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GIT Logs

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

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Package: wompwomp
Commit: a59395ce07729b7c2a994d71277d78249fb863b9
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-17 14:26:13 -0700
Commit message:

 removed python from readme
Package: wompwomp
Commit: f5912217abc86f15bf538df66c96eac3e39a0cf6
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-17 01:07:10 -0700
Commit message:

 removed python
Package: wompwomp
Commit: 4de05a03a27c7200d4ab4d12eb49194ae20ad8c6
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-16 18:34:56 -0700
Commit message:

 still working on removing python
Package: wompwomp
Commit: df1cf7ca57d24dd7dd34453444951f06f4491592
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-16 18:02:31 -0700
Commit message:

 in the process of removing python
Package: wompwomp
Commit: 4130b85db66bf393fc14f606136d7d6c84c6ed4b
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-16 15:49:49 -0700
Commit message:

 small readme change
Package: wompwomp
Commit: f67e31395f5c69bac1fe693d8c5e85091c193564
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-16 15:46:22 -0700
Commit message:

 small docker change
Package: wompwomp
Commit: 6201ba5adbc7efc888a955ee9b5b5ea4b5e9b102
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-16 15:45:21 -0700
Commit message:

 small docker change
Package: wompwomp
Commit: 012431eb79d80cc3922c0ddf211464032578e179
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-16 15:43:11 -0700
Commit message:

 adding docker
Package: CRISPRseek
Commit: cc307eae485b0e5c51bff27a50a881c68628aab1
Author: hukai916 <hukai916@gmail.com>
Date: 2025-10-17 16:40:04 -0400
Commit message:

 update testthat scripts and dataset to accomodate bioc 3.22 release
Package: MAST
Commit: 5c6e47f5279e14f6bea6e436da9ce588c2579bac
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2025-10-17 10:03:48 -0700
Commit message:

 remove an undeclared call to gdata in obsolete code
Package: ACE
Commit: 8427b046ee3d424fed3955ab20e15ae99dc96993
Author: jpoell <j.poell@amsterdamumc.nl>
Date: 2025-10-17 17:38:49 +0200
Commit message:

 Updated version in DESCRIPTION
Package: ACE
Commit: aa18de8541787c6e47cf1e38616e2ed48dc48f61
Author: jpoell <j.poell@amsterdamumc.nl>
Date: 2025-10-17 17:28:41 +0200
Commit message:

 Update accessory_functions.R

same updates to standard and linewidth as described for ACE.R
Package: ACE
Commit: f6f5e4a1d9a9a94955976f27a2a2485fe114f837
Author: jpoell <j.poell@amsterdamumc.nl>
Date: 2025-10-17 17:16:51 +0200
Commit message:

 also getadjustedsegments

there was also a calculation for the standard in getadjustedsegments
Package: ACE
Commit: 607579c40cf24ac647077a46e2f8091359700a30
Author: jpoell <j.poell@amsterdamumc.nl>
Date: 2025-10-17 17:05:15 +0200
Commit message:

 minor fixes ACE.R

changed size to linewidth in ggplot line functions and now the X and Y chromosomes are excluded when calculating the standard for singleplot (as they already were for the fitting functions)
Package: ACE
Commit: bc8e1608ac3b6f4138cc6314bacf9b4e23230896
Author: jpoell <j.poell@amsterdamumc.nl>
Date: 2025-10-17 16:41:18 +0200
Commit message:

 Merge pull request #15 from petanska/master

Add n=1 to tail() in ploidyplotloop to prevent multiple minima crash
Package: ACE
Commit: 164e1d3c725569986a01885e31c914f8a1aeb4a3
Author: petanska <50733801+petanska@users.noreply.github.com>
Date: 2025-10-03 10:45:58 +0200
Commit message:

 Add n=1 to tail() in ploidyplotloop to prevent multiple minima crash

Fix: prevent crash when multiple minima in rerror

Specify `n = 1` in `tail(which(rerror==min(rerror)))` to ensure a single index is returned.
This prevents `ploidyplotloop()` from crashing in rare cases where 
multiple minima exist, as reported in issues #10 and #11.
Package: SPOTlight
Commit: cd2d48ba4617a764112644eec90b4f91490b5046
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-10-17 11:56:58 -0400
Commit message:

 ggplot test update
Package: SPOTlight
Commit: 88812e318a211f1c64cd6269792fc30e46372590
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-10-01 11:10:48 -0400
Commit message:

 bump version
Package: SPOTlight
Commit: f83b6aaf53154c7f43b03753ebdb97ff237a68e1
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-10-01 11:10:06 -0400
Commit message:

 test ggplot 4.0.0
Package: SPOTlight
Commit: 47ccd8e678d0a230e83a17a4b7e56c176ff371a6
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-10-01 10:55:24 -0400
Commit message:

 dot-filter
Package: SPOTlight
Commit: 59ea875568bda278693ef57f2495c1a68cabd18a
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-10-01 10:54:57 -0400
Commit message:

 roxygen version
Package: SPOTlight
Commit: 9699ab5e35dba42162bd1a8089d03996a70afe2b
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-09-30 11:35:10 -0400
Commit message:

 bump version 1.13.2
Package: DESeq2
Commit: 2877f70a65cedc89c201947e6b971c1806614ca5
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-17 11:56:28 -0400
Commit message:

 version bump
Package: DESeq2
Commit: 3af71a756963cdf63bb7bc692100b8d61e84ae3c
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-17 11:41:55 -0400
Commit message:

 fix for useT + greaterAbs from @rrross
Package: DESeq2
Commit: 885ac787daf370cd3d7cf72547eb25b937d2b96e
Author: Michael Love <mikelove@users.noreply.github.com>
Date: 2025-10-17 11:34:41 -0400
Commit message:

 Merge pull request #118 from rrross/patch-1

bug fix for greaterAbs when useT=TRUE
Package: DESeq2
Commit: 01c54bb1320563e288bde681bb1c67c0e7f7247e
Author: rrross <57932933+rrross@users.noreply.github.com>
Date: 2025-10-16 14:53:34 -0500
Commit message:

 greaterAbs useT=TRUE bug fix

greaterAbs would return an error when useT=TRUE, due to the df environmental variable being a vector and not a scalar.
Package: TabulaMurisSenisData
Commit: f35b2cbe938409aef01b05673457d6d3307c890c
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-17 16:32:21 +0200
Commit message:

 Bump version
Package: TabulaMurisSenisData
Commit: 588a1d6bf42d235f0edaa2406ea2bd5499db6fcd
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-17 16:31:41 +0200
Commit message:

 Update roxygen version
Package: TabulaMurisSenisData
Commit: 238f7871cf1428540351d0105200210c00974d5d
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-17 16:31:28 +0200
Commit message:

 Document "_PACKAGE" instead of deprecated package documentation
Package: TabulaMurisSenisData
Commit: 47d6a2c194d6ac85dd97210d09a774848a6093e3
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-17 16:31:00 +0200
Commit message:

 Fix links in documentation
Package: TabulaMurisSenisData
Commit: 6e935046b32b9f878a4547aa3722b8dc3db1377b
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-17 16:25:31 +0200
Commit message:

 Add README.Rmd to .Rbuildignore
Package: scRepertoire
Commit: 74605e178570a711ca8e1fc9b3f669eea45df320
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-17 10:17:01 -0500
Commit message:

 Update DESCRIPTION
Package: scRepertoire
Commit: 77b772b58627dd663d1d163860c58eaf52818dab
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-13 10:49:05 -0400
Commit message:

 Merge pull request #542 from BorchLab/vizGenes-BCR

Viz genes bcr
Package: scRepertoire
Commit: 48ef37283d53a61dbb2f7960bc7fdd5d4abf63ab
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-13 09:12:31 -0500
Commit message:

 Update Ibex.Rmd
Package: scRepertoire
Commit: 6ebdd1997fa00411becbb18d9e4d971965d08bd2
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-13 08:30:51 -0500
Commit message:

 ensure chains Heavy and Light passed to getIR

#541
Package: RGMQLlib
Commit: 64be27b6eff0cb90c2980811be5f1aa88bef04f2
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-17 09:58:19 -0400
Commit message:

 Deprecated

 - Software deprecated in 3.21 for unresponsive
Package: chromstaRData
Commit: 3ccaf6be325a825a58d59fa988fcb0ed9b04244b
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-17 09:56:38 -0400
Commit message:

 Deprecated
 - Softare package deprecated in 3.21 for unresponsive
Package: AneuFinderData
Commit: 5fc87a5e2dd551b4c8c106e2988f4c2734173cfa
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-17 09:55:42 -0400
Commit message:

 Deprecate

 - Software package deprecated in 3.21 for unresponsive
Package: netZooR
Commit: d918f07e19e221ea967fe5d7c31d21f9572fa4ba
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-17 09:54:25 -0400
Commit message:

 Deprecated

  Failing for over a year
Package: DMRcaller
Commit: 066119e0ae83e553b368a5bc95e7a5524bec0b82
Author: nrzabet <r.zabet@qmul.ac.uk>
Date: 2025-10-17 14:51:50 +0100
Commit message:

 improved multicores computing with BPPARAM
Package: metabom8
Commit: d99e264d5d0bb25eb5faef879ed68bd698086016
Author: tk <tkimhofer@gmail.com>
Date: 2025-10-17 15:36:04 +0200
Commit message:

 add  git.bioc
Package: metabom8
Commit: 0a752ae7d5534fe501099f166ff874fb3e24b02d
Author: tk <tkimhofer@gmail.com>
Date: 2025-10-17 15:26:16 +0200
Commit message:

 ignoring rstudio files
Package: proBatch
Commit: 01335d493207db3e4692f77b305bab72be1787af
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-15 14:07:41 +0200
Commit message:

 Remove deprecated .onAttach function from zzz.R
Package: proBatch
Commit: 439a6988fa8c113e21b4fadaaecbb8712e3e4bfd
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-15 14:05:41 +0200
Commit message:

 Align with Bioconductor devel (preserve both histories)
Package: proBatch
Commit: 4e78ce58a242e05522ff7f29afb07f956471ba1a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-15 13:38:47 +0200
Commit message:

 add back figure

(cherry picked from commit 5addb09fe3c978361cb0ef117c94a61e3011e798)
Package: proBatch
Commit: 5addb09fe3c978361cb0ef117c94a61e3011e798
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-15 13:38:47 +0200
Commit message:

 add back figure
Package: proBatch
Commit: a2cf996ef34d788b8709bd7c99d97798118e2649
Author: Yuliya Burankova <15180672+Freddsle@users.noreply.github.com>
Date: 2025-09-30 17:19:04 +0200
Commit message:

 Change project URLs to new GitHub repository

Updated repository URLs to reflect new ownership.
Package: proBatch
Commit: 18691e944af5e19107d255b23e4a2918559633d6
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-29 15:32:03 +0200
Commit message:

 Add 'limma' to Imports in DESCRIPTION
Package: proBatch
Commit: b0b20e130fc6be3699e73abd79e6127bb1aa0f66
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 20:25:23 +0200
Commit message:

 Refactor documentation and examples]; remove unused example dataset and update installation instructions in vignettes.
Package: proBatch
Commit: 087be75fdd8bda759e41f338cc8e052235c7b00d
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 20:05:29 +0200
Commit message:

 Update version to 1.99.1 in DESCRIPTION; remove example_multicenter_data.rda and update example_ecoli_data.rda
Package: proBatch
Commit: 8ed1932e7ff51be20a40aec2bb5209d025821297
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 19:36:02 +0200
Commit message:

 Bump version to 1.99.0 in DESCRIPTION and NEWS; update installation instructions in README and vignettes
Package: proBatch
Commit: 8d92cb842e6552d179e71b30ffd102c06599c0a2
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 19:02:44 +0200
Commit message:

 Add return value descriptions to functions in ProBatchFeatures
Package: proBatch
Commit: 4d7660f225c922ff3d963e9fd962fef367b12dab
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 14:16:08 +0200
Commit message:

 remove donottest from examples
Package: proBatch
Commit: 7f9418bad0d7cd94527f49966fa19521f297a7d6
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 14:14:56 +0200
Commit message:

 Added examples fot ProBatchFeatures functions
Package: proBatch
Commit: 44cf4ef3d20a6ddc88b0d81f22aec5f1f6717ea7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 14:13:23 +0200
Commit message:

 Update version number to odd number; rename chunks in vignettes
Package: proBatch
Commit: 5d994f09e4181ae8f85a6eb50231fde562570f64
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 00:26:50 +0200
Commit message:

 Enhance documentation and examples; add new exports and improve warnings in functions.
Package: proBatch
Commit: 6c5f67a25c46794575bf168f4f82dffef522f480
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 00:07:18 +0200
Commit message:

 Update documentation and examples; remove .travis.yml file and adjust .gitignore.
Package: proBatch
Commit: 3787edae4153079f18ad9b6aa761857acb00f0cf
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:23:07 +0200
Commit message:

 Chenges sapply to vapply, removed set.seed.
Package: proBatch
Commit: 52367cdee912515e8fc78ab41cb730120e5fa00d
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:17:30 +0200
Commit message:

 Rename code chunks in vignette
Package: proBatch
Commit: 72b2f2530dfb230e99dad252187c7436ee5dd4f1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:14:37 +0200
Commit message:

 Update NEWS to include changes for version 2.0.1:
Package: proBatch
Commit: 6e982dcccfc06db8b8ad0dafb49d9bdb0bd2a936
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:14:23 +0200
Commit message:

 Update DESCRIPTION file for version 2.0.1; add missing author and improve biocViews
Package: proBatch
Commit: fed18e2aa875a8048a8ce4fb068ef98275e9eb94
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:14:06 +0200
Commit message:

 export `plot_boxplot` and `plot_sample_mean` functions in NAMESPACE.
Package: proBatch
Commit: f6c145673fd9478c579bac185315593a42c75533
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 12:13:44 +0200
Commit message:

 R version change
Package: proBatch
Commit: 52c4a9c4acf184f695e7a8596fb8dfca37f246c5
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-26 19:54:05 +0200
Commit message:

 Update code to change imports using :: to importFrom
Package: proBatch
Commit: 3425f3e52f838d650d9a10cdfa90ad1de4ea2980
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-26 18:48:59 +0200
Commit message:

 Refactor plotting functions to improve axis labeling and fixed message formatting in missing value handling
Package: proBatch
Commit: d74988bc50af2101b266b2812ad138fd7d0e6e7e
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-26 18:22:18 +0200
Commit message:

 Update DESCRIPTION and code to include gridExtra; adjust base sizes in plotting functions and improve message formatting in handle_missing_values function
Package: proBatch
Commit: 7a27fabd38515724aa4e787d27beb900d9ab2dcf
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-25 16:39:22 +0200
Commit message:

 Update ProBatchFeatures vignette and documentation
Package: proBatch
Commit: d7ed30914215de5d4b5111c031025de788fc0424
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-25 02:25:14 +0200
Commit message:

 renamed ProBatchFeatures vignett
Package: proBatch
Commit: 6334567ca0a3f0b9d2b37f624d8bda1defb56ea7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-25 02:23:46 +0200
Commit message:

 Refactor missing value handling and add batch effect correction methods. (limma and combat for pbf)
Package: proBatch
Commit: 7d1ad4f5a36d52ce9956ae826b2bb79c8f67f8f2
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-24 18:56:54 +0200
Commit message:

 Refactor batch correction functions; update tests to  suppress unnecessary warnings.
Package: proBatch
Commit: 6dd1fabd083364cc3264a9a901b4de382f556d4f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-24 10:28:52 +0200
Commit message:

 Add return_gridExtra parameter to plotting functions and update tests accordingly
Package: proBatch
Commit: d63381fabcb37504550e09b16c003c1d141e41c1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-23 15:46:27 +0200
Commit message:

 updated plotting to support multiple assays; add new helper functions for better plot management.
Package: proBatch
Commit: 83059e29a7e006a5bf3a8ea713b417faeb4c831c
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-22 10:22:27 +0200
Commit message:

 Update pb_filterNA function to handle NULL pbf_name; update docs the vignette for clarity on missing data handling and normalization steps.
Package: proBatch
Commit: 491b972053cded22a7cdb9f664985bb76663c2a8
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-21 16:38:03 +0200
Commit message:

 fixed plots missing and tests
Package: proBatch
Commit: d7d1da5710c9b4598ec2636ebd9e9637d1982aee
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-21 15:52:35 +0200
Commit message:

 fixed missing helpers df tests
Package: proBatch
Commit: 65506c8e420934cd4fdceec9162ce795ac21a0e4
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-21 15:49:32 +0200
Commit message:

 Review added missing values plots
Package: proBatch
Commit: ed8ca79a98a1f86ac2ff71cf3f49cf1afa84dd5d
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-19 23:43:36 +0200
Commit message:

 missing values tables from QF
Package: proBatch
Commit: f6012b70bce6c57ddbad4e03727247b4ce56d873
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-19 17:06:50 +0200
Commit message:

 added missing values info operations
Package: proBatch
Commit: 1a96beef14c18e1a4669a544822bf9b648bb066d
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 16:21:54 +0200
Commit message:

 updated wide_diagnostics for pbf objects
Package: proBatch
Commit: 3458b9116efb1436b14e028403a9cb2223252142
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 16:13:37 +0200
Commit message:

 updated pca plotting for pbf
Package: proBatch
Commit: c08dee78b68d74af319dd25ece0bd7d077a366cf
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 13:55:18 +0200
Commit message:

 added plots from "fast" logs from operations
Package: proBatch
Commit: 7af1e8f9f4496afda1b66162805e7729bdfcdd40
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 11:19:47 +0200
Commit message:

 minor fixes in PBF logs
Package: proBatch
Commit: a33e2f92926705a117db0450430db2aedfd4a471
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 16:35:40 +0200
Commit message:

 update show in pbf class
Package: proBatch
Commit: 1007d7fd36f2f382a9dc30db2e21280df9e9a84c
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 14:35:50 +0200
Commit message:

 updated log and chain structure
Package: proBatch
Commit: 7afc8752344dbb615e79d33ea194b667979bb232
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 13:10:55 +0200
Commit message:

 added pbf support into initial_assesment funcs
Package: proBatch
Commit: 69a506368f8da6ec3f4e906b695f3eb01cc24edb
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 11:43:48 +0200
Commit message:

 fix a bug in metadata df creatid in pbf
Package: proBatch
Commit: e23e64c45aac51582d4550297464c9e33f191d9a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-10 16:34:52 +0200
Commit message:

 added levels links into PBF class
Package: proBatch
Commit: ca697d992bb82b333b04a0f9afbe00fbddc1ecf7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-08 15:38:43 +0200
Commit message:

 added E.coli test data
Package: proBatch
Commit: bdaefb0047aef068497c9e9b3359c61ce8530f25
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-08 13:53:06 +0200
Commit message:

 probatch class added
Package: proBatch
Commit: 31d82df4691ea1c9e308d4a2fc2b55f9eca57ab7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-08-27 21:16:16 +0200
Commit message:

 updated ProBatchFeatures class
Package: proBatch
Commit: 172c8b1e73f6ab6a8bf76b552a9f815be26d4b84
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-08-27 16:49:36 +0200
Commit message:

 probatch class
Package: proBatch
Commit: ec6810bdc2d653532b54aa07cde8f117c6b38c51
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-08-25 23:47:35 +0200
Commit message:

 added new TMT dataset
Package: proBatch
Commit: 5d718c23e88851eefd77b479cc7a2d599ccdb907
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-07-02 21:00:44 +0200
Commit message:

 vignett updated (citation autoformatting added)
Package: proBatch
Commit: 11b4705d2d5f7d059ec7a2b03c9fa00bc3aad173
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-23 00:16:26 +0200
Commit message:

 typer checks, added tmp  files ignores
Package: proBatch
Commit: 00dd1a95510f49c5cbd5ec24b4fd912c3635c003
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-23 00:10:58 +0200
Commit message:

 Refactor feature level diagnostics tests to include warnings for missing values; update vline_color handling in plots.
Package: proBatch
Commit: 02c7b171209527f13bc5439d38e8a89418746d13
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 23:57:13 +0200
Commit message:

 Fixed warnings in proteome_wide_diagnostics
Package: proBatch
Commit: 30c03fb05aca02886ae0e34f51c568f8441f8f32
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 23:18:37 +0200
Commit message:

 Add tests for normalize_data_dm to verify offset handling; include example_sample_annotation in hierarchical clustering test
Package: proBatch
Commit: b6c148d6fb57f8f5d08889a8ed89510e4452d2cc
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:58:34 +0200
Commit message:

 Refactor plot_boxplot function (remove default NULL for sample_annotation); Added in log_transform_dm call in normalize_data_dm  offset parameter. Adjust save_ggplot call position in plot_PVCA.df function. Added tests for adjust_units.
Package: proBatch
Commit: 1e0678dec696b10bcdaf030d591d3f0c91f8b6cb
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:50:28 +0200
Commit message:

 Fix typos in documentation in feature_level_diagnostics.R
Package: proBatch
Commit: d47998ce64ee2d3c68e654e80acf919c65a8830a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:47:20 +0200
Commit message:

 Improve fit_nonlinear function warnings and handling of insufficient data; added rle_func tests
Package: proBatch
Commit: 499b939d04a339cb4a6027d0238dc77cb6fcfe4f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:35:13 +0200
Commit message:

 Refactor documentation in date conversion functions for clarity, improve error messages in fit_non_linear, and enhance tests for rle_func and fit_nonlinear behavior.
Package: proBatch
Commit: 3509d8d2a7bf65ff57b84396fe12c80448a172de
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 21:37:30 +0200
Commit message:

 Update adjust_batch_trend_dm to return corrected data directly and added fit column handling in error messages
Package: proBatch
Commit: 4f008121a05fd588145c22fdcabe6e42d760943a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 21:25:46 +0200
Commit message:

 Enhance adjust_batch_trend functions with additional parameters and improve error handling in date conversion tests
Package: proBatch
Commit: 76179a5a9250ab51c26b81174f9680e87ba7f1f2
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 21:15:38 +0200
Commit message:

 Update return documentation in convert_annotation_classes for clarity
Package: proBatch
Commit: 5a9d0f2ca07d3679d63dfe5c0dddb53868962de7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 21:11:21 +0200
Commit message:

 Refactor ggsave usage in plot_CV_distr.df, fix typo in auxiliary.R, and enhance date conversion tests
Package: proBatch
Commit: ebd8e19003297430c68602e5ecb7620321c0befa
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 20:44:13 +0200
Commit message:

 Fix typo in warning message for asymmetrical heatmap and update horizontal line intercept in split violin plot
Package: proBatch
Commit: 815c6b27bbd06067942fe5d889f10db679f47e48
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 20:21:44 +0200
Commit message:

 added and fixed for handle_missing_values
Package: proBatch
Commit: c606a0179ac50c02dcbf7d740e9039f0769e6ae5
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 16:02:46 +0200
Commit message:

 Improve error messages for missing columns in create_peptide_annotation and fix typo in normalize_sample_medians_df
Package: proBatch
Commit: 8e30cc4916eca41c682f52bc2436e07f31315e12
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 15:54:57 +0200
Commit message:

 refactored handle_missing_values function and added tests (fail now)
Package: proBatch
Commit: 22f0b7ac704d107900d23c8368a7226e79942afd
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 15:39:59 +0200
Commit message:

 fixed typos in call plot_heatmap_generic
Package: proBatch
Commit: 1fd7ae4ff703dec682047c3596b828b918e0f26f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 15:38:47 +0200
Commit message:

 refactored handle missing values function
Package: proBatch
Commit: e72f019951a18a69cd6578a445ceaa16eb49398a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 15:18:46 +0200
Commit message:

 color scheme fixes in initial assesment
Package: proBatch
Commit: 9c32c06099d5ec0755d630c4d3c20033414b8e69
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 13:36:02 +0200
Commit message:

 refactored plot_boxplot, added tests for initial assesment
Package: proBatch
Commit: 7674326ab3118add8534bad741a51e747a2a9356
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 13:19:51 +0200
Commit message:

 updated and refactored  plot_sample_mean
Package: proBatch
Commit: 47960078785c2bc2b55ed325f05cfd35e49a31fd
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 12:56:11 +0200
Commit message:

 minor refactoring of plots in initial_assesment
Package: proBatch
Commit: 810f58f3924dce3e62c820d8ec5c9be7b329a295
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 22:30:55 +0200
Commit message:

 fixed warnings CV tests
Package: proBatch
Commit: e25187831dcab4022bb510269cd02023b06eddee
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 22:25:49 +0200
Commit message:

 fixed failed CV tests
Package: proBatch
Commit: aca754fe250f3839c1474288ca80a0774adb018f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 22:15:53 +0200
Commit message:

 fixed majority of CV tests
Package: proBatch
Commit: a61e214f1cfd2addcbcf1b79dbcdd7529f0aeca7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 21:52:17 +0200
Commit message:

 removed qual_value from columns code
Package: proBatch
Commit: fee264a00a85d42c91c51ad57b549ac1b4c07fe5
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 21:40:52 +0200
Commit message:

 added tests (not final) fo CV calculation
Package: proBatch
Commit: 56df5b68b0a81883de7d35b1efb9e7930f6e5893
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 21:39:05 +0200
Commit message:

 refactored calculate_feature_CV
Package: proBatch
Commit: 86591def32c521950fc77969b774862e28171c5f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 21:14:12 +0200
Commit message:

 fixed bugs in CV calculation
Package: proBatch
Commit: 9b6c44b213149ff3228a9b830f364fbc147c17ed
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:57:01 +0200
Commit message:

 fixed filtering in CV calculations]
Package: proBatch
Commit: 8ae738a6482cfc027d41c5545d24db09897006ec
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:39:24 +0200
Commit message:

 added warning catch to utility fuuncs
Package: proBatch
Commit: ae1c70bc7c2ac52112e85e5eb2e5d02060041a31
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:34:24 +0200
Commit message:

 fixed correct_batch_effects_dm and added check to subset_keep_cols
Package: proBatch
Commit: 0e75d71cd781c1901f002357f21348c7c6bf032d
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:02:31 +0200
Commit message:

 fixed switch in subset_keep_cols
Package: proBatch
Commit: 32b36adbd85e3a1043c2f16f0652a3f495d08b5f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:00:44 +0200
Commit message:

 fixed unwanted warnings
Package: proBatch
Commit: 0b7951f2e4cb9450d85771a34a5d7171a244bf02
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 19:16:20 +0200
Commit message:

 refactor define_sample_order in utility_funcs
Package: proBatch
Commit: 03d3c1a95b9fc904ed922033523a3b83b32bb777
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 17:24:45 +0200
Commit message:

 fixed  plotting, added check to check_sample_consistency
Package: proBatch
Commit: 4fcac1fdd2d666cdb07e666908a27b67bf857878
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 17:01:44 +0200
Commit message:

 fixed merge_df_with_annotation, correct_batch_effects_dm
Package: proBatch
Commit: 8f4760646afee3c17f5f4c4377b8768a9fab313f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 15:43:40 +0200
Commit message:

 fixed all_of in  subset_keep_cols
Package: proBatch
Commit: af70b5579db034f753673a7cb2de3e7565872f60
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 14:35:44 +0200
Commit message:

 fixed unwanted warnings in tests - correlation based diagnostic
Package: proBatch
Commit: 24557db453083d372963f710a21c43aad02cdb64
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 13:52:38 +0200
Commit message:

 fixed all_of selection, fixed tests warnings, added transform_raw tests
Package: proBatch
Commit: 7f231190c4a74ed4a24e9bbb576cdabc885513eb
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 12:54:16 +0200
Commit message:

 4 spaces (BioCheck), added test for  transform log funcs, fixed seed in colors to hex sorting
Package: proBatch
Commit: dd8fdfb454b17f567c01fa146b5a17a2718062ea
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 12:08:20 +0200
Commit message:

 fixed unwanted warnings in color mapping tests
Package: proBatch
Commit: ee60a184606da98d4d0f2d3b9d05fe23830e4869
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 11:32:54 +0200
Commit message:

 yepo in annnotation
Package: proBatch
Commit: c197a3f582738e85e522b6f08ad18cbe3ba87f52
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 11:27:16 +0200
Commit message:

 minor fixes in colors - n_base and pallets
Package: proBatch
Commit: 9b6a7be529ea57804f05a83161d692e9c627f5d3
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 23:08:02 +0200
Commit message:

 fixed one_of/all_of,
Package: proBatch
Commit: 199a6be16af652510e76d93ffc1583dcef9afaaf
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 22:14:18 +0200
Commit message:

 color typo fixes, added palette_type
Package: proBatch
Commit: 82541eee308080daf33ef44f419b253335da6fb9
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 18:22:09 +0200
Commit message:

 fixed no_fit_imputed tests (set to False)
Package: proBatch
Commit: 231943f65c30793865da38852014a871bd686e36
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 18:04:42 +0200
Commit message:

 fixed missing columns in center_feature_batch_medians_df
Package: proBatch
Commit: 8efe9d6df10fd7b58ad400ff22dd4e59709f9ae4
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 17:50:48 +0200
Commit message:

 expect_equivalent() was deprecated -> expect_equal(ignore_attr = TRUE), same expect_is
Package: proBatch
Commit: 08deba034bfef9b6cce4206632fc973a6548b534
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 16:14:59 +0200
Commit message:

 context() was deprecated - removed
Package: proBatch
Commit: d9b34aa64b5dd5c3aff94364735c5ba9731a0201
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 15:20:57 +0200
Commit message:

 fixed typo in loess fit?
Package: proBatch
Commit: 5c2f543de7d035851e680a4ce1659b011b7b0239
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 15:17:17 +0200
Commit message:

 styler run - formatting
Package: proBatch
Commit: 8f10560e0c40ad7bd4be653d688640138dbc8b0e
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 15:08:01 +0200
Commit message:

 subset_keep_cols
Package: proBatch
Commit: 4767850f3141aa1fe196a4c61b2527b22a522dcd
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 15:07:54 +0200
Commit message:

 removed repetitions and added subset_keep_cols helper
Package: proBatch
Commit: b8b2d4876e802af00a346a9e88127583d3e37657
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-13 14:39:55 +0200
Commit message:

 typo in docs fixes
Package: proBatch
Commit: e8ac7026353f3e94e75902480f8695ad67a156c8
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 22:08:17 +0100
Commit message:

 added mainteiner
Package: proBatch
Commit: 38cbca9ad04674cf0377eba0a9e56c9f08bf6ad6
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 22:04:46 +0100
Commit message:

 updated RMD and description
Package: proBatch
Commit: 6c660e49432324b549885182f5958947f7c59606
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 21:41:26 +0100
Commit message:

 updated .Rd files
Package: proBatch
Commit: e9b0c7ab0813fd62efb67aca0137f93bcd62cff6
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 21:41:07 +0100
Commit message:

 refactor funcs to reduce cyclomatic complexity
Package: proBatch
Commit: 554048e9168a7c7de7c602201c2df2d4820a1def
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 20:54:14 +0100
Commit message:

 fixed style issues
Package: proBatch
Commit: 4bb37c7e658ba725f8a1f674828c94e4de82d8c1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 19:27:53 +0100
Commit message:

 fixed style issues
Package: proBatch
Commit: 6325af083de0cd179305aba64fc61529cc77080b
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 19:27:39 +0100
Commit message:

 updated description
Package: proBatch
Commit: 05ed1df53ecd632a5064bb01b77fc3dcbd9f9fba
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 17:15:33 +0100
Commit message:

 fixed code style with styler
Package: proBatch
Commit: c9ca8e772ecde8e69050cf1afeac45fb85227342
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 16:49:21 +0100
Commit message:

 fixed data loading for examples
Package: proBatch
Commit: f4960b38188782e8ade0547a1f71aa8d634501cc
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 16:15:47 +0100
Commit message:

 fixed loading data for examples docs after LazyData: false
Package: proBatch
Commit: b766ad50efe2e3405a771f140aceed3843cbe4c0
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 16:03:09 +0100
Commit message:

 set LazyData: false
Package: proBatch
Commit: 7fdc4fb3ffa33d9a819cc47de1146b0f2c6090f2
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 16:02:49 +0100
Commit message:

 added loading teest data in examples
Package: proBatch
Commit: ae78c4bd21d9b5a191d91048f9178d13a9be7ef0
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 15:42:01 +0100
Commit message:

 added "_PACKAGE" to main func
Package: proBatch
Commit: 50e4fcd6db5f4a058d901a9015335aebe4091c14
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 15:40:47 +0100
Commit message:

 fixed plot_sample_mean aes y
Package: proBatch
Commit: 7d57e675ff7ec94cc2fd3062dc11f46cf0a419f8
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 15:38:30 +0100
Commit message:

 fixed plot_protein_corrplot title for >1 proteins
Package: proBatch
Commit: 5f702a27f861bcff3ee59b06fceaa08eb0d50e55
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 15:37:26 +0100
Commit message:

 added merge_rare_levels example
Package: proBatch
Commit: 57bba4e371420e9478dc071d9813fa223fdbfc6c
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2024-12-30 23:36:02 +0100
Commit message:

 fixed deprecated aes params
Package: proBatch
Commit: bb9aff84e6e872b4224c4f03a88108536fca4522
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2024-12-30 23:11:41 +0100
Commit message:

 fixed select (deprecated->all_of) and base_size param(added)
Package: proBatch
Commit: 97ea0bcbdf1779ad33b45481f88f6360d80d851c
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2023-10-07 22:47:57 +0200
Commit message:

 add default locale for dates_to_posix
Package: proBatch
Commit: d5cb21f595f3b768e9876917cc867207514ce3f4
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2023-10-07 20:45:56 +0200
Commit message:

 Update CITATION, DESCRIPTION
Package: proBatch
Commit: 1886a09cc73a88fd2650348b50815fa9feea49b7
Author: Jelena Čuklina <chuklina.jelena@gmail.com>
Date: 2023-04-01 09:58:32 +0200
Commit message:

 new maintainers
Package: proBatch
Commit: dd82f814477aaabad012311a37a8a59058c81b23
Author: Chloe H. Lee <43470195+ChloeHJ@users.noreply.github.com>
Date: 2021-11-26 14:17:20 +0000
Commit message:

 Update README.md
Package: proBatch
Commit: 6cff0e5ae08f5929f07d570bcad4db3733cfa853
Author: Chloe H. Lee <43470195+ChloeHJ@users.noreply.github.com>
Date: 2021-11-26 14:16:37 +0000
Commit message:

 Update README.md
Package: proBatch
Commit: ecc00183934a12f84b6a949b331b815b845064cc
Author: Chloe H. Lee <43470195+ChloeHJ@users.noreply.github.com>
Date: 2021-11-26 14:12:05 +0000
Commit message:

 Update CITATION
Package: proBatch
Commit: 30e4481b8a745978974a323d7dbe7582f71c655b
Author: Chloe H. Lee <43470195+ChloeHJ@users.noreply.github.com>
Date: 2021-08-31 17:24:40 +0100
Commit message:

 Update README.md
Package: proBatch
Commit: 17e1ff207126ae0e31046444dc451eda51fc4476
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-09-13 18:02:35 +0200
Commit message:

 updated mans
Package: proBatch
Commit: e021d00d6d312a7a12eb748a6fbf014a86117e51
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-08-30 15:17:59 +0200
Commit message:

 base_size = 20 for larger fonts in plots
Package: proBatch
Commit: 4ef10a7d0f47fe0bd9b4f01791efb764cfb2afa6
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-04-13 14:08:30 +0200
Commit message:

 corrected bug in multi-peptide facetting
Package: proBatch
Commit: 26880f96507ed2252023ff5e62393fe1f80119cd
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-04-13 13:55:11 +0200
Commit message:

 corrected bug, preventing multiple peptide plotting
Package: proBatch
Commit: 86c1cbba784100ae0511f8b4fa6e24ca4456a5e1
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-04-13 13:44:22 +0200
Commit message:

 updated documentation for requant plotting
Package: proBatch
Commit: 422bd039b2cc0d88556456ff0ab9ad0a2d2d2f2d
Author: Yuliya Burankova <15180672+Freddsle@users.noreply.github.com>
Date: 2025-09-30 17:19:04 +0200
Commit message:

 Change project URLs to new GitHub repository

Updated repository URLs to reflect new ownership.
Package: proBatch
Commit: 609a5fddeecbdeb50edc0dc2c7d0e587fbeaeb62
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-29 15:32:03 +0200
Commit message:

 Add 'limma' to Imports in DESCRIPTION
Package: proBatch
Commit: 690aa7fee7077264f5353acf548837483ab04670
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 20:25:23 +0200
Commit message:

 Refactor documentation and examples]; remove unused example dataset and update installation instructions in vignettes.
Package: proBatch
Commit: 0a6e06193077040fdc08015432a290ee39bde755
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 20:05:29 +0200
Commit message:

 Update version to 1.99.1 in DESCRIPTION; remove example_multicenter_data.rda and update example_ecoli_data.rda
Package: proBatch
Commit: 92b302c0ca583e9df89c542c135d565482957c89
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 19:36:02 +0200
Commit message:

 Bump version to 1.99.0 in DESCRIPTION and NEWS; update installation instructions in README and vignettes
Package: proBatch
Commit: 7f5f487c73fe842a4d57d7087d3b639f09806da8
Author: Yuliya Burankova <15180672+Freddsle@users.noreply.github.com>
Date: 2025-09-28 19:38:25 +0200
Commit message:

 Merge pull request #3 from Freddsle/new_class

Documentation fixes
Package: proBatch
Commit: cc140d11c03cfdfb62a9cc3bfbf3859693fb36ca
Author: Yuliya Burankova <15180672+Freddsle@users.noreply.github.com>
Date: 2025-09-28 19:16:39 +0200
Commit message:

 Merge pull request #2 from Freddsle/new_class

New proBatchFeatures class and limmaRBE
Package: proBatch
Commit: 25539ec83106d93912da53a55c6861292daeaae2
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 19:02:44 +0200
Commit message:

 Add return value descriptions to functions in ProBatchFeatures
Package: proBatch
Commit: 71d03627e07990873870aec44911f8743f733bc9
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 14:16:08 +0200
Commit message:

 remove donottest from examples
Package: proBatch
Commit: cf14d631c391bce22310c67d5641e6200c7fe274
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 14:14:56 +0200
Commit message:

 Added examples fot ProBatchFeatures functions
Package: proBatch
Commit: 55dd343e0f889de3617c7fa29c3249329bf632f1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 14:13:23 +0200
Commit message:

 Update version number to odd number; rename chunks in vignettes
Package: proBatch
Commit: 76ae8decb9837e1085e6b03fa16e517431793a53
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 00:26:50 +0200
Commit message:

 Enhance documentation and examples; add new exports and improve warnings in functions.
Package: proBatch
Commit: 49e93c860f4e9f551a659b7f4a9de42507171966
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 00:07:18 +0200
Commit message:

 Update documentation and examples; remove .travis.yml file and adjust .gitignore.
Package: proBatch
Commit: 8acbd1d5244445aa95717bf281066a95574d3ac7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:23:07 +0200
Commit message:

 Chenges sapply to vapply, removed set.seed.
Package: proBatch
Commit: 95e3a5d28e2080211e4ba7f56e042b8d1a118103
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:17:30 +0200
Commit message:

 Rename code chunks in vignette
Package: proBatch
Commit: 05539988aa8cde10da59ce1f8ed1bdba16c96542
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:14:37 +0200
Commit message:

 Update NEWS to include changes for version 2.0.1:
Package: proBatch
Commit: 89478f2278bc9461162f5624b973fa4c05bfe070
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:14:23 +0200
Commit message:

 Update DESCRIPTION file for version 2.0.1; add missing author and improve biocViews
Package: proBatch
Commit: 539fb058df844697d426cd0c15d70ee007d1a84f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:14:06 +0200
Commit message:

 export `plot_boxplot` and `plot_sample_mean` functions in NAMESPACE.
Package: proBatch
Commit: 69e1215744d68bf8bf5bdd678677a01170962954
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 12:13:44 +0200
Commit message:

 R version change
Package: proBatch
Commit: cf86cd21fcdd243ba4dde535eefc39f6930186de
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-26 19:54:05 +0200
Commit message:

 Update code to change imports using :: to importFrom
Package: proBatch
Commit: 5134ce898451b2eeff7f1e58a13bd1e70e715ce1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-26 18:48:59 +0200
Commit message:

 Refactor plotting functions to improve axis labeling and fixed message formatting in missing value handling
Package: proBatch
Commit: e9ec6ddc260bb029892161664bb9b48fbf2f16ec
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-26 18:22:18 +0200
Commit message:

 Update DESCRIPTION and code to include gridExtra; adjust base sizes in plotting functions and improve message formatting in handle_missing_values function
Package: proBatch
Commit: c80e38785aa666ca3e80b77d5248b069b4cdc806
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-25 16:39:22 +0200
Commit message:

 Update ProBatchFeatures vignette and documentation
Package: proBatch
Commit: 7e0fae8e7d9506ba7aaf384eb1c6e8f9eb987f43
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-25 02:25:14 +0200
Commit message:

 renamed ProBatchFeatures vignett
Package: proBatch
Commit: bbc19cb6afc929fb32126af642e460de9613efb3
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-25 02:23:46 +0200
Commit message:

 Refactor missing value handling and add batch effect correction methods. (limma and combat for pbf)
Package: proBatch
Commit: ad92f66feb96c002561bc343daee033b5a000677
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-24 18:56:54 +0200
Commit message:

 Refactor batch correction functions; update tests to  suppress unnecessary warnings.
Package: proBatch
Commit: bfd062afb77ebb925a559f68e901b97db3e176e7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-24 10:28:52 +0200
Commit message:

 Add return_gridExtra parameter to plotting functions and update tests accordingly
Package: proBatch
Commit: b03cfc76f4e39b115ecfbbec7110a021b4d7b039
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-23 15:46:27 +0200
Commit message:

 updated plotting to support multiple assays; add new helper functions for better plot management.
Package: proBatch
Commit: 3f6d4148523055f7ea411946eec8c0a4cda4f73e
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-22 10:22:27 +0200
Commit message:

 Update pb_filterNA function to handle NULL pbf_name; update docs the vignette for clarity on missing data handling and normalization steps.
Package: proBatch
Commit: 942639d22a043149b2eaa9df6d55a1391a8a8ba2
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-21 16:38:03 +0200
Commit message:

 fixed plots missing and tests
Package: proBatch
Commit: c92761553efae2306207d56c48c34693943cc4f8
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-21 15:52:35 +0200
Commit message:

 fixed missing helpers df tests
Package: proBatch
Commit: 8d2f9f4132cf96e3a249e9896c05e9aa91d57e1d
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-21 15:49:32 +0200
Commit message:

 Review added missing values plots
Package: proBatch
Commit: 5276084041a5cd930f758cb7434764bb6c967738
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-19 23:43:36 +0200
Commit message:

 missing values tables from QF
Package: proBatch
Commit: bb7f2df7cae8e9022958c6279f71cb91add4f209
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-19 17:06:50 +0200
Commit message:

 added missing values info operations
Package: proBatch
Commit: 9a762564d131e471f59e51c85dec11967c1bc0a3
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 16:21:54 +0200
Commit message:

 updated wide_diagnostics for pbf objects
Package: proBatch
Commit: 2b01d199d2dc8e5c884cb7cce7cce66bc23aba0a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 16:13:37 +0200
Commit message:

 updated pca plotting for pbf
Package: proBatch
Commit: 112883e16beac5389f2f7d194f063930f136f021
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 13:55:18 +0200
Commit message:

 added plots from "fast" logs from operations
Package: proBatch
Commit: be633f5a2efbf219acefe272cd76ed1e417c4f5f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 11:19:47 +0200
Commit message:

 minor fixes in PBF logs
Package: proBatch
Commit: 7aef1aaf77eaa7c7168cb4a1730d431ad4a21455
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 16:35:40 +0200
Commit message:

 update show in pbf class
Package: proBatch
Commit: 9f0d53de1e9230dbc27624cd848b4800dddedd49
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 14:35:50 +0200
Commit message:

 updated log and chain structure
Package: proBatch
Commit: c4a3191a69e05366a8f3d099ef65c70e0658bd50
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 13:10:55 +0200
Commit message:

 added pbf support into initial_assesment funcs
Package: proBatch
Commit: d3706c1a95d9f3a0cbdc6c606f17ba46002167c1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 11:43:48 +0200
Commit message:

 fix a bug in metadata df creatid in pbf
Package: proBatch
Commit: 60bf2cbf865e99b7eb3bf56e50a259b01c7106ee
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-10 16:34:52 +0200
Commit message:

 added levels links into PBF class
Package: proBatch
Commit: 028d6d513f13414276c91c94c1a93773490326c8
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-08 15:38:43 +0200
Commit message:

 added E.coli test data
Package: proBatch
Commit: eaac342ba499686b181d68c777bc21f79b298dc6
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-08 13:53:06 +0200
Commit message:

 probatch class added
Package: proBatch
Commit: eb84dbeecfd444abf1edaeb60a2b1723b54cb493
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-08-27 21:16:16 +0200
Commit message:

 updated ProBatchFeatures class
Package: proBatch
Commit: 7ca01b19eb1d5f07eb1bfcac243c63db7efda282
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-08-27 16:49:36 +0200
Commit message:

 probatch class
Package: proBatch
Commit: 80a37c5b1c8c396277fa42671790e8f960580707
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-08-25 23:47:35 +0200
Commit message:

 added new TMT dataset
Package: proBatch
Commit: c08551a124b7713ec57bc0abecfa831411ec9c18
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-07-02 21:00:44 +0200
Commit message:

 vignett updated (citation autoformatting added)
Package: proBatch
Commit: 368b93c5afff61d4d7e25d96b26c89de5f00c5a5
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-23 00:16:26 +0200
Commit message:

 typer checks, added tmp  files ignores
Package: proBatch
Commit: 7185ee849f7ea3f12de59064cdf90e47e074b79c
Author: Yuliya Burankova <15180672+Freddsle@users.noreply.github.com>
Date: 2025-06-23 00:14:31 +0200
Commit message:

 Merge pull request #1 from Freddsle/warning_fixes

Warning fixes, refactoring, typo fixes, and minor bug fixes.
Package: proBatch
Commit: 810fb31e358610e4302d351290640a821563da65
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-23 00:10:58 +0200
Commit message:

 Refactor feature level diagnostics tests to include warnings for missing values; update vline_color handling in plots.
Package: proBatch
Commit: 7bb7c6ddc8e6e2cc44bc6cc98d2907b632eb3644
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 23:57:13 +0200
Commit message:

 Fixed warnings in proteome_wide_diagnostics
Package: proBatch
Commit: 011a2f1deac144b5c6397acf7ca930e04d4f559c
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 23:18:37 +0200
Commit message:

 Add tests for normalize_data_dm to verify offset handling; include example_sample_annotation in hierarchical clustering test
Package: proBatch
Commit: 15fa176137bbf368ca6a4d84012b5ae347393590
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:58:34 +0200
Commit message:

 Refactor plot_boxplot function (remove default NULL for sample_annotation); Added in log_transform_dm call in normalize_data_dm  offset parameter. Adjust save_ggplot call position in plot_PVCA.df function. Added tests for adjust_units.
Package: proBatch
Commit: 2356af3be10374c7753649bdbffa0f9c291da139
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:50:28 +0200
Commit message:

 Fix typos in documentation in feature_level_diagnostics.R
Package: proBatch
Commit: 93ce5ebea36ec5dd212df9477aedad8afc18fe75
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:47:20 +0200
Commit message:

 Improve fit_nonlinear function warnings and handling of insufficient data; added rle_func tests
Package: proBatch
Commit: b26eae34ddf96b4e183044c7c79331678dfa54c1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:35:13 +0200
Commit message:

 Refactor documentation in date conversion functions for clarity, improve error messages in fit_non_linear, and enhance tests for rle_func and fit_nonlinear behavior.
Package: proBatch
Commit: 03d6fdeb00de22d76b9722f2d8db65d72bb2e745
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 21:37:30 +0200
Commit message:

 Update adjust_batch_trend_dm to return corrected data directly and added fit column handling in error messages
Package: proBatch
Commit: 80decb3e37db3050ce37432d10f80a53d1eebcde
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 21:25:46 +0200
Commit message:

 Enhance adjust_batch_trend functions with additional parameters and improve error handling in date conversion tests
Package: proBatch
Commit: 9005c19b0afd7dd6d9eea7d38b651572da0d3b65
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 21:15:38 +0200
Commit message:

 Update return documentation in convert_annotation_classes for clarity
Package: proBatch
Commit: 01cc1f110375219eb965b63d4710aedcd889c0cb
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 21:11:21 +0200
Commit message:

 Refactor ggsave usage in plot_CV_distr.df, fix typo in auxiliary.R, and enhance date conversion tests
Package: proBatch
Commit: d6bfafe22946326c955e9627ab9ef2a375d12ba0
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 20:44:13 +0200
Commit message:

 Fix typo in warning message for asymmetrical heatmap and update horizontal line intercept in split violin plot
Package: proBatch
Commit: 54d7861a9dbde24e3d103a25f3b94eab45e559bf
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 20:21:44 +0200
Commit message:

 added and fixed for handle_missing_values
Package: proBatch
Commit: 4f26e3ac91827a6c8afb85a30799756c0e299207
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 16:02:46 +0200
Commit message:

 Improve error messages for missing columns in create_peptide_annotation and fix typo in normalize_sample_medians_df
Package: proBatch
Commit: a7e6e3aeea4743d0425c0702481efdadcdb67ac3
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 15:54:57 +0200
Commit message:

 refactored handle_missing_values function and added tests (fail now)
Package: proBatch
Commit: bc4e629750fa4ec5161c4a0c23938ff87adf4b63
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 15:39:59 +0200
Commit message:

 fixed typos in call plot_heatmap_generic
Package: proBatch
Commit: 4980afdd88095855fe89977c785e14cf8f87dd75
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 15:38:47 +0200
Commit message:

 refactored handle missing values function
Package: proBatch
Commit: 05e48d9e5cbf0c8ba7ea9f234ae0eae8968b2510
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 15:18:46 +0200
Commit message:

 color scheme fixes in initial assesment
Package: proBatch
Commit: 4c70a0e0f3afe66ab2e4f408eb7431161ade95bd
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 13:36:02 +0200
Commit message:

 refactored plot_boxplot, added tests for initial assesment
Package: proBatch
Commit: 434331558414faf1b40014f4a74eff6b28da73be
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 13:19:51 +0200
Commit message:

 updated and refactored  plot_sample_mean
Package: proBatch
Commit: 40cb94f973491e0d6ea1fcc5f8361ab5c3b0ee3c
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 12:56:11 +0200
Commit message:

 minor refactoring of plots in initial_assesment
Package: proBatch
Commit: e25fb237024d4b4b5707f2dc8bdb3d72ac0c14ec
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 22:30:55 +0200
Commit message:

 fixed warnings CV tests
Package: proBatch
Commit: 28f6dd7bbc4faba2638967fa7a95ba72bd6ed389
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 22:25:49 +0200
Commit message:

 fixed failed CV tests
Package: proBatch
Commit: 0a7f8a56c33fd6789915f251ca1ba697bc5489db
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 22:15:53 +0200
Commit message:

 fixed majority of CV tests
Package: proBatch
Commit: 6efa00055b19bbab5b653f5116d4eda92dbc8337
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 21:52:17 +0200
Commit message:

 removed qual_value from columns code
Package: proBatch
Commit: c5806dfbe1deccb5082e2746781170a3cb97dde1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 21:40:52 +0200
Commit message:

 added tests (not final) fo CV calculation
Package: proBatch
Commit: 73316eafbe492c9d226909c18052c772d4506d2d
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 21:39:05 +0200
Commit message:

 refactored calculate_feature_CV
Package: proBatch
Commit: d19e322e923eadf3c3b0852d989f91cc76f75420
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 21:14:12 +0200
Commit message:

 fixed bugs in CV calculation
Package: proBatch
Commit: ad704b00bbb707e613832de5ad2adf5684b79502
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:57:01 +0200
Commit message:

 fixed filtering in CV calculations]
Package: proBatch
Commit: ca0d0a9db1f9596d5c7f738d53e29a20d3e353d8
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:39:24 +0200
Commit message:

 added warning catch to utility fuuncs
Package: proBatch
Commit: 6f548a0090d92706c10aa1f2ca4c32e715b18967
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:34:24 +0200
Commit message:

 fixed correct_batch_effects_dm and added check to subset_keep_cols
Package: proBatch
Commit: 280f840a9a7b7fd92521fb24f1067056fe373227
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:02:31 +0200
Commit message:

 fixed switch in subset_keep_cols
Package: proBatch
Commit: 73fc94c894915df8949e12dd901c01ee6a792dd5
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:00:44 +0200
Commit message:

 fixed unwanted warnings
Package: proBatch
Commit: 69e29b2514d7d7d7d100e4aa4402c719064685d3
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 19:16:20 +0200
Commit message:

 refactor define_sample_order in utility_funcs
Package: proBatch
Commit: c628ca70499e932838affd0a2cfbc53585122ca7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 17:24:45 +0200
Commit message:

 fixed  plotting, added check to check_sample_consistency
Package: proBatch
Commit: f2a6eed52318600e87d93b7780470c78287b03b3
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 17:01:44 +0200
Commit message:

 fixed merge_df_with_annotation, correct_batch_effects_dm
Package: proBatch
Commit: 524d4dce3a398dc64a0e5fe689d684a6674d0ed6
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 15:43:40 +0200
Commit message:

 fixed all_of in  subset_keep_cols
Package: proBatch
Commit: 42e8af702d1e9139d0daaf8aed5e801fe5489231
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 14:35:44 +0200
Commit message:

 fixed unwanted warnings in tests - correlation based diagnostic
Package: proBatch
Commit: 2e200a5fde07eb245045e93a0dce0577e4f98848
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 13:52:38 +0200
Commit message:

 fixed all_of selection, fixed tests warnings, added transform_raw tests
Package: proBatch
Commit: 919d359ccf164b76f9cbe7a57a01128c3e170d52
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 12:54:16 +0200
Commit message:

