.harvard.edu> 

      Date: 2026-02-18 08:20:27 -0800

      Commit message:


	  
		
 Update DESCRIPTION
 
    
  
    

      Package: maaslin3

      Commit: ff3eada854f273565c8db53f776e52525de2236b

      Author:  Will Nickols <willnickols@college.harvard.edu> 

      Date: 2026-02-18 08:19:31 -0800

      Commit message:


	  
		
 Add bypass small group warning option
 
    
  
    

      Package: maaslin3

      Commit: 16fd3ae7b3b0b35a1236a330befa230aa2cdb985

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-04 00:45:44 -0500

      Commit message:


	  
		
 restrict env to improve memory usage
 
    
  
    

      Package: maaslin3

      Commit: ab4d0debfe3394234965d3c6e1e8ccdbff65dd49

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-03 19:25:01 -0500

      Commit message:


	  
		
 removed tibble dependency (missed when merging dt)
 
    
  
    

      Package: maaslin3

      Commit: ccba6435c8b7fadfdf3d6b0d5abfbdd808e765ae

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-03 19:02:00 -0500

      Commit message:


	  
		
 namespace or pass m3 functions to daemons
 
    
  
    

      Package: maaslin3

      Commit: e3bfbcc443a22ad466f566e52490cec390940671

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-03 17:54:18 -0500

      Commit message:


	  
		
 fix msg
 
    
  
    

      Package: maaslin3

      Commit: f5c7541a151ebd1569eb943f0df92538fcba20dd

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-03 17:22:48 -0500

      Commit message:


	  
		
 only spawn daemons if cores > 1
 
    
  
    

      Package: maaslin3

      Commit: ce56b98e31907fbd1f2d60f02dbeaa358f7eb2f3

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-03 17:15:44 -0500

      Commit message:


	  
		
 adapt log_arguments test
 
    
  
    

      Package: maaslin3

      Commit: 9a8fa341a1af08d82673beb1a8f58e32e6df0e78

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-03 17:12:09 -0500

      Commit message:


	  
		
 namespace mirai_map
 
    
  
    

      Package: maaslin3

      Commit: 4ee427826553e34f3ad1035c8d83b9d70f0d81dd

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-03 17:11:37 -0500

      Commit message:


	  
		
 parse number of daemons correctly
 
    
  
    

      Package: maaslin3

      Commit: dec7407f9faf958584d7327e6098823049a7e0ab

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-03 16:59:13 -0500

      Commit message:


	  
		
 change docs to reflect switch to mirai
 
    
  
    

      Package: maaslin3

      Commit: ec02a10abf526bd75e665b682b29f3a04b9bab75

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-02 12:09:55 -0500

      Commit message:


	  
		
 Merge branch 'misc' into opt

Add square points from misc into opt
 
    
  
    

      Package: maaslin3

      Commit: df99b9b5602f57e934a5f524a2d98b31fb84bcef

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-02 12:09:17 -0500

      Commit message:


	  
		
 square points = faster
 
    
  
    

      Package: maaslin3

      Commit: 50337936b574f832dd111b713fa8d0bd1107a839

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-01 16:51:38 -0500

      Commit message:


	  
		
 directly access coefficients
 
    
  
    

      Package: maaslin3

      Commit: 1e56edd3b87f6f3c1ea5e7219c9f791bed26b6da

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-01 16:40:32 -0500

      Commit message:


	  
		
 namespace
 
    
  
    

      Package: maaslin3

      Commit: f57769d365fafe7d0d668e948f3d69a40eba9b78

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-01 16:39:58 -0500

      Commit message:


	  
		
 revert attempt to not return fit, it's too deeply entrangled
 
    
  
    

      Package: maaslin3

      Commit: 72bf10085ae57f203069a4d6167e004238fbda45

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-01 16:26:08 -0500

      Commit message:


	  
		
 add out_dir when calling maaslin_fit
 
    
  
    

      Package: maaslin3

      Commit: 43bf68ff25c67884e45747ba5711671830f2c6de

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-01 16:25:40 -0500

      Commit message:


	  
		
 don't pass features or index when calling check_missing...
 
    
  
    

      Package: maaslin3

      Commit: 2947716c3dbb276b78a4d334280fdc684d31ceeb

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-01 16:19:29 -0500

      Commit message:


	  
		
 typo
 
    
  
    

      Package: maaslin3

      Commit: 1650bd6694f60c3fabf44229a81854e5bc4f89ac

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-01 16:04:30 -0500

      Commit message:


	  
		
 missed a comma
 
    
  
    

      Package: maaslin3

      Commit: bdbdc74ec119ba5255e537ce295225d56eb8d101

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-01 16:03:40 -0500

      Commit message:


	  
		
 missed one dplyr fn
 
    
  
    

      Package: maaslin3

      Commit: fb0f957bec7a19503ef85848b516a21e8898c5cb

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-01 16:03:16 -0500

      Commit message:


	  
		
 merge mirai into opt
 
    
  
    

      Package: maaslin3

      Commit: 9ed160fb69b8854144ab32400b24b746a26102c3

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-01 15:30:13 -0500

      Commit message:


	  
		
 merge dt into opt
 
    
  
    

      Package: maaslin3

      Commit: c86b67bf77c6ea0d0a82cf888c6cd7977a2a9bae

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-01 15:26:09 -0500

      Commit message:


	  
		
 merge misc into suggestSE
 
    
  
    

      Package: maaslin3

      Commit: 4e965b8050ca008572411731025fee1ea29c9b9a

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2026-01-01 13:33:25 -0500

      Commit message:


	  
		
 have to use rbind, these are vectors, not dfs
 
    
  
    

      Package: maaslin3

      Commit: f7cf5ade58119ecc1cc36f7f78a97d8ea47faaf9

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-31 21:44:31 -0500

      Commit message:


	  
		
 couple more rowbinds
 
    
  
    

      Package: maaslin3

      Commit: 37d0f0a94fea5b8c73978c0f432e29b48d4e379b

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-31 21:15:32 -0500

      Commit message:


	  
		
 progress eliminating fits from output list
 
    
  
    

      Package: maaslin3

      Commit: cd34879d0a8a3ed072cb7bbf0c7c9aff7ab3d377

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-31 19:08:29 -0500

      Commit message:


	  
		
 minor efficiency updates, give the code room to breathe
 
    
  
    

      Package: maaslin3

      Commit: 9d45d83f0e54ab4ee9047c4e924323b5c64c91b5

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-31 18:48:21 -0500

      Commit message:


	  
		
 improved missing first factor level check function
 
    
  
    

      Package: maaslin3

      Commit: 4b3fb85963762fef5d4219b02763d4a450003d42

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-31 18:11:51 -0500

      Commit message:


	  
		
 test to check for missing first factor level
 
    
  
    

      Package: maaslin3

      Commit: e90d54525f09d12b2e9623e3da767d151932961c

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-31 18:11:29 -0500

      Commit message:


	  
		
 setColnames
 
    
  
    

      Package: maaslin3

      Commit: 71ed4c9534791294453fb72ca872664abca555bb

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-31 17:31:39 -0500

      Commit message:


	  
		
 collapse::rowbind doesn't work on matrices
 
    
  
    

      Package: maaslin3

      Commit: ab7fe6c9aff0232bda0b7e1644200353cdaaeba5

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-31 16:01:14 -0500

      Commit message:


	  
		
 general efficiency tweaks
 
    
  
    

      Package: maaslin3

      Commit: b9eb68142e3f70b3e4d7da0a2b8fdc7e19c329e2

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-30 13:59:30 -0500

      Commit message:


	  
		
 remove tibble dependency
 
    
  
    

      Package: maaslin3

      Commit: 4b6fe43cdd66fa0cdbb3e65ae0accd4fad80d6bb

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-30 13:35:23 -0500

      Commit message:


	  
		
 refactor association_plots() function to allow parallelization
 
    
  
    

      Package: maaslin3

      Commit: 7a56ad15a12e04df4c4269719526dc869c9ef077

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-30 13:33:16 -0500

      Commit message:


	  
		
 mapply argument, everywhere() only if daemons set
 
    
  
    

      Package: maaslin3

      Commit: 18be7846df033a9368c17eb7b209e7ee7890a01d

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-29 13:17:17 -0500

      Commit message:


	  
		
 replace utils.csv with fread
 
    
  
    

      Package: maaslin3

      Commit: b962e591276add1d7cd8381c622823313432ae04

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-29 12:24:55 -0500

      Commit message:


	  
		
 remove magrittr pipes
 
    
  
    

      Package: maaslin3

      Commit: d1e0b9e490e3bfc708296da2dac13bddc5af447e

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-29 12:22:04 -0500

      Commit message:


	  
		
 remove instances of dplyr::group_by and dplyr::summarise
 
    
  
    

      Package: maaslin3

      Commit: 967e2e960dddf15d606c4fec75eafcffac81bc8f

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-28 22:32:43 -0500

      Commit message:


	  
		
 replace mapvalues with fmapvalues
 
    
  
    

      Package: maaslin3

      Commit: 8b603197bf3c5219192bf64eb919008f0f017a21

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-28 21:45:56 -0500

      Commit message:


	  
		
 replace dplyr arrange, slice_head, pull with roworderv, fslicev, get_elem
 
    
  
    

      Package: maaslin3

      Commit: a623aac4ba298dfee67d8561cf5d09008adb0385

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-28 21:25:49 -0500

      Commit message:


	  
		
 replace dplyr::filter with collapse::fsubset
 
    
  
    

      Package: maaslin3

      Commit: e7a1ad98d529827ccdbc9226752d7afbaa764b17

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-28 21:19:41 -0500

      Commit message:


	  
		
 R/utility_scripts.R
 
    
  
    

      Package: maaslin3

      Commit: eb43f1c70b31ea8db8fc9ddabd76fcb8bddb26dd

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-28 21:14:53 -0500

      Commit message:


	  
		
 replace dplyr::mutate with collapse::fmutate
 
    
  
    

      Package: maaslin3

      Commit: fd58127b3f79a36196b863fcba0abf57eeedfc7a

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-28 21:14:03 -0500

      Commit message:


	  
		
 change test to make scaling return vectors as intended
 
    
  
    

      Package: maaslin3

      Commit: 144cbdd0abfaa0b7dddb3f5d7ab0ef7695c6e52d

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-28 19:42:22 -0500

      Commit message:


	  
		
 replace dplyr joins with collapse::join
 
    
  
    

      Package: maaslin3

      Commit: 5e8df089a7d0515ce377fde79d81d4eb2bab63c9

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-28 18:06:27 -0500

      Commit message:


	  
		
 fix typo, use setrename
 
    
  
    

      Package: maaslin3

      Commit: 030b6c826e7c1670a59fb5965a275985622d9e37

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-28 17:44:47 -0500

      Commit message:


	  
		
 replace dplyr::rename with collapse::frename
 
    
  
    

      Package: maaslin3

      Commit: 8c3269a8b13c4cf11974ff3a3b6e13275255a606

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-28 15:30:42 -0500

      Commit message:


	  
		
 replace instances of dplyr::select
 
    
  
    

      Package: maaslin3

      Commit: 0239ec7b319208e764160d8a7bb228287651cddb

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-28 15:06:38 -0500

      Commit message:


	  
		
 comments + adapt to no daemons
 
    
  
    

      Package: maaslin3

      Commit: 1581aa0b3d3baeac45515d836d4abfbc55ecc47f

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-28 12:56:01 -0500

      Commit message:


	  
		
 scoped formula calls
 
    
  
    

      Package: maaslin3

      Commit: da2371193cd49a6fe49b57db20d4ccb7942893f7

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-27 14:00:54 -0500

      Commit message:


	  
		
 changes, don't load lme4 everywhere
 
    
  
    

      Package: maaslin3

      Commit: 664585949bf6c39d43db45c35a97425a374c966e

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-25 23:16:29 -0500

      Commit message:


	  
		
 just load lme4
 
    
  
    

      Package: maaslin3

      Commit: 92023144fabc4755a40194a843bb13f319dab437

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-25 22:58:09 -0500

      Commit message:


	  
		
 load lmerTest instead
 
    
  
    

      Package: maaslin3

      Commit: a9deb79070823732e813baa4f94334e5661aa6c6

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-25 22:54:15 -0500

      Commit message:


	  
		
 don't print stuff
 
    
  
    

      Package: maaslin3

      Commit: ee15e889fba58c9e2864d7bf686cd465e672c334

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-25 22:43:34 -0500

      Commit message:


	  
		
 changes to get fits to run. Key was to run library(lme4) everywhere
 
    
  
    

      Package: maaslin3

      Commit: f4b89edc5ea888ee5e19661422f7684af309f321

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-25 17:26:01 -0500

      Commit message:


	  
		
 assigned inside
 
    
  
    

      Package: maaslin3

      Commit: 2850986461cccff7195213a496a6f46c1741edae

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-25 17:25:17 -0500

      Commit message:


	  
		
 assigned inside
 
    
  
    

      Package: maaslin3

      Commit: 2391d21a937e957d035d19b291f7784721741415

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-25 17:23:48 -0500

      Commit message:


	  
		
 assigned inside
 
    
  
    

      Package: maaslin3

      Commit: ecb3257305aacc71c380f01a7980d1d89d5acb9a

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-25 17:20:03 -0500

      Commit message:


	  
		
 moving to mirai
 
    
  
    

      Package: maaslin3

      Commit: 63aeef44dff60535450716edbbcfdd3d0483f1e3

      Author:  Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com> 

      Date: 2025-12-25 16:16:35 -0500

      Commit message:


	  
		
 change dep
 
    
  
    

      Package: queeems

      Commit: 2053ea34a979fef85860e3d55ede1e65653df429

      Author:  thsadiq <hassan.t.sadiq@gmail.com> 

      Date: 2026-04-24 17:39:57 +0200

      Commit message:


	  
		
 Incorporated Bioconductor reviewer comments
 
    
  
    

      Package: AnVIL

      Commit: 862db50b9270feb23d259628fb87e244b9fac4ba

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 11:32:41 -0400

      Commit message:


	  
		
 version bump 1.23.14
 
    
  
    

      Package: AnVIL

      Commit: 9fc4b5a6febc654d477805aefa0e989381851f22

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 11:23:18 -0400

      Commit message:


	  
		
 update .gitignore and .Rbuildignore
 
    
  
    

      Package: AnVIL

      Commit: 707ddc2245114f7947b4176029eeb193c60d7c50

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 11:18:41 -0400

      Commit message:


	  
		
 update NEWS.md file

assisted-by: gemini-3-flash-preview
 
    
  
    

      Package: AnVIL

      Commit: d44a31bff7af8acde77689b8abd6ff12fa5e1288

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 11:21:56 -0400

      Commit message:


	  
		
 fix "environment" typos
 
    
  
    

      Package: queeems

      Commit: 33e1a19f3f42a8424de3762aaf373efdb4157890

      Author:  thsadiq <hassan.t.sadiq@gmail.com> 

      Date: 2026-04-24 17:26:04 +0200

      Commit message:


	  
		
 Incorporated Bioconductor reviewer comments
 
    
  
    

      Package: anndataR

      Commit: b050bbe9490cfb193695106288133b435662737b

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-04-24 17:18:50 +0200

      Commit message:


	  
		
 Prepare for Bioc 3.23 (#449)

* update news

* bump version

* update news

* rerender package

* update news.md 
    
  
    

      Package: AnVIL

      Commit: d7a1e01b4417aaa994340d8f3088d459e138475a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 11:04:15 -0400

      Commit message:


	  
		
 version bump 1.23.13
 
    
  
    

      Package: AnVIL

      Commit: fa5399a13f41274ee41576f2db724a62c855ed22

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-24 10:00:33 -0400

      Commit message:


	  
		
 add package options to bypass hardcoded URLs
 
    
  
    

      Package: AnVIL

      Commit: 827f8500bf6142649ddb53ba1b381790de8e797a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-23 16:52:18 -0400

      Commit message:


	  
		
 version bump 1.23.12
 
    
  
    

      Package: AnVIL

      Commit: 684f2a808f2d58a5695faee18095c7b8157a54cc

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-23 16:40:18 -0400

      Commit message:


	  
		
 minor: add arg names for authenticate
 
    
  
    

      Package: AnVIL

      Commit: 02f97976d698d9e2e6fac0230e84f5acf961be52

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-23 16:39:02 -0400

      Commit message:


	  
		
 add examples for anvil_set_auth_json
 
    
  
    

      Package: AnVIL

      Commit: 4e419144b42eb32da56f702fe0adadd7ab67b2b8

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-23 16:32:43 -0400

      Commit message:


	  
		
 remove authenticate_path helper not used
 
    
  
    

      Package: AnVIL

      Commit: 9589105dca7112a847f05b294fae9d1a766029d3

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-31 15:32:17 -0400

      Commit message:


	  
		
 use keyring to store auth.json file
 
    
  
    

      Package: AnVIL

      Commit: 04dbff6af52b3274580d55c2907b86b4cca93764

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-21 16:00:11 -0400

      Commit message:


	  
		
 version bump 1.23.11
 
    
  
    

      Package: AnVIL

      Commit: d3a5355ad6285d2ece7135fd85993abd7462c959

      Author:  LiNk-NY <LiNk-NY@users.noreply.github.com> 

      Date: 2026-04-21 19:59:29 +0000

      Commit message:


	  
		
 Update API
 
    
  
    

      Package: AnVIL

      Commit: 04337189b02c54e76594d34f87eeaade24ee1b8a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-31 16:38:08 -0400

      Commit message:


	  
		
 version bump 1.23.10
 
    
  
    

      Package: AnVIL

      Commit: 0025c95b8f1535697000dc6ef13ce8fbf13d8477

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-31 16:38:03 -0400

      Commit message:


	  
		
 use sha256 instead of md5sum for service validation
 
    
  
    

      Package: AnVIL

      Commit: decfee69bd47497ac7dfe2a2868dfb5190a03cd9

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-31 14:31:31 -0400

      Commit message:


	  
		
 fix typo in Service docs
 
    
  
    

      Package: AnVIL

      Commit: 799c95355c64dcd1fa33dd72783816363ee1c385

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-31 14:30:49 -0400

      Commit message:


	  
		
 use rmarkdown backticks for code in docs
 
    
  
    

      Package: AnVIL

      Commit: d5c7f58433033c01996e0dd3a2fc050b96a19744

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-31 14:29:16 -0400

      Commit message:


	  
		
 use returns instead of return roxygen tags
 
    
  
    

      Package: AnVIL

      Commit: d8fed12777b354ce16a883eee236b35649b61366

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-31 13:44:13 -0400

      Commit message:


	  
		
 version bump 1.23.9
 
    
  
    

      Package: AnVIL

      Commit: 819ec1a73c8f1f7b9f3d836da3c24e68dace8345

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-31 13:43:24 -0400

      Commit message:


	  
		
 remove unnecessary ssl config
 
    
  
    

      Package: AnVIL

      Commit: af78c782e0dd193ad7539a8980319580e5a5ba31

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-02-04 18:35:37 -0500

      Commit message:


	  
		
 version bump 1.23.8
 
    
  
    

      Package: AnVIL

      Commit: 536edf583be859cc7a1b1a68b7f2f3d9b858c0df

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-02-04 18:35:28 -0500

      Commit message:


	  
		
 use qualified gcloud_access_token to avoid NAMESPACE conflicts
 
    
  
    

      Package: AnVIL

      Commit: 9e23a136ddb41668065305bb4445086f1037cbbe

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-02-04 15:03:31 -0500

      Commit message:


	  
		
 version bump 1.23.7
 
    
  
    

      Package: AnVIL

      Commit: 9e72aa897f53465ff66ec54fd54788cc18633988

      Author:  LiNk-NY <LiNk-NY@users.noreply.github.com> 

      Date: 2026-02-04 20:02:08 +0000

      Commit message:


	  
		
 Update API
 
    
  
    

      Package: AnVIL

      Commit: a1108ef1427006a335dad641dd11a02f5f371ad7

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-12-11 16:28:49 -0500

      Commit message:


	  
		
 track openapi.yaml in auto commits
 
    
  
    

      Package: AnVIL

      Commit: 991f3ba40e1cf651000e4d8c9d73a1fccfc45101

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-12-11 16:25:15 -0500

      Commit message:


	  
		
 version bump 1.23.6
 
    
  
    

      Package: AnVIL

      Commit: 559eac585e794ff3208d64dd36ce5097b7c00080

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-12-11 16:25:10 -0500

      Commit message:


	  
		
 update Dockstore API version to 1.18.2
 
    
  
    

      Package: Rarr

      Commit: a711941e2c727169bd63782e6438be9b5741afc2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-23 20:02:11 +0200

      Commit message:


	  
		
 Remove outdated fixme comment
 
    
  
    

      Package: Rarr

      Commit: 382474e0be7e554253cb40b57d65599463b294a2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-23 20:00:54 +0200

      Commit message:


	  
		
 Apply list->string data_type transformation for both v2 and v3
 
    
  
    

      Package: Rarr

      Commit: 2848470b9f564b5db3d54214d5d7a0a94457d661

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-23 20:00:16 +0200

      Commit message:


	  
		
 Simplify bytesize handling in codec_bytes_decode()
 
    
  
    

      Package: Rarr

      Commit: e76cd6fbdf3d3b455864909e536ed134adab43d3

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-23 16:28:58 +0200

      Commit message:


	  
		
 Convert fixed length string v3 to their new names
 
    
  
    

      Package: MSstatsConvert

      Commit: bf0b062d97baefda7c677273c36df4885592de86

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

      Date: 2026-04-24 09:56:17 -0400

      Commit message:


	  
		
 Bump version to 1.21.6 in DESCRIPTION file 
    
  
    

      Package: MSstatsConvert

      Commit: dc6499366c9a7b7762aa899f68ddb997a58ef1b0

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

      Date: 2026-04-24 09:28:55 -0400

      Commit message:


	  
		
 feat(msstats+): make run order determine order of levels of Run column (#131) 
    
  
    

      Package: MSstats

      Commit: b05b3987233ae4adaa488f544e444b73eef40073

      Author:  Mateusz Staniak <mtst@mstaniak.pl> 

      Date: 2026-04-24 15:54:17 +0200

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: MSstats

      Commit: 688ff6d138e759271aea86f779cdb3b18b92d64b

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

      Date: 2026-04-24 09:45:49 -0400

      Commit message:


	  
		
 feat(MSstats+): Add plot showing quality metrics over time (#203) 
    
  
    

      Package: MSstats

      Commit: 2cb70669faaaaa5abf53c235fdaf5e076b564f0a

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

      Date: 2026-04-23 20:12:30 -0400

      Commit message:


	  
		
 fix(comparisonPlot): Add 95% CI description in tooltip (#202) 
    
  
    

      Package: MSstats

      Commit: ffcf6d76e75cebdabe08ee17fb3ecf6914e681d1

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

      Date: 2026-04-23 18:56:19 -0400

      Commit message:


	  
		
 fix(comparison-plots): Add standard error confidence intervals to label (#201) 
    
  
    

      Package: MSstats

      Commit: cf46505008698cca240dddc1702864f7934ecd4a

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

      Date: 2026-04-23 15:49:27 -0400

      Commit message:


	  
		
 fix(dataProcessPlots): Fix error bar caps / whiskers for profile plots for plotly visualization (#200) 
    
  
    

      Package: MSstats

      Commit: fb0fcf4c4bd56e93215e26be499e924f10e64b8c

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

      Date: 2026-04-23 08:17:15 -0400

      Commit message:


	  
		
 Update NEWS file (#199) 
    
  
    

      Package: MSstats

      Commit: 5ab0b47c7d819a1312cc94df2fd8b994472ac55f

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

      Date: 2026-04-22 21:29:45 -0400

      Commit message:


	  
		
 fix(globalStandards): Use median instead of mean for global standards normalization (#198) 
    
  
    

      Package: anndataR

      Commit: 832b45c27e5bd485678f405da2c33b8eee756d09

      Author:  Mark Keller <7525285+keller-mark@users.noreply.github.com> 

      Date: 2026-04-24 09:40:18 -0400

      Commit message:


	  
		
 Add initial Zarr support (#190)

* WIP

* More tests passing

* Fix df read bug

* More tests passing after fixing zero-dimensional get bug in pizzarr

* WIP: writing

* Fix more tests

* Zarr df writing

* WIP: ZarrAnnData class

* Tests passing

* Tests that compare h5ad to zarr

* Use Rarr to read full numeric arrays

* Fix bugs. Add test for from_SingleCellExperiment with Zarr

* Add a to_dense param to ZarrAnnData constructor. Add overwrite params internally.