 4 spaces (BioCheck), added test for  transform log funcs, fixed seed in colors to hex sorting
Package: proBatch
Commit: 32512377b11d88573b7b5b8d08bc5c75f5ed4f68
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 12:08:20 +0200
Commit message:

 fixed unwanted warnings in color mapping tests
Package: proBatch
Commit: 18053bb64d9a20fc9edb8aff040f23b1a6fe3c52
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 11:32:54 +0200
Commit message:

 yepo in annnotation
Package: proBatch
Commit: c362fe3c4723f11b101fbb7665189c05f471cf19
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 11:27:16 +0200
Commit message:

 minor fixes in colors - n_base and pallets
Package: proBatch
Commit: 259712e7518089eb1a06d9d6b19d4b21903c1250
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 23:08:02 +0200
Commit message:

 fixed one_of/all_of,
Package: proBatch
Commit: cc9f1716a8e3ea742f6ef2123cf39346047bd89f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 22:14:18 +0200
Commit message:

 color typo fixes, added palette_type
Package: proBatch
Commit: 77ae3fb129923623e85fb0c27042166b73e64932
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 18:22:09 +0200
Commit message:

 fixed no_fit_imputed tests (set to False)
Package: proBatch
Commit: b0b900571270c426e097c7bb7fdc8a78d49678d3
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 18:04:42 +0200
Commit message:

 fixed missing columns in center_feature_batch_medians_df
Package: proBatch
Commit: 34fed2d552ace672ce03f71aee460823427fc6be
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 17:50:48 +0200
Commit message:

 expect_equivalent() was deprecated -> expect_equal(ignore_attr = TRUE), same expect_is
Package: proBatch
Commit: 3487bea26cbfcdbbde5fa1553f822a008be2554d
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 16:14:59 +0200
Commit message:

 context() was deprecated - removed
Package: proBatch
Commit: 7391a46fcb79e4d435868b6a68b77bb31edf98a3
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 15:20:57 +0200
Commit message:

 fixed typo in loess fit?
Package: proBatch
Commit: 8cfb4523c1dde097412dd4ce0f250345948c93d0
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 15:17:17 +0200
Commit message:

 styler run - formatting
Package: proBatch
Commit: e53051467437076c738ee6ebddf621752e781e3a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 15:08:01 +0200
Commit message:

 subset_keep_cols
Package: proBatch
Commit: 3e01d2b2e18fbf181871bfe8a4288e58137a7f79
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 15:07:54 +0200
Commit message:

 removed repetitions and added subset_keep_cols helper
Package: proBatch
Commit: 4b5f85c19e097a500548e82e547c2fc6481d1cbf
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-13 14:39:55 +0200
Commit message:

 typo in docs fixes
Package: proBatch
Commit: 524249ee9db539ca0e93442ca698bb14cf827d90
Author: Jelena Čuklina <chuklina.jelena@gmail.com>
Date: 2025-04-25 11:26:42 +0200
Commit message:

 Merge pull request #16 from Freddsle/master

Fixed errors in build
Package: proBatch
Commit: 566d8c530ccd99ec54326dc3aa8a30d89fd5eb3a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 22:08:17 +0100
Commit message:

 added mainteiner
Package: proBatch
Commit: 06ce42366734891083986309321d387ceeefe952
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 22:04:46 +0100
Commit message:

 updated RMD and description
Package: proBatch
Commit: 5991f206c8d362a081eb50665854ad62c34b6da6
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 21:41:26 +0100
Commit message:

 updated .Rd files
Package: proBatch
Commit: d667c4e7ddacde200c97275de84396379d8472b1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 21:41:07 +0100
Commit message:

 refactor funcs to reduce cyclomatic complexity
Package: proBatch
Commit: 3d1c8ff32fac91d338d60956c9299a14ac8a66ca
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 20:54:14 +0100
Commit message:

 fixed style issues
Package: proBatch
Commit: 714aa2193ee359dfe1f15ff9cbf0bc2a2e57262a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 19:27:53 +0100
Commit message:

 fixed style issues
Package: proBatch
Commit: 01f79ea63fe60d26eb279b205ff56952af433ea1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 19:27:39 +0100
Commit message:

 updated description
Package: proBatch
Commit: de5a8b5afeb3d6bf9df01c71ac07b27e8c02d0f9
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 17:15:33 +0100
Commit message:

 fixed code style with styler
Package: proBatch
Commit: 782fa7d09aae8ba276356de0a0fdb12674e9a1d8
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 16:49:21 +0100
Commit message:

 fixed data loading for examples
Package: proBatch
Commit: 867382d66ed24cea270838ca769d24f35f2451e6
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 16:15:47 +0100
Commit message:

 fixed loading data for examples docs after LazyData: false
Package: proBatch
Commit: 17639a662c78f93af7e82a6199e487122c02a16a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 16:03:09 +0100
Commit message:

 set LazyData: false
Package: proBatch
Commit: da89694cb1b8d68b118f7108622a9ebb22162188
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 16:02:49 +0100
Commit message:

 added loading teest data in examples
Package: proBatch
Commit: 1a3314b17b64081967301551a590bbc691cd94d4
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 15:42:01 +0100
Commit message:

 added "_PACKAGE" to main func
Package: proBatch
Commit: e02f3ae87bdbcb7389dd92316a42bb929cce2bde
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 15:40:47 +0100
Commit message:

 fixed plot_sample_mean aes y
Package: proBatch
Commit: 0d7c0a68ffadb6a96b315d1e7935cb13ac38e45c
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 15:38:30 +0100
Commit message:

 fixed plot_protein_corrplot title for >1 proteins
Package: proBatch
Commit: c95b44313b07cd7a33c5bccc8a0c0f8f60792e15
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 15:37:26 +0100
Commit message:

 added merge_rare_levels example
Package: proBatch
Commit: a3665390e67070369332546448abafe28cf3e479
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2024-12-30 23:36:02 +0100
Commit message:

 fixed deprecated aes params
Package: proBatch
Commit: 89858419838ab8ec9de5a4f68f7953e16d8d25e9
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2024-12-30 23:11:41 +0100
Commit message:

 fixed select (deprecated->all_of) and base_size param(added)
Package: proBatch
Commit: d4c9f2206216f19718d737be9ca4de61443e5b24
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2023-10-07 22:47:57 +0200
Commit message:

 add default locale for dates_to_posix
Package: proBatch
Commit: 8394239203dd792b6baf30d0125daf3bdea8e868
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2023-10-07 20:45:56 +0200
Commit message:

 Update CITATION, DESCRIPTION
Package: proBatch
Commit: 84322c0fc45dc60117e37c19bbd499496d7ae384
Author: Jelena Čuklina <chuklina.jelena@gmail.com>
Date: 2023-04-01 09:58:32 +0200
Commit message:

 new maintainers
Package: proBatch
Commit: 4342c3f3aec7b34299ebd69b6d67bf888b8bc334
Author: Chloe H. Lee <43470195+ChloeHJ@users.noreply.github.com>
Date: 2021-11-26 14:17:20 +0000
Commit message:

 Update README.md
Package: proBatch
Commit: b17e394e2667e471339ac84435e63fac1decd51e
Author: Chloe H. Lee <43470195+ChloeHJ@users.noreply.github.com>
Date: 2021-11-26 14:16:37 +0000
Commit message:

 Update README.md
Package: proBatch
Commit: aef7b2e58944df0063d62f79d2e426e64501b653
Author: Chloe H. Lee <43470195+ChloeHJ@users.noreply.github.com>
Date: 2021-11-26 14:12:05 +0000
Commit message:

 Update CITATION
Package: proBatch
Commit: f23007649399285bf9091c6db8181d5d6f9ae38e
Author: Chloe H. Lee <43470195+ChloeHJ@users.noreply.github.com>
Date: 2021-08-31 17:24:40 +0100
Commit message:

 Update README.md
Package: proBatch
Commit: 8fae15049be67693bd0d4a4383b51bfb4fb287a6
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-09-13 18:02:35 +0200
Commit message:

 updated mans
Package: proBatch
Commit: 3507a3e7b427ebe1f8bc048934ee080b546e30a4
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-08-30 15:17:59 +0200
Commit message:

 base_size = 20 for larger fonts in plots
Package: proBatch
Commit: 5d52759e98bdc71f30eb976e99e0eb17a94a76d0
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-04-13 14:08:30 +0200
Commit message:

 corrected bug in multi-peptide facetting
Package: proBatch
Commit: 59c84d7eb7026c15b8bc78bf4f8994689ac760c8
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-04-13 13:55:11 +0200
Commit message:

 corrected bug, preventing multiple peptide plotting
Package: proBatch
Commit: 34201b8d1da9930e65ee8157ebbebdc39fb4bc12
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-04-13 13:44:22 +0200
Commit message:

 updated documentation for requant plotting
Package: SynExtend
Commit: 6662838ff5caedcdded65874e34fed7bec99f8b9
Author: npcooley <npcooley@gmail.com>
Date: 2025-10-17 08:59:08 -0400
Commit message:

 fixed function name case
Package: SynExtend
Commit: 0150dbc87375c7044966da0c26b245294118854d
Author: npcooley <npcooley@gmail.com>
Date: 2025-07-28 23:33:33 -0400
Commit message:

 remove duplicate line
Package: SynExtend
Commit: 40380e21fc90dcee60aad80233b3f9bcb64b54bf
Author: Nicholas Cooley <39340402+npcooley@users.noreply.github.com>
Date: 2025-07-28 12:43:35 -0400
Commit message:

 Merge pull request #80 from ahl27/master

fix: code cleanup
Package: SynExtend
Commit: b5a57a917cc1b55e22afe97845a781ebe34f4ed3
Author: npcooley <npcooley@gmail.com>
Date: 2025-07-28 12:42:09 -0400
Commit message:

 Merge branch 'devel' of https://github.com/npcooley/SynExtend into devel
Package: SynExtend
Commit: b0fda1d69a15fd83733af0861344c68485c9a302
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-07-28 12:39:36 -0400
Commit message:

 minor formatting update for consistency
Package: SynExtend
Commit: 72e3a321d811eb11ccef51af1d28c04493cf248d
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-07-28 12:31:52 -0400
Commit message:

 masks R-specific functionality in ExoLabel
Package: SynExtend
Commit: 82d97dde57c6b6b81b73ee23fa82186eb2145e06
Author: npcooley <npcooley@gmail.com>
Date: 2025-07-28 12:30:27 -0400
Commit message:

 c file clean up
Package: SynExtend
Commit: d1b42456c00652c98bd2e7e9a289e2f76348f5ca
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-07-28 12:27:50 -0400
Commit message:

 adds fallback defines for compilation outside of R
Package: SynExtend
Commit: e507c74771f43f8a681d81fbfa1c1a6bab2ae645
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-07-24 13:21:11 -0400
Commit message:

 minor consistency update
Package: SynExtend
Commit: 266090c1561d0b7f39aaa6cff2d97fce76a6e249
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-07-24 13:16:06 -0400
Commit message:

 add important note to header
Package: SynExtend
Commit: c1f0755f8afe2e46db093364b069a02b2cec2b46
Author: Nicholas Cooley <39340402+npcooley@users.noreply.github.com>
Date: 2025-07-24 13:06:44 -0400
Commit message:

 Merge pull request #79 from ahl27/master

fix: tech debt cleanup
Package: SynExtend
Commit: 49752e8c7f709164b5046fa494efdc949d78bd19
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-07-16 13:38:23 -0400
Commit message:

 bump description and update NEWS
Package: SynExtend
Commit: 1506e043153bc204c7dd2c95b9930fc5415d4733
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-07-24 13:03:19 -0400
Commit message:

 update documentation to reflect gzip-compression support
Package: SynExtend
Commit: ec997c9609fcad2007457e26d80c7b4fe2e12331
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-07-24 12:55:32 -0400
Commit message:

 Adds support for gz-compressed files
Package: SynExtend
Commit: 203d5520dfc752b0d582a3b98f4feb88e392fbe1
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-07-16 13:42:48 -0400
Commit message:

 fix issue where numeric input to header would break ExoLabel
Package: SynExtend
Commit: 0cdd45c12169418305a69cc6b7f7c1428b8e00f0
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-07-16 13:24:20 -0400
Commit message:

 Adds header argument to ExoLabel
Package: SynExtend
Commit: 46aac2291b115b0dbb3d1b3696a3e6b7d0542045
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-07-16 12:54:24 -0400
Commit message:

 Remove consensus clustering stuff
Package: SynExtend
Commit: 5692f673231083a0d1708a1397a603f1809b8caa
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-07-16 12:42:44 -0400
Commit message:

 Fix some examples to make them run faster
Package: SynExtend
Commit: be95daf897cb7d9a956cffa841a9d2f9b616b12d
Author: npcooley <npcooley@gmail.com>
Date: 2025-05-27 11:27:28 -0400
Commit message:

 first c subfunction for SummarizePairs
Package: SynExtend
Commit: 39ed7e34ad13d07200ce62a2dc1640d1c4f0f469
Author: Nicholas Cooley <39340402+npcooley@users.noreply.github.com>
Date: 2025-05-27 11:25:57 -0400
Commit message:

 Merge pull request #78 from ahl27/master

fix: code cleanup
Package: SynExtend
Commit: dcd1dd4fff0adf477d6429aca7332b76a04f38b1
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-05-16 13:34:23 -0400
Commit message:

 update description
Package: SynExtend
Commit: 7583cedc7c3a998b3247714ef14f45151aca2fb1
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2025-05-16 13:29:43 -0400
Commit message:

 Merge branch 'devel' into master
Package: SynExtend
Commit: ec4154bd23d4c56a3a91be038c52640076085cfd
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-05-16 13:28:21 -0400
Commit message:

 add final newlines for some files
Package: SynExtend
Commit: 27aed5f9022a4c1f00fca63c19f9d09ead75451e
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-05-16 13:17:50 -0400
Commit message:

 fix documentation errors
Package: SynExtend
Commit: 85291373383ceec55d018281e429c2e66820ae16
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-05-16 13:05:01 -0400
Commit message:

 add cleanup script
Package: SynExtend
Commit: 0b66d9e268c09d5a93a00c6f6116a623848d8fca
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-05-16 13:04:49 -0400
Commit message:

 remove processors argument
Package: SynExtend
Commit: 150e1c087acb465ff61283c593926aae5b32f7a1
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-05-16 09:00:34 -0400
Commit message:

 add exolabel header
Package: SynExtend
Commit: 8d247cd3e5cd768ac113d3f4b0be6b92a71ebcf5
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-05-16 09:00:11 -0400
Commit message:

 Add argument passthrough to supertree
Package: SynExtend
Commit: 8d448fd481dedf7358804260cec621b446f2c8bb
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-05-09 10:39:41 -0400
Commit message:

 Makevars is finally working
Package: SynExtend
Commit: eca0b5c72ec8a32bab71b7a80d7f87419a6d9a2a
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-05-09 09:38:56 -0400
Commit message:

 update includes for ExoLabel
Package: SynExtend
Commit: 4687f3749ab3a956b7000720573565970b4bf4bb
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-05-09 08:36:30 -0400
Commit message:

 rename ExoLabel file
Package: SynExtend
Commit: a438bc990face129a955ad192f5b1311cbd6a10f
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-05-09 08:34:49 -0400
Commit message:

 move ExoLabel source files into their own folder
Package: SynExtend
Commit: 45dc238a4247311c6704422767c4c9b1e031880d
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2025-05-09 08:35:05 -0400
Commit message:

 Merge branch 'npcooley:devel' into master
Package: SynExtend
Commit: 756e6f1594c112528e53de2b9a39c19d7543dc27
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-16 09:10:58 -0400
Commit message:

 fixes precision issue causing discrepancy between self_loops and actual weights
Package: SynExtend
Commit: 0438597f69b3e6450da829523df61e7eb11c4868
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-14 11:25:36 -0400
Commit message:

 minor output fixes
Package: scviR
Commit: e3b36fd6e7272eff14b4f02b8fe6155b9f00e72f
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-10-17 08:40:17 -0400
Commit message:

 remove apptest from devel repo
Package: scviR
Commit: 71b9782ea4f42ab9aeab247b9448045f39ef8968
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-10-17 07:56:00 -0400
Commit message:

 Merge branch 'nobas' of https://github.com/vjcitn/scviR into nobas
Package: scviR
Commit: a2a83510e73b6678b6a2e01fd33a04141cfc9dd8
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-10-17 07:33:33 -0400
Commit message:

 trying to sync suitably
Package: scviR
Commit: b3495f24da97b952bd865e03c1e68c132cbb7588
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-10-17 07:28:23 -0400
Commit message:

 Merge branch 'devel' of https://github.com/vjcitn/scviR into nobas
Package: scviR
Commit: 64860e5a322c5ba77b594a3964bdfc2bfdd7188e
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-10-17 07:23:04 -0400
Commit message:

 trying to convert to py_require discipline, blocking use of basilisk
Package: scviR
Commit: 1e6d83920c9be8c0d1ce2873f550d1895bd7e202
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-12 06:02:12 -0400
Commit message:

 Merge branch 'main' of https://github.com/vjcitn/scviR into HEAD
Package: scviR
Commit: f39e0a394f820f611c2f0d852c12e1a56da63d99
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2025-05-12 06:01:11 -0400
Commit message:

 Merge pull request #4 from vjcitn/newvince

Newvince - bringing main into sync with bioc
Package: scviR
Commit: 44c0eef385a6bcce3d3544ef641f92a901d36546
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-12 05:57:52 -0400
Commit message:

 Merge branch 'newvince' into HEAD -- moving from 1.1.1 to 1.9.10
Package: scviR
Commit: bafd3f8ffc66ed602a8b5e620f055d034c6c7eb4
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-07 22:31:54 -0400
Commit message:

 better content for pkgdown
Package: scviR
Commit: c3ed506b4fd69b42444e83322fbcd925a03dfa4a
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2023-09-26 09:10:03 -0400
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: scviR
Commit: fe34047eab78fc23a9c851c80c42619c9ac2288c
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2023-03-07 06:08:30 -0500
Commit message:

 adding app and tests
Package: scviR
Commit: 5c875264b757bf2bac6bf42e3f0f901f568e298a
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2023-03-07 05:57:24 -0500
Commit message:

 remove .Rhistory
Package: scviR
Commit: afbb3773c79ac6d588c4c6e1b8e8862115e3bb0a
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2023-03-07 05:54:50 -0500
Commit message:

 adding a shinytest test suite
Package: scviR
Commit: 54f9e7322f26edf43036385c2c515b38aba695d8
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2023-03-07 05:36:41 -0500
Commit message:

 adding testable app
Package: scviR
Commit: 3d4b46b70759ae15942d82ad78c837119cc914a0
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2023-03-07 05:35:28 -0500
Commit message:

 trying to sync suitably
Package: Rvisdiff
Commit: ce11c9f2d488f9a1bc124a30c2bc7113a5fef57f
Author: BioinfoUSAL <bioinfo@usal.es>
Date: 2025-10-17 10:55:59 +0200
Commit message:

 1.7.1 merged
Package: Rvisdiff
Commit: 9315091a5387096c6610a76d956b6d423b76d011
Author: BioinfoUSAL <bioinfo@usal.es>
Date: 2025-10-17 10:47:14 +0200
Commit message:

 1.7.1
Package: Rvisdiff
Commit: 5928a86d451aaabb0b0dc533f9d6b2bbd99b5b48
Author: BioinfoUSAL <bioinfo@usal.es>
Date: 2024-12-12 10:52:57 +0100
Commit message:

 1.3.1
Package: Rvisdiff
Commit: 3afe60053074ef9adb7b6f0e45040d6a8d4834f8
Author: BioinfoUSAL <bioinfo@usal.es>
Date: 2024-09-25 09:58:29 +0200
Commit message:

 1.3.1
Package: dar
Commit: 9e7cc1205ae5b22dc8ceee1fdac13781a74f4992
Author: Francesc Català-Moll <70643921+xec-cm@users.noreply.github.com>
Date: 2025-10-17 09:32:02 +0200
Commit message:

 bump
Package: dar
Commit: 43704f41a514862852baf74b79d61e50b756d991
Author: Francesc Català-Moll <70643921+xec-cm@users.noreply.github.com>
Date: 2025-10-17 09:30:26 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: dar
Commit: 4cb8571f69c4dc7caa13a442bb1e6d24b7ee1274
Author: Francesc Català-Moll <70643921+xec-cm@users.noreply.github.com>
Date: 2025-10-17 09:24:37 +0200
Commit message:

 add GenomeInfoDb to avoid error on testing
Package: anndataR
Commit: e4c4e0e2d82e5bd4d690fec65c652199dc758be5
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2025-10-17 08:58:16 +0200
Commit message:

 Bump version number
Package: anndataR
Commit: 0e801d373e5806121543476414a05ea9f6707560
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-10-17 08:55:01 +0200
Commit message:

 Improve handling in conversion from `Seurat` (#369)

* Handle converting Seurat graphs without assays

* Add check_dims_and_skip() util function

* Check dimensions and skip in from_Seurat

* Fix layer processing in from_Seurat()

* Style

* Adjust defaults in conversion man pages
Package: anndataR
Commit: fb6cfafe5f801391a8437352317f1a57d135e6a3
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2025-10-16 12:35:15 +0200
Commit message:

 Add agents file (#367)

* Add agents.md file

* add agents to buildignore

* update changelog

* Apply suggestions from code review

Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com>

---------

Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com>
Package: Ibex
Commit: 124a6b38d19f1131567c0157bea276a4d179b7c5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-16 15:53:21 -0700
Commit message:

 Ibex 0.99.34: Restore pre-0.99.33 ibex_vdj.rda
Package: BiocGenerics
Commit: e33e990405279c99ebd99580dd961c98e2de6f7c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-16 15:23:29 -0700
Commit message:

 BiocGenerics 0.55.4: Small tweak to updateObject(data.frame)
Package: scrapper
Commit: 7f61f83db0150d95ebe1f33a87e83af7140aa06f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-16 14:57:40 -0700
Commit message:

 Updated bindings to scran_markers functions.

- Added call to score_markers_best() if all.pairwise= is an integer.
- Added min.rank.limit= so users can choose how much min-rank they want.
- Allow users to disable group-wise means and detected if not needed.
Package: assorthead
Commit: 87148384820b2be468884d15a6506da2a7d59b99
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-16 14:58:54 -0700
Commit message:

 Updated version of scran_markers and topicks.
Package: assorthead
Commit: dd9711980b6cbfe352d6cb069978b9878cf142c5
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-09 11:24:41 -0700
Commit message:

 Updated the version of tatami_hdf5.
Package: epiregulon
Commit: 591e442fe9f75677a5154ea401e5c3c9b7682a57
Author: TomVuod <tomasz.wlodarczyk@contractors.roche.com>
Date: 2025-10-16 19:43:25 +0000
Commit message:

 v1.99.2
Package: epiregulon
Commit: 38da628e3f5c1eeee0cde1715884f487fffe9c86
Author: TomVuod <tomasz.wlodarczyk@contractors.roche.com>
Date: 2025-10-16 18:35:19 +0000
Commit message:

 small corrections
Package: epiregulon
Commit: 2ae21c3affce10c9dee16a6500c68a548b404f76
Author: TomVuod <tomasz.wlodarczyk@contractors.roche.com>
Date: 2025-10-16 15:39:13 +0000
Commit message:

 calculate FDR from all p-values at once
Package: OSTA
Commit: 29eccde04ca33615a98dff3f0bb5d68e96969620
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-16 14:34:37 -0400
Commit message:

 version and date
Package: OSTA
Commit: 6fec36768386a565782abfc513f2504af98f8be6
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-16 14:29:42 -0400
Commit message:

 Merge pull request #235 from lmweber/python-reticulate

Update Python interoperability to use Miniconda, Conda, and reticulate
Package: OSTA
Commit: 87dd86c884143585b3b38cf0e23036ec38f93d8f
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-16 00:51:56 -0400
Commit message:

 install BS from Bioc
Package: OSTA
Commit: a6323b8b7f50f03630f07e8e7a15af337dbd9973
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-15 22:47:01 -0400
Commit message:

 update text to clarify re-using an existing Python installation
Package: OSTA
Commit: 6a023f6729fe15a28c99f35b69a7f7b3b2be6911
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-15 21:28:00 -0400
Commit message:

 fix outs/ directories with updated TENxVisium()
Package: OSTA
Commit: c14eb44770f2a1fa4cdb13c9604f811d503d0493
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-15 21:22:08 -0400
Commit message:

 add GenomeInfoDb manually as dependency due to changes to GenomicRanges
Package: OSTA
Commit: 1c66798f88fd7c7f985db91d4afd3e1ef358eb90
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-15 19:22:56 -0400
Commit message:

 fix outs/ directory for updated TENxVisium()
Package: OSTA
Commit: 507742bc2e27f7ab194bfe95f1d33f3d1c620955
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-15 17:33:36 -0400
Commit message:

 revert eval=FALSE now with correct BS dependencies
Package: OSTA
Commit: 34a9c21335651706e7e5299fb937e4cd70c84d01
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-15 16:57:54 -0400
Commit message:

 install correct devel versions of dependencies for BayesSpace
Package: OSTA
Commit: 4a03125779ec13e977ecb6be0ae34b28389956e2
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-15 11:47:38 -0400
Commit message:

 skip plot
Package: OSTA
Commit: 7f5c413cb49edec58660b83674d1280e4230df14
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-15 11:46:28 -0400
Commit message:

 additional gc
Package: OSTA
Commit: 5fda99baf6771b917cd30a564bbaf2bafa9260b3
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-15 09:45:41 -0400
Commit message:

 pause imcRtools
Package: OSTA
Commit: 529ffb89a52e9ac641c79ab54fb4adbe03008315
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-15 09:43:06 -0400
Commit message:

 gc() to reduce memory usage
Package: OSTA
Commit: 4c57345c3224f97e705a7502758ae7b8c4144066
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-13 15:22:24 -0400
Commit message:

 install BS from GitHub
Package: OSTA
Commit: 800ac13e1dee084349f332a93d9c24871a0e3d66
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-13 15:21:30 -0400
Commit message:

 pause SpotSweeper
Package: OSTA
Commit: e5cf82768fc22ffa8fa740f51db618e01ee98e60
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-13 14:52:56 -0400
Commit message:

 comment and wording
Package: OSTA
Commit: ef073db32d73fd382aeadbed14b7996d67ad5a2b
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-13 14:10:15 -0400
Commit message:

 skip basilisk
Package: OSTA
Commit: 5566b74c82e18fe6e530ed6877b7de1700f3a107
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-13 11:38:07 -0400
Commit message:

 reorganize python interoperability chapter to start with conda and reticulate
Package: OSTA
Commit: bf2906a5deab7bdf29234fa07e5a6b92701cd2e3
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-10-09 10:19:07 +0200
Commit message:

 +`SpaceTrooper` in "img-quality-control"
Package: OSTA
Commit: 7dad11441c4d12a49279d2203322e09f924225a4
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 10:07:38 +0200
Commit message:

 rmv caching
Package: OSTA
Commit: 6fb9beb93aac57fa893633ca373c42b4df9d03b6
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-10-09 10:01:25 +0200
Commit message:

 Merge pull request #37 from HelenaLC/img-qc

revise intro; reformat plot
Package: OSTA
Commit: af8890fa40114c56968a8373c6f39e531d5986fc
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 09:55:42 +0200
Commit message:

 revise intro; reformat plot
Package: OSTA
Commit: e8ac905f7524e2a176fe1d3fa971390502fcf2f2
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-10-08 20:00:12 +0200
Commit message:

 +`SpaceTrooper` in "img-quality-control" chp
Package: OSTA
Commit: 9f7db74451e19a2c38a825f8dbdda4b3da17728a
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-08 19:58:52 +0200
Commit message:

 +Imports:SpaceTrooper
Package: OSTA
Commit: 07a2f3753b4c4418d886134373b75e7352c6e227
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-08 19:58:21 +0200
Commit message:

 incorporate SpaceTrooper
Package: OSTA
Commit: 73c8df8707439d9cd64028fc34a0a2633733430c
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-10-08 17:30:24 +0200
Commit message:

 decon/Visium HD revision
Package: OSTA
Commit: d8bd694897ba2d8f2c40e6c8534634710703f4ca
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-08 16:43:12 +0200
Commit message:

 simpilfy hyperlink to workshop
Package: OSTA
Commit: 21dbed6356ae3c471cb97763aa9eec5efcfadedf
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-08 16:40:44 +0200
Commit message:

 increase png rendering size
Package: OSTA
Commit: f7b2f6d88d4d443d907acdd02a28f4ca65072c82
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-08 16:30:40 +0200
Commit message:

 Merge branch 'sandbox' into vhd_hlc
Package: OSTA
Commit: ad9369e065998460c7b965eb799ae5930c343103
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-08 16:30:17 +0200
Commit message:

 hlc revision
Package: OSTA
Commit: cfde6fe0af061b267fea091c1ffb0387a4d37ecf
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-10-08 14:02:33 +0200
Commit message:

 aesthetic revision of `spatialFDA` updates
Package: OSTA
Commit: 09ccb83845ca725c5db76c98bc60daab291d0307
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-08 14:01:46 +0200
Commit message:

 spatialFDA HLC revision
Package: OSTA
Commit: e5393e868545b00a1d49b70eb2ff72b7a9b53d34
Author: Estella Yixing Dong <estelladong729@gmail.com>
Date: 2025-10-08 10:03:12 +0200
Commit message:

 Merge pull request #12 from estellad/vhdcell

remove tidyverse from load libraries
Package: OSTA
Commit: e02b9d3ceb8fc1a658b52df4420a483ede4580fc
Author: estellad <estelladong729@gmail.com>
Date: 2025-10-08 10:01:10 +0200
Commit message:

 remove tidyverse from load libraries
Package: OSTA
Commit: 355f34cd1cc2adba1111eeaca1aabbdde20e346b
Author: Estella Yixing Dong <estelladong729@gmail.com>
Date: 2025-10-08 08:59:45 +0200
Commit message:

 Merge pull request #11 from estellad/vhdcell

add tidyverse to DESCRIPTION, needed in VHD chapter
Package: OSTA
Commit: 55c954f59252d1b6c77c1fff2844ee3c3a8c81d2
Author: estellad <estelladong729@gmail.com>
Date: 2025-10-08 08:59:02 +0200
Commit message:

 add tidyverse to DESCRIPTION, needed in VHD chapter
Package: OSTA