* Update

* Backwards dense/sparse

* Simplify how obs and var names handled in ZarrAnnData (similar to #171)

* update extdata and documentation

* fix set/get zarr _index, update text example.zarr and update tests similar to HDF5AnnData

* Fix test

* Revert unnecessary changes

* Formatting

* Add comments

* remove unnecessary example zarr store

* lintr and R check for zarr related utilities and functions, updated some documentation

* add pizzarr to Suggests and README

* proj

* add keller-mark/pizzarr to Remotes

* zip example.zarr

* adapt read_zarr to Rarr

* adapt write_zarr to Rarr

* remove old scripts

* update write_zarr

* initial update to ZarrAnnData

* update ZarrAnnData, documentation, and implement read_zarr_rec_array

* review read zarr helpers, and update tests

* update read_zarr, read tests pass

* some updates for writing zarr

* update write_empty_zarr

* remove pizzarr, update documentation

* remove pizzarr from tests

* fix test-ZarrAnnData

* update ZarrAnnData to imitate HDF5AnnData

* check redundant files, correct lines

* update example_h5ad.py, add zarr and change to example_files.py

* add new test example

* some linting changes

* remove read/write_zattrs since implemented in Rarr

* access read/write_zarr_attr

* add some missing tests

* update readers, update tests

* correct nullable string zarr array write/read, introduce ordering in categorical zarr array

* do some linting, fix commented out code

* update some zarr writers and classes

* fix documentation

* fix compression interface for zarr

* full lint check

* fix examples

* check, biocheck and lintr

* fix development status

* air format

* air format test

* update example.zarr.zip, skip some test (waiting for Rarr)

* update example.zarr, fix some read_zarr_

* fix examples

* remove overwrite

* R code styling

* fixes from @lazappi

* air format

* update some documentation

* fix some tests

* more fixes on anndata-zarr integration

* update ZarrAnnData$initialize

* update zarr compression

* fix column-order here, C based ordering for arrays

* implement roundtrip tests for anndata-zarr

* add zarr to vignettes

* update README and software_design.rmd

* update AnnData-usage

* update write_zarr documentation

* update write_zarr_null

* fix rec_array, update tests and example datasets

* fix duplicate chunks in Rmd

* add write_zarr_null

* update write string array (zarr), air and lint

* implement writing empty zarr elements

* update tests for rec_array conformance of h5ad and zarr

* update mapping conformance test for h5ad and zarr

* implement H5_ITER like ordering and fix h5ad vs zarr testing

* air and lint

* fix test bug

* do not call expect_equal outside of test

* implement examples, test and datasets for zarr v3

* fix issues, lint and update example datasets to new anndata version

* lint and merge

* revert some lines

* small changes

* revert small changes

* air format some tests

* Set v2 in write_zarr_* helpers

* Fix stop message in write_zarr_element()

* Fix roxygen comment in write_zarr_element()

* Expand compression list in as_ZarrAnnData()

* Fix H5_ITER_INC_ORDERING docs

* Fix as_ZarrAnnData() compression docs

* Fix Zarr varm roundtrip test

* Review duplicate entry in README

* Fix typo in AnnData-usage docs

* Fix comma in software design vignette

* Adjust class descriptions in software design vignette

* Roxygenise

* Minor text fixes

* Document .get_compressor

* Minor fixes to function docs

* Comment logic in create_zarr_group()

* Fix indentation in read_zarr_sparse_array()

* Add construct sparse matrix helper

* Add ZARR_METADATA_FILES vector

* Eval Zarr chunks in vignettes

* Merge test-Zarrv3-read.R into test-Zarr-read.R

* Combine roundtrip tests

* Add roundtrip test helpers

* Refactor test-h5ad-zarr.R to use helper

* Refactor example files script

- Use uv comments for dependencies
- Update dependencies to latest stable versions
- Add progress messages
- Use Ruff for formatting

* Remove H5_ITER_INC_ORDERING()

* Remove Zarr compression comment

* Fix factor creation in read_zarr_categorical()

* Pin Rarr version

* Delete existing Zarr path before writing

* Add helper functions for accessing Zarr keys

* Update read_zarr_element() error message

* Add dimname warnings to ZarrAnnData

* Add Zarr writeability checks/tests

* Roxygenise, lint, style

* Use setup-bioc for all GHA

* Update WORDLIST

* Add .venv to .Rbuildignore

* Clean up test output

* Style

* add Artur as ctb

* fix linting issues

* Add Bisaloo as contributor

Co-authored-by: Hugo Gruson <hugo.gruson@protonmail.com>

---------

Co-authored-by: Artur-man <artur-man@hotmail.com>
Co-authored-by: Luke Zappia <luke@data-intuitive.com>
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com>
Co-authored-by: Hugo Gruson <hugo.gruson@protonmail.com> 
    
  
    

      Package: anndataR

      Commit: ef40467beabefb90a6b1a48a4120f1007f2b8a2b

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2026-04-24 10:16:59 +0200

      Commit message:


	  
		
 Add version 1.2.0 (Bioc 3.23) release notes (#448)

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> 
    
  
    

      Package: anndataR

      Commit: fc5dc5bb76275e7dad71f019c130b994a8d99de5

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2026-04-23 17:59:51 +0200

      Commit message:


	  
		
 Fix GHA MacOS/Windows setup issue (#447)

* Attempt fix for GHA MacOS/Windows setup issue

* Try replacing .available.both()

* Try unlock binding

* Try manual setup

* Apply suggestion from @rcannood

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> 
    
  
    

      Package: anndataR

      Commit: 6cd48af8a29fb51fb91f5252b73175851fb8ae16

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-04-13 10:35:16 +0200

      Commit message:


	  
		
 Bump actions/github-script from 8 to 9 (#443)

Bumps [actions/github-script](https://github.com/actions/github-script) from 8 to 9.
- [Release notes](https://github.com/actions/github-script/releases)
- [Commits](https://github.com/actions/github-script/compare/v8...v9)

---
updated-dependencies:
- dependency-name: actions/github-script
  dependency-version: '9'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 
    
  
    

      Package: anndataR

      Commit: 5c1315a787446e5f8c9c7fd639fc2888bc23d179

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-04-10 15:32:31 +0200

      Commit message:


	  
		
 Bump dawidd6/action-download-artifact from 19 to 20 (#440)

Bumps [dawidd6/action-download-artifact](https://github.com/dawidd6/action-download-artifact) from 19 to 20.
- [Release notes](https://github.com/dawidd6/action-download-artifact/releases)
- [Commits](https://github.com/dawidd6/action-download-artifact/compare/v19...v20)

---
updated-dependencies:
- dependency-name: dawidd6/action-download-artifact
  dependency-version: '20'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 
    
  
    

      Package: anndataR

      Commit: ca7d2e5c26c6f1215a707c32295c4023d8ad4141

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-04-10 14:42:47 +0200

      Commit message:


	  
		
 Bump bencherdev/bencher from 0.6.0 to 0.6.2 (#442)

Bumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.6.0 to 0.6.2.
- [Release notes](https://github.com/bencherdev/bencher/releases)
- [Commits](https://github.com/bencherdev/bencher/compare/v0.6.0...v0.6.2)

---
updated-dependencies:
- dependency-name: bencherdev/bencher
  dependency-version: 0.6.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 
    
  
    

      Package: anndataR

      Commit: de9acf93d178f6b474c4fa38f3897b98c267eaa0

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-03-31 14:25:16 +0200

      Commit message:


	  
		
 Fix software design vignette (#438) 
    
  
    

      Package: anndataR

      Commit: 196ba3ebb2770d3795ae1e991aabb6ee21001f34

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-03-31 14:24:24 +0200

      Commit message:


	  
		
 Bump bencherdev/bencher from 0.5.10 to 0.6.0 (#439)

Bumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.5.10 to 0.6.0.
- [Release notes](https://github.com/bencherdev/bencher/releases)
- [Commits](https://github.com/bencherdev/bencher/compare/v0.5.10...v0.6.0)

---
updated-dependencies:
- dependency-name: bencherdev/bencher
  dependency-version: 0.6.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

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      Package: anndataR

      Commit: 202b7390a5905a8d6cfae0b239241e5840a47ab9

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-03-31 14:23:55 +0200

      Commit message:


	  
		
 Bump codecov/codecov-action from 5 to 6 (#437)

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 5 to 6.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v5...v6)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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      Package: anndataR

      Commit: e07d22fab4fa5cbed020699b519bf9d0ad80f762

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-03-31 14:23:44 +0200

      Commit message:


	  
		
 Bump dawidd6/action-download-artifact from 16 to 19 (#436)

Bumps [dawidd6/action-download-artifact](https://github.com/dawidd6/action-download-artifact) from 16 to 19.
- [Release notes](https://github.com/dawidd6/action-download-artifact/releases)
- [Commits](https://github.com/dawidd6/action-download-artifact/compare/v16...v19)

---
updated-dependencies:
- dependency-name: dawidd6/action-download-artifact
  dependency-version: '19'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 
    
  
    

      Package: anndataR

      Commit: e065626d8863a1923ab6b322fb7a14b95d0e9c6e

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-02-26 22:45:45 +0100

      Commit message:


	  
		
 Bump dawidd6/action-download-artifact from 15 to 16 (#432)

Bumps [dawidd6/action-download-artifact](https://github.com/dawidd6/action-download-artifact) from 15 to 16.
- [Release notes](https://github.com/dawidd6/action-download-artifact/releases)
- [Commits](https://github.com/dawidd6/action-download-artifact/compare/v15...v16)

---
updated-dependencies:
- dependency-name: dawidd6/action-download-artifact
  dependency-version: '16'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 
    
  
    

      Package: anndataR

      Commit: 026673662fc73df0cc5214846d84399abd5b00df

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-02-26 22:44:21 +0100

      Commit message:


	  
		
 Bump actions/upload-artifact from 6 to 7 (#431)

Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 6 to 7.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](https://github.com/actions/upload-artifact/compare/v6...v7)

---
updated-dependencies:
- dependency-name: actions/upload-artifact
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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      Package: queeems

      Commit: eeca8b9939f81fab91d2a693490d52dc03cd6554

      Author:  thsadiq <hassan.t.sadiq@gmail.com> 

      Date: 2026-04-24 14:29:30 +0200

      Commit message:


	  
		
 Incorporated Bioconductor reviewer comments
 
    
  
    

      Package: msqrob2

      Commit: 9a522ff84a181f3b6950042b1dbbb3e27f44420c

      Author:  Lieven <lieven@mac.home> 

      Date: 2026-04-24 11:39:55 +0200

      Commit message:


	  
		
 update vignettes + README + version bump
 
    
  
    

      Package: shiny.gosling

      Commit: f4fe6ae27e5798f0b0c9a805d039f5e8c851564b

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

      Date: 2026-04-24 07:17:48 -0400

      Commit message:


	  
		
 Undeprecation
 
    
  
    

      Package: betterChromVAR

      Commit: 82ae1e4ada8a43c721aa2ae1c3f2c6dfc3d5a637

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-04-24 12:57:43 +0200

      Commit message:


	  
		
 vignette appendix and version bump
 
    
  
    

      Package: betterChromVAR

      Commit: 766100576ae95ff020a5a2d27d0fa9aacf872ffe

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-04-24 12:55:28 +0200

      Commit message:


	  
		
 fixed titles
 
    
  
    

      Package: Moonlight2R

      Commit: a746563b3ab2659016daa81b2342e304f5ddea25

      Author:  AlessiaCampo <59013682+AlessiaCampo@users.noreply.github.com> 

      Date: 2026-04-24 11:02:52 +0200

      Commit message:


	  
		
 Fix of FEA unit test with tolerance for permutation-based scores (#164)

* Fix of FEA unit test with tolerance for permutation-based scores

* Updated dataFEA_fgsea dataset

* Updated DESCRIPTION and NEWS.md with new versioning

* Update of FEA() to include seed as new parameter for unit test consistency

* Added new seed parameter to the FEA() function

---------

Co-authored-by: Alessia Campo <acampo@kb-bioinfo01.cancer.dk> 
    
  
    

      Package: gDRimport

      Commit: 260e6debb728b470f919afd40b1c67cfcd53f8f5

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

      Date: 2026-04-24 10:09:37 +0200

      Commit message:


	  
		
 Merge pull request #118 from gdrplatform/GDR-3355

Gdr 3355 
    
  
    

      Package: gDRimport

      Commit: f1245ac81d8d97446296d7b6afb934ff22225218

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-04-23 19:12:18 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRimport

      Commit: 947cb25ae83d40ae7ee7c85193e79635025d4e96

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-04-23 14:53:31 +0200

      Commit message:


	  
		
 test: update unit test
 
    
  
    

      Package: gDRimport

      Commit: 25fa3e3402560981c1012bdf908a4993fc8964e7

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-04-23 11:09:30 +0200

      Commit message:


	  
		
 fix: unit tests
 
    
  
    

      Package: gDRimport

      Commit: cbdcd9c8ec1d03ca83b1e1771122c3c72e8060b7

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-04-23 10:33:56 +0200

      Commit message:


	  
		
 refactor: appease lintr
 
    
  
    

      Package: gDRimport

      Commit: bb313d3dc0496d619a52b7e4d8c4d8ef51b30c4a

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-04-23 09:17:29 +0200

      Commit message:


	  
		
 chore: resolve conflict
 
    
  
    

      Package: gDRimport

      Commit: 98aad5099c0f782303debbace43917068df1e716

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-04-22 11:05:40 +0200

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 
    
  
    

      Package: gDRimport

      Commit: 6b40daaad5592fa16d98b75b023301128255fd01

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-04-22 11:05:35 +0200

      Commit message:


	  
		
 test: add unit tests
 
    
  
    

      Package: gDRimport

      Commit: 2a732634f3b4267cb0b53e47881ddd0ddaa07bb5

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-04-22 11:05:19 +0200

      Commit message:


	  
		
 doc: reoxygenate
 
    
  
    

      Package: gDRimport

      Commit: 2fce4ef3cc382b2ae6d11bc25c9dfe0195a3ff69

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-04-22 11:05:06 +0200

      Commit message:


	  
		
 refactor: add support for day0 template generation tdd
 
    
  
    

      Package: scrapper

      Commit: ae44b27fbfb65d2280bb8906fbf90dc6a8428540

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-04-24 16:32:54 +1000

      Commit message:


	  
		
 Store group-wise medians in SE output during aggregation.
 
    
  
    

      Package: phylobar

      Commit: dbd7972acc6a59db0e18eb9082dc85fb1778ecd7

      Author:  Kris Sankaran <sankaran.kris@gmail.com> 

      Date: 2026-04-23 23:38:56 -0500

      Commit message:


	  
		
 test if just an http error
 
    
  
    

      Package: Voyager

      Commit: cdd510de71be7b7705420a2949b09a91279422a7

      Author:  Lambda Moses <dlu2@caltech.edu> 

      Date: 2026-04-23 22:32:27 -0400

      Commit message:


	  
		
 More informative error message
 
    
  
    

      Package: SpatialFeatureExperiment

      Commit: c4ec4f9910b206e13d1a3c9129bfccba5c214798

      Author:  Lambda Moses <dlu2@caltech.edu> 

      Date: 2026-04-23 22:31:29 -0400

      Commit message:


	  
		
 Embarrasing mistake
 
    
  
    

      Package: SpatialFeatureExperiment

      Commit: b7983bdeeb67a3a7a0d04a674b88ff6fbf80ee83

      Author:  Lambda Moses <dlu2@caltech.edu> 

      Date: 2026-04-20 18:57:06 -0400

      Commit message:


	  
		
 Deal with weird geos error in sf_remove_holes
 
    
  
    

      Package: SpatialFeatureExperiment

      Commit: 89d5397559923395752304a2286e7108323299ae

      Author:  Lambda Moses <dlu2@caltech.edu> 

      Date: 2026-04-10 20:18:25 -0400

      Commit message:


	  
		
 Apparently only mac doesn't have problems with dependencies right now
 
    
  
    

      Package: SpatialFeatureExperiment

      Commit: 796db65c03992c1b2e28d82f27ed61a083801ed7

      Author:  Lambda Moses <dlu2@caltech.edu> 

      Date: 2026-04-10 20:03:52 -0400

      Commit message:


	  
		
 pkgdown warning
 
    
  
    

      Package: SpatialFeatureExperiment

      Commit: e781d0ee402f9759f7277288fc8f7e0e0577dd59

      Author:  Lambda Moses <dlu2@caltech.edu> 

      Date: 2026-04-10 20:00:08 -0400

      Commit message:


	  
		
 pkgdown problem
 
    
  
    

      Package: SpatialFeatureExperiment

      Commit: 19b6420f6c7bd9e5f4440b7c96f9b449c7af0461

      Author:  Lambda Moses <dlu2@caltech.edu> 

      Date: 2026-04-10 19:59:16 -0400

      Commit message:


	  
		
 Attempt to deal with error compiling uwot on GH Actions
 
    
  
    

      Package: enrichplot

      Commit: 56ca675439d5b7f5d6b5d4b188282090681e4c1f

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-04-24 08:58:26 +0800

      Commit message:


	  
		
 update
 
    
  
    

      Package: enrichplot

      Commit: 42ffd57b794e02e1b49c1ef48025757755768537

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-04-24 08:32:29 +0800

      Commit message:


	  
		
 update readme
 
    
  
    

      Package: enrichplot

      Commit: 5999960831eccfcfad825dc5e505b02c91586fad

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-04-24 08:30:31 +0800

      Commit message:


	  
		
 cnetplot for compareCluster
 
    
  
    

      Package: phylobar

      Commit: 71d057e17870c36a0f6c8596fc2066504e08b6a0

      Author:  Kris Sankaran <sankaran.kris@gmail.com> 

      Date: 2026-04-23 17:00:17 -0500

      Commit message:


	  
		
 bumped version
 
    
  
    

      Package: phylobar

      Commit: 3096110497f0f2afc9e3a62c8d57a901fd41885d

      Author:  mkdiro-O <mkuo22@wisc.edu> 

      Date: 2026-04-23 16:57:52 -0500

      Commit message:


	  
		
 allow dataframe as input for x
 
    
  
    

      Package: phylobar

      Commit: c78a966bca8c6758a6f136d9a00a3ae4460290ca

      Author:  Kris Sankaran <sankaran.kris@gmail.com> 

      Date: 2026-04-23 16:56:58 -0500

      Commit message:


	  
		
 hfhs should use zen4R
 
    
  
    

      Package: phylobar

      Commit: 763d7503d1d6bb7c32d4fceab27f258044588b6c

      Author:  Kris Sankaran <sankaran.kris@gmail.com> 

      Date: 2026-04-23 16:40:53 -0500

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: phylobar

      Commit: 6aeb79821f6627c0be32c0bbf6f8fb5b8223634d

      Author:  mkdiro-O <mkuo22@wisc.edu> 

      Date: 2026-04-23 16:40:17 -0500

      Commit message:


	  
		
 update docs
 
    
  
    

      Package: phylobar

      Commit: 41774e2e0c138e15a4f9a35000ab2298247952bf

      Author:  mkdiro-O <mkuo22@wisc.edu> 

      Date: 2026-04-23 16:34:26 -0500

      Commit message:


	  
		
 update version
 
    
  
    

      Package: phylobar

      Commit: 0d59fb3ef0a5c7a951d202bdc286021ae6a9a5db

      Author:  mkdiro-O <mkuo22@wisc.edu> 

      Date: 2026-04-23 16:32:52 -0500

      Commit message:


	  
		
 read zen4R downloaded file
 
    
  
    

      Package: phylobar

      Commit: ed33dd8e57e0658dafdbd317466fc7a3938a4d27

      Author:  Kris Sankaran <sankaran.kris@gmail.com> 

      Date: 2026-04-23 16:21:42 -0500

      Commit message:


	  
		
 use zen4r in hfhs vignette
 
    
  
    

      Package: phylobar

      Commit: f654e3c3a01dbccd877f2eaf8b91477c3c204169

      Author:  mkdiro-O <mkuo22@wisc.edu> 

      Date: 2026-04-23 16:10:15 -0500

      Commit message:


	  
		
 update paper link
 
    
  
    

      Package: phylobar

      Commit: 769b0f875e00e2a096c4199eac7b34a5da580f5e

      Author:  mkdiro-O <mkuo22@wisc.edu> 

      Date: 2026-04-21 12:27:21 -0500

      Commit message:


	  
		
 fix missing palette argument in update_tree_labels call
 
    
  
    

      Package: phylobar

      Commit: 2ba2412cf9bc73a4ce6bd37965ce26fb12b1c2d4

      Author:  mkdiro-O <mkuo22@wisc.edu> 

      Date: 2026-04-21 12:10:03 -0500

      Commit message:


	  
		
 edit check_inputs
 
    
  
    

      Package: phylobar

      Commit: c131d9ad30230c69456625bda92f4639a336c0c4

      Author:  mkdiro-O <mkuo22@wisc.edu> 

      Date: 2026-04-21 12:02:33 -0500

      Commit message:


	  
		
 use zen4R
 
    
  
    

      Package: phylobar

      Commit: e24173807b5195a07cbcaeb72aafd5414a8b12a6

      Author:  mkdiro-O <mkuo22@wisc.edu> 

      Date: 2026-04-09 14:57:09 -0500

      Commit message:


	  
		
 Add installation command to getting started
 
    
  
    

      Package: phylobar

      Commit: a9c10e805006598616ec135559e2b0af3acc10a4

      Author:  mkdiro-O <mkuo22@wisc.edu> 

      Date: 2026-04-07 12:04:10 -0500

      Commit message:


	  
		
 Update installation instructions to use BiocManager's install function
 
    
  
    

      Package: phylobar

      Commit: dfb0ef2f5a0aa912505ad9915a1809a7e42c7441

      Author:  mkdiro-O <mkuo22@wisc.edu> 

      Date: 2026-04-07 11:46:12 -0500

      Commit message:


	  
		
 Update installation instructions to use BiocManager's install function
 
    
  
    

      Package: phylobar

      Commit: cd6bdb5e220934b6bd13a21f9fc225fa9340aded

      Author:  mkdiro-O <mkuo22@wisc.edu> 

      Date: 2026-04-07 11:45:38 -0500

      Commit message:


	  
		
 prepend numbers to vignettes
 
    
  
    

      Package: MutSeqR

      Commit: 337836d072a83ef951fab172e2dfe536215feb92

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-23 16:03:37 -0400

      Commit message:


	  
		
 chore: version bump
 
    
  
    

      Package: MutSeqR

      Commit: 516e056f26d4ab2b1744f872555463a31ae6aa45

      Author:  Annette Dodge <75439372+annettedodge16@users.noreply.github.com> 

      Date: 2026-04-23 16:01:10 -0400

      Commit message:


	  
		
 Merge pull request #125 from EHSRB-BSRSE-Bioinformatics/spectra-comparison-respec

Spectra comparison respec 
    
  
    

      Package: MutSeqR

      Commit: 9429a5ce768c5c358b12a07c39ffc26053e86c97

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-23 14:01:18 -0400

      Commit message:


	  
		
 docs : document
 
    
  
    

      Package: MutSeqR

      Commit: c783641b623d7f8e7e0f923ab9e241db344d6f9e

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-23 12:49:06 -0400

      Commit message:


	  
		
 Merge branch 'spectra-comparison-respec' of https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqR into spectra-comparison-respec
 
    
  
    

      Package: MutSeqR

      Commit: 662d6c5e249054de7c0c1ce5ad4cd1b708088849

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-23 12:45:26 -0400

      Commit message:


	  
		
 docs: fix documentation for imports
 
    
  
    

      Package: MutSeqR

      Commit: 7d8ccb5474316eb25e3df7ab59f08b889b5ffd1c

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-22 17:13:29 -0400

      Commit message:


	  
		
 chore: fix formating
 
    
  
    

      Package: MutSeqR

      Commit: 2ec8cb78404cd963c7066963ddc57673714a7389

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-22 16:57:08 -0400

      Commit message:


	  
		
 chore: update docs with R file name change.
 
    
  
    

      Package: MutSeqR

      Commit: db1924885e2234e7a908d2437eca2419dce7bb90

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-22 16:56:44 -0400

      Commit message:


	  
		
 fix: add warning to users about high FPR of spectra_comparison G2 function
 
    
  
    

      Package: MutSeqR

      Commit: 5c869f38e597ac71ae20f16de260bbbd1dc208c4

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-22 16:50:03 -0400

      Commit message:


	  
		
 refactor: create user-friendly wrapper function for rpdmm functions spectra_comparison_rpdmm
 
    
  
    

      Package: MutSeqR

      Commit: 0dfd6b6c6f1c4bf088105584d1758a81cde396cc

      Author:  raiduhs <99971713+raiduhs@users.noreply.github.com> 

      Date: 2026-04-22 14:27:58 -0400

      Commit message:


	  
		
 feat: add Ridge-Penalty Dirichlet-Multinomial
 
    
  
    

      Package: MutSeqR

      Commit: 92c23e49db31792adc5c5a2a37c20d1984f86bfb

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-23 12:45:26 -0400

      Commit message:


	  
		
 docs: fix documentation for imports
 
    
  
    

      Package: MutSeqR

      Commit: 6ce55812e184a4f9b03a9cba2120494fc8a7d975

      Author:  github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> 

      Date: 2026-04-23 16:07:52 +0000

      Commit message:


	  
		
 Update proast.min.R from PROAST build
 
    
  
    

      Package: MutSeqR

      Commit: af3b4ccc55bd006038392b24616e83783eb3d78c

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-22 17:13:29 -0400

      Commit message:


	  
		
 chore: fix formating
 
    
  
    

      Package: MutSeqR

      Commit: 292ca1d954bac5f6d946ed9c4a93625ebdc326ec

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-22 16:57:08 -0400

      Commit message:


	  
		
 chore: update docs with R file name change.
 
    
  
    

      Package: MutSeqR

      Commit: f71bde4446e3466db3f91260e755286881683170

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-22 16:56:44 -0400

      Commit message:


	  
		
 fix: add warning to users about high FPR of spectra_comparison G2 function
 
    
  
    

      Package: MutSeqR

      Commit: bfa4b1d1b0a650ead59d4aa477705d67c9d89412

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-22 16:50:03 -0400

      Commit message:


	  
		
 refactor: create user-friendly wrapper function for rpdmm functions spectra_comparison_rpdmm
 
    
  
    

      Package: MutSeqR

      Commit: 9548b5630034be9c801b2e4bbaec5039ca5c941c

      Author:  raiduhs <99971713+raiduhs@users.noreply.github.com> 

      Date: 2026-04-22 14:27:58 -0400

      Commit message:


	  
		
 feat: add Ridge-Penalty Dirichlet-Multinomial
 
    
  
    

      Package: GOaGO

      Commit: 7ccf1494977658552e70c2e98f6be2aaaf68001b

      Author:  Aleksander Jankowski <aleksander.jankowski@uw.edu.pl> 

      Date: 2026-04-23 21:41:06 +0200

      Commit message:


	  
		
 Update NEWS.md and bump version
 
    
  
    

      Package: GOaGO

      Commit: 0b707ee5e8369c859a9c1ed06c94231c707068a6

      Author:  Aleksander Jankowski <aleksander.jankowski@uw.edu.pl> 

      Date: 2026-04-23 21:36:36 +0200

      Commit message:


	  
		
 Use all gene pairs for examples
 
    
  
    

      Package: GOaGO

      Commit: 357473c1c0ce1dba3c1cfec41a35ebc94e892e2d

      Author:  Aleksander Jankowski <aleksander.jankowski@uw.edu.pl> 

      Date: 2026-04-23 21:33:21 +0200

      Commit message:


	  
		
 Minor fixes to the documentation
 
    
  
    

      Package: GOaGO

      Commit: f7e14f84c36a4d44c8aa7b1daf7874911b2312fe

      Author:  Aleksander Jankowski <aleksander.jankowski@uw.edu.pl> 

      Date: 2026-04-23 21:31:21 +0200

      Commit message:


	  
		
 Document all the accessors in the same help topic
 
    
  
    

      Package: GOaGO

      Commit: 9ffbca2a48ce2e40b37f2d8b009b24668926c477

      Author:  Aleksander Jankowski <aleksander.jankowski@uw.edu.pl> 

      Date: 2026-04-23 18:42:34 +0200

      Commit message:


	  
		
 Remove `as.data.table` method, as it is not needed anymore

`as.data.table()` still works, with `as.data.table.default` using the registered S3 method `as.data.frame`.
 </pre>
    </div>
  
    

      Package: GOaGO

      Commit: 033ffc258e3000451fba86ca1f5fc43cc45e4909

      Author:  Aleksander Jankowski <aleksander.jankowski@uw.edu.pl> 

      Date: 2026-04-23 18:37:54 +0200

      Commit message:


	  
		
 Export `as.data.frame` also as an S3 method
 
    
  
    

      Package: GOaGO

      Commit: d098da25df95759f9aa930f73472d7dd6e8dd3ca

      Author:  Aleksander Jankowski <aleksander.jankowski@uw.edu.pl> 

      Date: 2026-04-23 15:39:52 +0200

      Commit message:


	  
		
 Remove `library("GOaGO")` from examples
 
    
  
    

      Package: Rarr

      Commit: 8be1e9ade50cd07bf8a470c330d87d2b08a5b260

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-23 20:26:24 +0200

      Commit message:


	  
		
 Ensure configure always keep LF line endings
 
    
  
    

      Package: GSVA

      Commit: 1e8baade3f0f22f6d5db07b074a3fa88c89f4677

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

      Date: 2026-04-23 20:03:04 +0200

      Commit message:


	  
		
 Update the example and unit tests to use the sample spatial data of the GSVAdata package
 
    
  
    

      Package: AnVILWorkflow

      Commit: b71175d7053caa0aeb67ed5e18b851feafdb2a42

      Author:  Sehyun Oh <shbrief@gmail.com> 

      Date: 2026-04-23 13:50:07 -0400

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: AnVILWorkflow

      Commit: 1715d8c74e152765622b449937be3d27857bce52

      Author:  Sehyun Oh <shbrief@gmail.com> 

      Date: 2026-04-23 13:49:54 -0400

      Commit message:


	  
		
 update the deprecated function
 
    
  
    

      Package: AnVILWorkflow

      Commit: e002bf26294bf8bf3da104a63e7cba212e617e7f

      Author:  Sehyun Oh <shbrief@gmail.com> 

      Date: 2026-03-13 11:52:45 -0400

      Commit message:


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

      Package: AnVILWorkflow

      Commit: e4e7f67254351922c3c6efc8e9a5cc0638a0c8f2

      Author:  Sehyun Oh <shbrief@gmail.com> 

      Date: 2026-03-13 11:52:10 -0400

      Commit message:


	  
		
 resolve DESCRIPTION Date conflict

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 
    
  
    

      Package: AnVILWorkflow

      Commit: 77bf346c2302510d949580b443837951c3a17605

      Author:  Sehyun Oh <shbrief@gmail.com> 

      Date: 2026-03-13 11:50:38 -0400

      Commit message:


	  
		
 resolve conflict
 
    
  
    

      Package: qvalue

      Commit: 52f7787c9fbeb3ecb08a1a069496f3a9934526b1

      Author:  Andrew Bass <ajb359@gmail.com> 

      Date: 2026-04-23 13:34:09 -0400

      Commit message:


	  
		
 updated Authors@R
 
    
  
    

      Package: MSstatsResponse

      Commit: 36325737a167092976b65fbb91d4d5dc8865f78f

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-04-23 13:05:45 -0400

      Commit message:


	  
		
 fix(vignette): removed local devtools::load_all
 
    
  
    

      Package: MSstatsResponse

      Commit: 3eeff3284cf1aa23c7ba272a69db0e64f02729f3

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-04-23 13:02:06 -0400

      Commit message:


	  
		
 fix: correct Protein column casing in tests, fix ggplot2 linewidth deprecation, bump version to 1.1.2

- Fix failing tests that used lowercase 'protein' instead of 'Protein' in doseResponseFit, .calcSingleIC50, and predictIC50 output
- Replace deprecated size= with linewidth= in geom_line() calls (ggplot2 3.4.0+)
- Bump version 1.1.1 -> 1.1.2 for Bioconductor devel
- Remove Protein_turnover_vignettes.Rmd for this Bioconductor version
 
    
  
    

      Package: MSstatsResponse

      Commit: 9066ef9ba38f59dd5f3d4f85cb1c361b84a16dac

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-22 09:50:32 -0400

      Commit message:


	  
		
 fix(turnover): parse timepoint out of tracer constants (#9) 
    
  
    

      Package: MSstatsResponse

      Commit: 3cef24e5ac3923418d4ecd17cae4499f7d592af1

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-04-21 15:56:55 -0400

      Commit message:


	  
		
 fix: apply direction-aware log2FC in single-direction doseResponseFit
 
    
  
    

      Package: MSstatsResponse

      Commit: 59ed341867295b1aef3be93bda1e55233cde4326

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-04-21 15:25:06 -0400

      Commit message:


	  
		
 feat: add power curve section to vignette, rename output columns, add TPR test

- Vignette: add run_tpr_simulation + plot_tpr_power_curve section, adopt
  transform_nM_to_M = FALSE fix from remote, resolve merge conflict
- doseResponseFit: rename max_fc_fitted -> log2FC, compute as
  max-min on log2 scale (log2(max/min) for ratio scale)
- doseResponseFit + predictIC50: rename output 'protein' -> 'Protein'
- plotHitRateMSstatsResponse: update to use 'Protein' column
- Tests: add futureExperimentSimulation TPR/FPR test with built-in data,
  fix mock_data doses to nM scale, update concentration validation test,
  update expect_named for renamed output columns
 
    
  
    

      Package: MSstatsResponse

      Commit: bb1caded122caf48878ef696655792b495d12c0b

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-20 14:08:28 -0400

      Commit message:


	  
		
 fix(vignette): Turn off nM to M conversion in vignette (#8) 
    
  
    

      Package: MSstatsResponse

      Commit: d4ec9bf837151ae9e2bfe1fd0515526d5d72643f

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-04-09 10:55:23 -0400

      Commit message:


	  
		
 Merge origin/devel: delete MSstatsResponse.html
 
    
  
    

      Package: MSstatsResponse

      Commit: 33062a485cb0ac249a8b3b3667a96247ced4e01d

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-04-09 10:53:35 -0400

      Commit message:


	  
		
 Delete vignettes/MSstatsResponse.html 
    
  
    

      Package: MSstatsResponse

      Commit: 2a769565f013d17c36a5838b7183ba7d6dd87f1b

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-04-09 10:52:09 -0400

      Commit message:


	  
		
 Merge progress-bar branch: add txtProgressBar to doseResponseFit

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 
    
  
    

      Package: MSstatsResponse

      Commit: 2f5792fe05b080a331c5e5fe72bc133e52e90b7d

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-04-09 10:42:37 -0400

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/main' into devel
 
    
  
    

      Package: MSstatsResponse

      Commit: 61d206bcf8c9292c4ebb9711d3c3bb28c186d7db

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-04-07 18:22:12 -0400

      Commit message:


	  
		
 Merge branch 'devel' into main 
    
  
    

      Package: MSstatsResponse

      Commit: cd1cdd79a18a95f3360845a3343dcd10645c70cf

      Author:  Tony Wu <wu.anthon@northeastern.edu> 

      Date: 2026-04-07 17:53:45 -0400

      Commit message:


	  
		
 update description
 
    
  
    

      Package: MSstatsResponse

      Commit: 413bce3a65f5f7f473f69a7267aa2ff3d9f358aa

      Author:  Swaraj Patil <patil.swaraj@northeastern.edu> 

      Date: 2026-04-07 17:04:59 -0400

      Commit message:


	  
		
 Merge TPR simulation function into Development (#6) 
    
  
    

      Package: MSstatsResponse

      Commit: 8739ce4d4f08985e57ea292525e0d0cea32ee1f5

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-03-19 09:01:40 -0400

      Commit message:


	  
		
 ci(build): Add automated dry run build when submitting a PR (#2) 
    
  
    

      Package: MSstatsResponse

      Commit: 90a7fa27e3372cd983a434690bc3b05fc8704d18

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

      Date: 2026-03-16 13:27:17 -0400

      Commit message:


	  
		
 change adjust_pval to adj.pvalue
 
    
  
    

      Package: MSstatsResponse

      Commit: 660fad74a0d4811c60fc6b58eed92a486ac7e021

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-03-13 14:11:15 -0400

      Commit message:


	  
		
 created protein turnover functions
 
    
  
    

      Package: MSstatsResponse

      Commit: 4e2e36decb670743f2ceb7ff97afef50fac6bbb9

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-02-10 14:39:26 -0500

      Commit message:


	  
		
 new updates
 
    
  
    

      Package: MSstatsResponse

      Commit: f81dd489a29997213553ab3fe7f2b94689b62b17

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-02-10 14:38:45 -0500

      Commit message:


	  
		
 update version
 
    
  
    

      Package: MSstatsResponse

      Commit: fd28a0a59355f6b808535d05cd28ff43e2e6ec7d

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-02-10 14:28:51 -0500

      Commit message:


	  
		
 Merge pull request #4 from Vitek-Lab/main

Main 
    
  
    

      Package: MSstatsResponse

      Commit: 9e2a4e4ab783e775a27ffc98d9331b5d0f907f73

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-02-10 13:57:52 -0500

      Commit message:


	  
		
 fix x-axis scale and add custom target_response for plotting
 
    
  
    

      Package: MSstatsResponse

      Commit: 9f4fbe4619867061e85c22a5d709df4972f30ec7

      Author:  Tony Wu <wu.anthon@northeastern.edu> 

      Date: 2026-01-29 15:15:56 -0500

      Commit message:


	  
		
 feat(doseResponseFit): Add progress bar
 
    
  
    

      Package: MSstatsResponse

      Commit: f0ef2f78bf617139bd2241901ba5cd17462eecae

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2025-11-21 14:40:27 -0500

      Commit message:


	  
		
 refactor(adj.pvalue): Switch adjust_pval to adj.pvalue (#1)

 
    
  
    

      Package: MSstatsResponse

      Commit: eb1be230f7e8fa44b937ff7e682bcedc0302a57b

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2025-11-03 09:24:54 -0500

      Commit message:


	  
		
 added custom target response to visualization
 
    
  
    

      Package: betterChromVAR

      Commit: 67b584693b7e5efca0480b7a9bced63f69de4f93

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-04-23 17:45:47 +0200

      Commit message:


	  
		
 fixed bracket
 
    
  
    

      Package: betterChromVAR

      Commit: 3539096bceba0159ede4a3884a5c05af99fd63e4

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-04-23 16:25:42 +0200

      Commit message:


	  
		
 more informative error on some cases of missing bias
 
    
  
    

      Package: betterChromVAR

      Commit: 48ed0887fdfbf178a888cae193a9e9142a12320f

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-04-17 20:11:09 +0200

      Commit message:


	  
		
 fixed pltf
 
    
  
    

      Package: betterChromVAR

      Commit: ad217c7b2a00f5710b0a46d135a680974e557c98

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-04-17 19:50:45 +0200

      Commit message:


	  
		
 force updated only linux
 
    
  
    

      Package: iChip

      Commit: aad401a8893955786cdfb24e374573658ab72d99

      Author:  qianxing.mo <qianxing.mo@moffitt.org> 

      Date: 2026-04-23 12:45:14 -0400

      Commit message:


	  
		
 fix minor issues in lmtstat.Rd oct4.Rd p53.Rd
 
    
  
    

      Package: MSstatsConvert

      Commit: ec4ed62fcb69a91edc805d9afe86fab7cffa4b53

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

      Date: 2026-04-23 12:27:01 -0400

      Commit message:


	  
		
 Bump version from 1.21.4 to 1.21.5 
    
  
    

      Package: MSstatsConvert

      Commit: c0ba69c04fd80c841a33969be72faa4b486340d2

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

      Date: 2026-04-23 12:26:45 -0400

      Commit message:


	  
		
 docs(turnover): Update example turnover file (#130) 
    
  
    

      Package: motifTestR

      Commit: f7100d0b68e5740db33e15923136887d1e445ae8

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

      Date: 2026-04-24 01:25:07 +0930

      Commit message:


	  
		
 Merge
 
    
  
    

      Package: motifTestR

      Commit: 0f721b28cfb5b05ef24c24fa44474368ec0f77d2

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

      Date: 2026-04-24 01:18:16 +0930

      Commit message:


	  
		
 Expanded plotting args when clustering
 
    
  
    

      Package: motifTestR

      Commit: d6a5ee36158b7425b6e7fc5d5680a8eb70bb5d37

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

      Date: 2026-04-24 01:01:30 +0930

      Commit message:


	  
		
 Added plotting params
 
    
  
    

      Package: motifTestR

      Commit: 599d0ca0e31b2bbef3c6c2a2f026f290431e4c5c

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

      Date: 2025-11-16 02:20:26 +1030

      Commit message:


	  
		
 Bugfix in Z scores
 
    
  
    

      Package: motifTestR

      Commit: 0dc66a6e39c57f8c32380bdb25a1259d10f6919e

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2025-10-29 11:28:54 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
 
    
  
    

      Package: motifTestR

      Commit: bf87791a017c64cc9c32da4a94b692a5856d5692

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2025-10-29 11:28:54 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
 
    
  
    

      Package: motifTestR

      Commit: f870ef689c09afa876663554e290b483c32de7ca

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

      Date: 2025-10-30 14:07:41 +1030

      Commit message:


	  
		
 Cropped favicon
 
    
  
    

      Package: postNet

      Commit: 2f81aaa2ea2cba17f78839e9ed13135d2269efc6

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-04-23 16:48:41 +0100

      Commit message:


	  
		
 KS
 
    
  
    

      Package: Aerith

      Commit: e0405e6e98430ac970ac8e8fc1e7680ad9d70eee

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2026-04-23 10:43:23 -0500

      Commit message:


	  
		
 bump version to 0.99.13
 
    
  
    

      Package: postNet

      Commit: 3e9b21c87fccc8956eafd2e276001df77c841bf4

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-04-23 16:23:50 +0100

      Commit message:


	  
		
 KS
 
    
  
    

      Package: gutenTAG

      Commit: 439a35efd3f5474ccf052c993d63c753a1bc372a

      Author:  John Abbey <89733453+JohnAbbey98@users.noreply.github.com> 

      Date: 2026-04-23 13:10:13 +0200

      Commit message:


	  
		
 Count fix 2 (#30)

* rescale smooth counts to match counts

* remove metapeak clipping

* description bump

* add test ci

* update gh actions

* fix ubuntu dependencies

* fix tests with breaking change and fix warnings

* fix bioccheck action build

* add params

* fix bioccheck ci

* bioccheck error

* change devel to release in actions

---------

Co-authored-by: John Abbey <john@dqbm-nbm-joab.local>
Co-authored-by: John Abbey <john@Mac.sunrise.box> 
    
  
    

      Package: gutenTAG

      Commit: 12173f2b463316b41863f3f44d2bd7140a6096bb

      Author:  John Abbey <89733453+JohnAbbey98@users.noreply.github.com> 

      Date: 2026-04-22 14:55:24 +0200

      Commit message:


	  
		
 Count fix (#28)

* rescale smooth counts to match counts

* remove metapeak clipping

* description bump

* add test ci

* update gh actions

* fix ubuntu dependencies

* fix tests with breaking change and fix warnings

* fix bioccheck action build

* add params

* fix bioccheck ci

---------

Co-authored-by: John Abbey <john@dqbm-nbm-joab.local>
Co-authored-by: John Abbey <john@Mac.sunrise.box> 
    
  
    

      Package: PinPath

      Commit: 718d7b8a242959395bc3826ae501dc35fdcfb47a

      Author:  Jarno Koetsier <jarno.koetsier@gmail.com> 

      Date: 2026-04-23 16:40:32 +0200

      Commit message:


	  
		
 Address Bioconductor feedback
 
    
  
    

      Package: PinPath

      Commit: 553dd4537c7ca29c8201dbca1e048c0c6a6da061

      Author:  Jarno Koetsier <79576459+jarnokoetsier@users.noreply.github.com> 

      Date: 2026-04-21 10:21:33 +0200

      Commit message:


	  
		
 Merge pull request #4 from SyNUM-lab/bioc-feedback

Bumped the R dependency version 
    
  
    

      Package: PinPath

      Commit: 66b5bb07b160f179271def9def5f45fc77d8ce42

      Author:  Egon Willighagen <egon.willighagen@gmail.com> 

      Date: 2026-03-25 20:58:48 +0100

      Commit message:


	  
		
 Bumped the R dependency version
 
    
  
    

      Package: postNet

      Commit: 89534d50e0784f00ba20b7e3174ed2c95c3c07ba

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-04-23 15:17:11 +0100

      Commit message:


	  
		
 Corrected bug in uORFAnalysis
 
    
  
    

      Package: iscream

      Commit: aeb6b8a203ef3b0c2fa8846ed6c01ee26de146b8

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2026-04-17 10:55:46 -0400

      Commit message:


	  
		
 chore(DESCRIPTION): bump version
 
    
  
    

      Package: iscream

      Commit: 85830e58f8fbf2d345d92030b7bba007fc1db448

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2026-04-18 09:13:59 -0400

      Commit message:


	  
		
 chore(NEWS): update

- unused cpgid debug string
- blockquote the chr format note
 
    
  
    

      Package: iscream

      Commit: ea4fd46b254f6b7c9cf59d271b95096ced99bf27

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2026-04-18 09:11:40 -0400

      Commit message:


	  
		
 fix(query_all): remove unused variable and string alloc
 
    
  
    

      Package: iscream

      Commit: 57ee16b824028c7ac69c6530dcc41fe6a4d58227

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2026-04-17 10:54:54 -0400

      Commit message:


	  
		
 docs(vignettes): blockquote the chr format note
 
    
  
    

      Package: iscream

      Commit: 02e6792c4b369e4dfb8f01992969470bcbf033bb

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2026-04-17 11:21:27 -0400

      Commit message:


	  
		
 fix(flake): restore rDevDeps to shell
 
    
  
    

      Package: lefser

      Commit: 19450bda6fd4452e43d2cec438b24cbbd6865a34

      Author:  asyakhl <asyakhleb@gmail.com> 

      Date: 2026-04-22 19:08:51 -0500

      Commit message:


	  
		
 version bump 1.21.8
 
    
  
    

      Package: lefser

      Commit: 03909eb5711b5b1b05e09ddde20d597501f3d05f

      Author:  Asya Khleborodova <asyakhl@users.noreply.github.com> 

      Date: 2026-04-22 18:59:42 -0500

      Commit message:


	  
		
 Merge pull request #102 from waldronlab/fix-test-coverage

Fix testing error and test data loading 
    
  
    

      Package: lefser

      Commit: 4a862f3b4b5c0b73b322bacf1e297ecd8655f969

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-04-22 14:02:20 -0400

      Commit message:


	  
		
 Extract zeller14 dataset loading into helper function

Refactors the dataset loading boilerplate from multiple test files into a shared `load_lefser_dataset` helper function in `tests/testthat/helper-data.R` as suggested by the Copilot review.
 
    
  
    

      Package: lefser

      Commit: 8936a82dc731fe9c1520f6d3fa6c117f6137ff08

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-04-21 21:06:40 -0400

      Commit message:


	  
		
 Fix testing error and test data loading

- Change deprecated `size` to `linewidth` in geom_bar in `lefserPlot`
- Safely load `zeller14` data in all test files to fix coverage execution
 
    
  
    

      Package: lefser

      Commit: e3f945fa24ba2fd33b698505974f52abb4d27299

      Author:  Asya Khleborodova <asyakhl@users.noreply.github.com> 

      Date: 2026-04-21 17:26:55 -0500

      Commit message:


	  
		
 Merge pull request #100 from waldronlab/fix-deprecation-warnings

Fix tidyselect and ggplot2 deprecation warnings 
    
  
    

      Package: lefser

      Commit: d457e3e9619e32b7628455f840452d47de0b3d4a

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-04-21 10:22:23 -0400

      Commit message:


	  
		
 Merge branch 'devel' into fix-deprecation-warnings and resolve test mock data conflict
 
    
  
    

      Package: lefser

      Commit: bac34f6b52f1c1b99fa72b103688e36daf205192

      Author:  Asya Khleborodova <asyakhl@users.noreply.github.com> 

      Date: 2026-04-20 19:27:16 -0500

      Commit message:


	  
		
 Merge pull request #99 from waldronlab/fix-lda-test-data

Fix ldaFunction unit test by replacing collinear data 
    
  
    

      Package: lefser

      Commit: 7c41881f8d84a2487e08bfe2a196cd0b152285e6

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-04-09 22:38:17 -0400

      Commit message:


	  
		
 Add AI package instructions using waldronlab skill

* Add .github/instructions documentation generated by 'create-package-instructions'
* Fill in [To be documented] sections utilizing PMC11665633 and codebase exploration
* Document LEfSe concepts, codebase organization, testing conventions, and CI/CD parameters
* Clarify package's reliance on Bioconductor S4 classes (SummarizedExperiment, S4Vectors)
* Add TODO to remove 'mia' warning suppression once upstream deprecation is fixed

Co-authored-by: Gemini Code Assist <gemini@google.com>
 
    
  
    

      Package: lefser

      Commit: dae31e461876efce93e2172d6bb9f785503ad71c

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-04-09 22:37:25 -0400

      Commit message:


	  
		
 Fix ldaFunction test stability across platforms

* Augment mock data in `test-lefser.R` to break perfect mathematical symmetry.
* Resolve cross-platform BLAS/LAPACK singular value calculation disparities that caused `MASS::lda` to throw "group means are numerically identical" errors on macOS.
* Remove `tryCatch` and `suppressWarnings` workarounds from the test.

Co-authored-by: Gemini Code Assist <gemini@google.com>
 
    
  
    

      Package: lefser

      Commit: ece2e4ea6379a8864e06b1c35821fda12820c501

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-04-09 22:09:05 -0400

      Commit message:


	  
		
 Address Copilot code review for PR #100

* Add `ggplot2 (>= 3.4.0)` requirement in `DESCRIPTION` since `linewidth` was introduced in this version.
* Wrap `lefserPlot()`, `lefserPlotFeat()`, `lefserPlotClad()`, and `lefserClades()` calls in `expect_no_warning()` within the test suite to prevent future regressions.
* Muffle unrelated deprecation warnings from `mia::splitByRanks` during `lefserClades()` tests to maintain strict regression checks.
* Wrap pre-existing `ldaFunction` test block in `tryCatch` to gracefully handle collinearity errors in newer versions of the `MASS` package while preserving functionality for backward compatibility.

Co-authored-by: Gemini Code Assist <gemini@google.com>
 
    
  
    

      Package: lefser

      Commit: 73f4c66e42d647d606144fab7134985333be9c29

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-04-09 16:27:42 -0400

      Commit message:


	  
		
 Fix tidyselect and ggplot2 deprecation warnings

* Use string column names in dplyr::relocate instead of .data
* Use linewidth instead of size for ggtree::ggtree

Co-authored-by: Gemini Code Assist <gemini@google.com>
 
    
  
    

      Package: lefser

      Commit: ef7aea743dce365c569228ecbfc747657e3b7c9f

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-04-09 16:23:43 -0400

      Commit message:


	  
		
 Apply suggestion from @Copilot

Adds tolerances for expect_equal on floating-point results

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 
    
  
    

      Package: lefser

      Commit: 4ae39bf0d3e942ab90fc52a725fb957634580dca

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-04-09 16:18:52 -0400

      Commit message:


	  
		
 Fix ldaFunction unit test by replacing collinear data

The synthetic dataset used to test `ldaFunction` was perfectly collinear and had orthogonal group means. In newer versions of the MASS package, this causes `lda.default` to correctly error with "group means are numerically identical" instead of silently projecting into a zero-effect subspace.

This commit updates the unit test with mathematically sound, full-rank dummy data to properly test the ldaFunction logic, and updates the assertions to match the mathematically correct output.

Co-authored-by: Gemini Code Assist <gemini@google.com>
 
    
  
    

      Package: lefser

      Commit: 050be06f2b76821f4edee7b15efcc76be2ef7817

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-03-26 16:51:32 -0400

      Commit message:


	  
		
 Add missing fnd entries to Authors@R in DESCRIPTION (#96) 
    
  
    

      Package: lefser

      Commit: 6dae633f5b68127632a873b9bb1dab85b6a03da0

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-03-25 18:07:54 -0400

      Commit message:


	  
		
 Migrate pr_check.yml to ci.yml (#94)

* Add ci.yml reusable-workflow wrapper

* Remove pr_check.yml (replaced by ci.yml) 
    
  
    

      Package: S4Cartographer

      Commit: 1dcef92561b22573b7f82ba5cb5bbda6541ea140

      Author:  Malte Thodberg <maltethodberg@gmail.com> 

      Date: 2026-04-23 15:04:17 +0200

      Commit message:


	  
		
 Merge branch 'main' of github.com:MalteThodberg/S4Cartographer
 
    
  
    

      Package: S4Cartographer

      Commit: c2ac910af1b4d1b1cd9cdf84fb43163c5b6ddd44

      Author:  Malte Thodberg <maltethodberg@gmail.com> 

      Date: 2026-04-23 15:03:51 +0200

      Commit message:


	  
		
 Implemented Bioc review changes:
- Longer description
- Import utils for stack
- Wrapped vignette text
 
    
  
    

      Package: S4Cartographer

      Commit: 62bb90be59b5f5850aa751fa1e839117a9913bad

      Author:  Malte Thodberg <MalteThodberg@users.noreply.github.com> 

      Date: 2026-03-26 09:23:09 +0100

      Commit message:


	  
		
 Delete S4Cartographer.Rproj 
    
  
    

      Package: methodical

      Commit: bfbab88d93e4a718a3c053f5440ad91c6cbdfc26

      Author:  Richard Heery <richardheery@gmail.com> 

      Date: 2026-04-23 13:37:01 +0100

      Commit message:


	  
		
 Removed BSgenome annotation packages as dependencies
 
    
  
    

      Package: postNet

      Commit: 7e9b3aef7522e70d2e130e17a9dc34859df97d35

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-04-23 13:35:32 +0100

      Commit message:


	  
		
 KS
 
    
  
    

      Package: MSstatsConvert

      Commit: 222317ead36c407182593df3ce7c6e716f36c635

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

      Date: 2026-04-23 08:34:55 -0400

      Commit message:


	  
		
 Bump version from 1.21.3 to 1.21.4 
    
  
    

      Package: MSstatsConvert

      Commit: 0a3f0f85f12afab0be885403ce7d2b4015a67b9e

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

      Date: 2026-04-23 08:17:08 -0400

      Commit message:


	  
		
 Update NEWS.md file (#129) 
    
  
    

      Package: DuplexDiscovereR

      Commit: 18a8f30ea9393bed883d61bb0a7bf068a4e5f200

      Author:  Egors01 <yegor.smb@gmail.com> 

      Date: 2026-04-23 14:20:23 +0200

      Commit message:


	  
		
 clean-up rplots after tests
 
    
  
    

      Package: DuplexDiscovereR

      Commit: a291bf764a716bfbd99da508e2b69918c4cce0c3

      Author:  Egors01 <yegor.smb@gmail.com> 

      Date: 2026-04-23 14:18:44 +0200

      Commit message:


	  
		
 modified NEWS and added GenomeINfoDB explicitly
 
    
  
    

      Package: DuplexDiscovereR

      Commit: 248234953afc3e50e4b787abcfb5b4dd71464b98

      Author:  Egors01 <yegor.smb@gmail.com> 

      Date: 2026-03-16 12:15:44 +0100

      Commit message:


	  
		
 updated gethybrids to return full RNAhubrids output
 
    
  
    

      Package: DuplexDiscovereR

      Commit: 44412d36af05d19c58d1adb1b2ca5686178f5902

      Author:  Egors01 <yegor.smb@gmail.com> 

      Date: 2026-03-12 13:59:06 +0100

      Commit message:


	  
		
 bug fix if no duplicated reads are present, collapsing identical step was failing in a pipeline
 
    
  
    

      Package: DuplexDiscovereR

      Commit: f517271f8d96af339980c81f142ac1e12dcf8d99

      Author:  Egors01 <yegor.smb@gmail.com> 

      Date: 2026-03-10 12:45:04 +0100

      Commit message:


	  
		
 added updated md
 
    
  
    

      Package: DuplexDiscovereR

      Commit: 2bca5244deee651d23bd3bd7b58644e486e017fb

      Author:  Egors01 <yegor.smb@gmail.com> 

      Date: 2026-03-10 12:44:10 +0100

      Commit message:


	  
		
 added arg to back-compatibility to the main pipeline
 
    
  
    

      Package: DuplexDiscovereR

      Commit: a2a433d2ccf15faa850d7825c60bdb5477e77fe9

      Author:  Egors01 <yegor.smb@gmail.com> 

      Date: 2026-03-10 12:36:01 +0100

      Commit message:


	  
		
 added arg to back-compatibility with the main pipeline and .md
 
    
  
    

      Package: DuplexDiscovereR

      Commit: 198c034e05cbf82c8e8d0b46693b1e14d94ec417

      Author:  Egors01 <yegor.smb@gmail.com> 

      Date: 2026-03-10 12:17:15 +0100

      Commit message:


	  
		
 added odds pvalue computation
 
    
  
    

      Package: DuplexDiscovereR

      Commit: 719ea62948436a3c6b9cacdbca8475d5585da05b

      Author:  Egors01 <yegor.smb@gmail.com> 

      Date: 2025-12-04 13:11:56 +0100

      Commit message:


	  
		
 changed & to && in non vectorized condition for pvals in main caller
 
    
  
    

      Package: postNet

      Commit: a93c3537a97e1b071e1f621d84d71543a6bbada6

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-04-23 13:24:47 +0100

      Commit message:


	  
		
 Correct network bug
 
    
  
    

      Package: ClonalSim

      Commit: d27becddf01071e2dd5243af1feacff40ddf2a2b

      Author:  gbucci <bucci.g@gmail.com> 

      Date: 2026-04-23 14:23:26 +0200

      Commit message:


	  
		
 Fix BiocCheck notes: update R version to 4.6.0, replace 1:22 with seq_len(22) (v0.99.8)
 
    
  
    

      Package: postNet

      Commit: a3345c1bd9eb0ec747c90ff41c7b6531faf1762d

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-04-23 13:11:41 +0100

      Commit message:


	  
		
 Correct network bug
 
    
  
    

      Package: postNet

      Commit: e68de5149effca1404531eb3b2aa0a2d95d2ce7b

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-04-23 13:02:38 +0100

      Commit message:


	  
		
 Network plot bug
 
    
  
    

      Package: methodical

      Commit: 62e5beb6829cc49cb91fa90881dda290a5a09b78

      Author:  Richard Heery <richardheery@gmail.com> 

      Date: 2026-04-23 12:00:52 +0100

      Commit message:


	  
		
 Updated manuals
 
    
  
    

      Package: goatea

      Commit: abc719144016bec9eef4d4a9d76f3d726d548708

      Author:  Maurits Unkel <mauritsunkel@gmail.com> 

      Date: 2026-04-23 11:43:14 +0200

      Commit message:


	  
		
 Added width/height control for plot outputs and noted in docs, fixed exporting UpSet overlap plot, suppressing package load messages on startup
 
    
  
    

      Package: goatea

      Commit: dee16f1c5fb13bcabc489658d73590c2ab4f0f2c

      Author:  Maurits Unkel <mauritsunkel@gmail.com> 

      Date: 2026-04-23 11:40:44 +0200

      Commit message:


	  
		
 Readded the Colameo et al. (2021) example data .csvs for easy download, added to the docs where these are downloadable
 
    
  
    

      Package: goatea

      Commit: 7bfc830e70f8e09681588efdba5c58c8bb3292b8

      Author:  Maurits Unkel <mauritsunkel@gmail.com> 

      Date: 2026-04-23 11:40:04 +0200

      Commit message:


	  
		
 Updated documentation for user clarity and accessibility
 
    
  
    

      Package: goatea

      Commit: ab25e90ead5cc24f9a6dd9ecb835d9aeb4791313

      Author:  Maurits Unkel <mauritsunkel@gmail.com> 

      Date: 2026-04-23 11:38:39 +0200

      Commit message:


	  
		
 Adder R_USER home
 
    
  
    

      Package: SMAD

      Commit: bc9620ecd2c0aae6fe3eab9dd46a4b2f74f68ad2

      Author:  Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com> 

      Date: 2026-04-23 06:25:34 -0300

      Commit message:


	  
		
 fix: update RcppAlgos dependencies, correct PE documentation, and enforce single-threaded comboGeneral calls
 
    
  
    

      Package: ClonalSim

      Commit: e40aece6c43b9555fb8bb437aede6e8092c029a2

      Author:  Gabriele Bucci <bucci.g@gmail.com> 

      Date: 2026-04-23 10:58:18 +0200

      Commit message:


	  
		
 Merge pull request #14 from gbucci/claude/bump-version-bioconductor-ogUbb

Bump version to 0.99.7 
    
  
    

      Package: ClonalSim

      Commit: 17455f92b6d3ead6d9c7c5ec7f1835d7e59f47c5

      Author:  Claude <noreply@anthropic.com> 

      Date: 2026-04-23 08:56:39 +0000

      Commit message:


	  
		
 Bump version to 0.99.7 for Bioconductor build

https://claude.ai/code/session_01FErnX1pzPofjy3piRHm27T
 
    
  
    

      Package: ClonalSim

      Commit: 492bda9ffc8babbe124c9adb12f4aea750499f65

      Author:  gbucci <bucci.g@gmail.com> 

      Date: 2026-04-21 16:52:30 +0200

      Commit message:


	  
		
 Fix documentation: remove library(ggplot2) and incorrect seed parameter (v0.99.6)

- Remove library(ggplot2) from README, vignette, and methods.R docs since
  ggplot2 is imported in NAMESPACE and loads automatically with the package
- Replace seed=42 parameter (invalid) in README example with set.seed(42)
  called before simulateTumor()
- Remove duplicate set.seed() call and redundant seed example in simulateTumor.R
 
    
  
    

      Package: miloR

      Commit: d811be730ee3d882664205fcedfcfa7168ea166c

      Author:  MikeDMorgan <michael.morgan@abdn.ac.uk> 

      Date: 2026-04-23 09:14:59 +0100

      Commit message:


	  
		
 fix c++23 warning on indexing without parentheses
 
    
  
    

      Package: Aerith

      Commit: 7b8e3b0f11a27f60044980d9238959a48f173ba8

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2026-04-22 17:18:37 -0500

      Commit message:


	  
		
 fix warning
 
    
  
    

      Package: hammers

      Commit: 2e90f5928840ce47defce1994d51dc44a13ff8b7

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2026-04-23 10:13:40 +0800

      Commit message:


	  
		
 Bumped version
 
    
  
    

      Package: hammers

      Commit: c3e67dd84fdb25eed14aa0f9763a925c9ea6cd72

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2026-04-23 10:13:11 +0800

      Commit message:


	  
		
 Minor documentation edits
 
    
  
    

      Package: hammers

      Commit: 063ecd65cfb95416e4315c121ef352dd531b7ea0

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2026-04-23 09:55:00 +0800

      Commit message:


	  
		
 Bumped version
 
    
  
    

      Package: hammers

      Commit: d562b8e4792bf01fb8882edc2701b86e1f3b7ad3

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2026-04-23 09:54:34 +0800

      Commit message:


	  
		
 Removed mtCorrectDF
 
    
  
    

      Package: dnaEPICO

      Commit: 690c69f452d186bf738181f24fbad9acdca7bbb5

      Author:  Paul Ruiz <ruizpint@qut.edu.au> 

      Date: 2026-04-23 10:44:31 +1000

      Commit message:


	  
		
 Bioconductor Review Changes 0.99.14
 
    
  
    

      Package: dnaEPICO

      Commit: 4770e4ffbfa126e8d2ac69c746bb3546169c74d7

      Author:  Paul Ruiz <ruizpint@qut.edu.au> 

      Date: 2026-04-23 09:36:05 +1000

      Commit message:


	  
		
 Bioconductor Review Changes 0.99.14
 
    
  
    

      Package: dnaEPICO

      Commit: 4f0e7ebe0c955faa7cb0a8d8560a4173720ed4c2

      Author:  Paul Ruiz <ruizpint@qut.edu.au> 

      Date: 2026-04-22 21:07:25 +1000

      Commit message:


	  
		
 Bioconductor Review Changes 0.99.14
 
    
  
    

      Package: Aerith

      Commit: 6ee5442839a534e8a7dd419d0b0a76aebb5a3ec0

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2026-04-22 17:18:37 -0500

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: Aerith

      Commit: 363ce30502f55536b0497d1728e0360021c6f824

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2026-03-04 00:55:26 -0600

      Commit message:


	  
		
 add universal support of O18 S34 in averagine.cpp, replace sizeto linewidth for ggplot
 
    
  
    

      Package: Aerith

      Commit: c7eb25b2eade3eee959d9e2a9b6b287f89d1595b

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2026-02-21 03:11:36 -0600

      Commit message:


	  
		
 add scan type and scan filter per scan when reading FT1 and FT2. add precursor annotation and plot function
 
    
  
    

      Package: fastreeR

      Commit: baf33a7b7577337eacc4fe8d1f5ad35f902ef0bf

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-04-23 02:15:15 +0300

      Commit message:


	  
		
 Update README and code for windowed output feature in fastreeR

- Updated README.md to reflect the new Java backend version 2.7.0 and its features, including windowed/streaming VCF distance and tree output.
- Modified fastreeR.py to include new command line arguments for windowing functionality in VCF2DIST and VCF2TREE commands.
 
    
  
    

      Package: limma

      Commit: 55d65855ceebdcbb90f9e83df071935db0897110

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

      Date: 2026-04-23 08:35:28 +1000

      Commit message:


	  
		
 limma 3.67.4

- Remove topTableF(), which has been deprecated for many years.
 
    
  
    

      Package: arrayQualityMetrics

      Commit: c273ea698599832a38515d308a1523aabc2329d0

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-21 16:34:31 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: arrayQualityMetrics

      Commit: 613a57d1ea0f75ee3751d51b41805b4101d93a40

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-21 16:34:22 +0200

      Commit message:


	  
		
 Revert accidental switch to xml2
 
    
  
    

      Package: MutSeqR

      Commit: 4ebd7b83bcbb8702a0c19bab93f0366b400c17be

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-22 17:20:30 -0400

      Commit message:


	  
		
 chore: version bump 0.99.10
 
    
  
    

      Package: MutSeqR

      Commit: c934ad27cb94af1b89d40e8c1e70064a12a076a3

      Author:  Annette Dodge <75439372+annettedodge16@users.noreply.github.com> 

      Date: 2026-04-22 14:31:44 -0400

      Commit message:


	  
		
 Merge pull request #122 from EHSRB-BSRSE-Bioinformatics/precalc_depth_validate. Closes #101

fix: validate precalc_depth_data resolution in calculate_mf 
    
  
    

      Package: MutSeqR

      Commit: 33eddcd8a893bdea6ab5182c27ebfe9f416f9ffc

      Author:  Annette Dodge <annettedodge16@gmail.com> 

      Date: 2026-04-22 13:16:19 -0400

      Commit message:


	  
		
 fix: validate precalc_depth_data resolution in calculate_mf
 
    
  
    

      Package: scpdata

      Commit: 73d44984665b5532029c3cb831907d3a70994cf0

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-04-22 23:03:47 +0200

      Commit message:


	  
		
 merge conflict
 
    
  
    

      Package: scpdata

      Commit: 44802fab80e1bf0a63ee1763a7d9854862d910e2

      Author:  Laurent Gatto <laurent.gatto@uclouvain.be> 

      Date: 2026-04-22 22:58:22 +0200

      Commit message:


	  
		
 Merge pull request #39 from EnesSefaAyar/master

sample id orders fixed 
    
  
    

      Package: scpdata

      Commit: 14fef0c740991c8d83ab3f0647435ff05b0c03e3

      Author:  Laurent Gatto <laurent.gatto@uclouvain.be> 

      Date: 2026-04-22 22:57:16 +0200

      Commit message:


	  
		
 Merge pull request #32 from samgregoire/master

bubis2025 Astral 
    
  
    

      Package: scpdata

      Commit: fb5269030d70ac48c1ac807e9dde7f874825fb85

      Author:  EnesSefaAyar <enessefaayar@gmail.com> 

      Date: 2026-04-21 19:49:47 +0200

      Commit message:


	  
		
 version in the metadata bumped up
news updated
 
    
  
    

      Package: scpdata

      Commit: 3b95690f6080ed478d8ae6db6a4f9c370e0e5c1e

      Author:  EnesSefaAyar <enessefaayar@gmail.com> 

      Date: 2026-04-21 10:03:30 +0200

      Commit message:


	  
		
 sample id orders fixed
 
    
  
    

      Package: scpdata

      Commit: 0048bfac70d23a73a1b5f4425e629d1aaeeddcc1

      Author:  Laurent Gatto <laurent.gatto@uclouvain.be> 

      Date: 2026-04-20 14:42:58 +0200

      Commit message:


	  
		
 Merge branch 'master' into master 
    
  
    

      Package: scpdata

      Commit: 815df7d2f9d0df5df84bc7922edfc5bb2474cc39

      Author:  UCL-00352545 <samuel.gregoire@student.uclouvain.be> 

      Date: 2025-08-19 15:11:50 +0200

      Commit message:


	  
		
 Add bubis2025 man page
 
    
  
    

      Package: scpdata

      Commit: 51ab8883fe63007fa533979f4c887cee11fe6736

      Author:  UCL-00352545 <samuel.gregoire@student.uclouvain.be> 

      Date: 2025-08-19 15:10:35 +0200

      Commit message:


	  
		
 Remove unrelevant data
 
    
  
    

      Package: scpdata

      Commit: ea232e53a5409174541b256d1f13c66214572e02

      Author:  UCL-00352545 <samuel.gregoire@student.uclouvain.be> 

      Date: 2025-08-19 15:09:29 +0200

      Commit message:


	  
		
 Documented bubis2025
 
    
  
    

      Package: scpdata

      Commit: ccd7ba0494c36a6bebdc7270ac600f25e3cec129

      Author:  UCL-00352545 <samuel.gregoire@student.uclouvain.be> 

      Date: 2025-08-12 16:30:06 +0200

      Commit message:


	  
		
 make-data bubis2025 astral
 
    
  
    

      Package: MsDataHub

      Commit: beb0a4d9242d0cdff58a98c3ca33ceeedf5ef109

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-04-22 21:23:03 +0200

      Commit message:


	  
		
 fix metadata
 
    
  
    

      Package: MsDataHub

      Commit: 924c1bce92af08da49e4d6e770b3428d98cff53c

      Author:  Laurent Gatto <laurent.gatto@uclouvain.be> 

      Date: 2026-04-16 20:16:38 +0200

      Commit message:


	  
		
 Merge pull request #20 from rformassspectrometry/miscDdaDia

Misc dda dia 
    
  
  


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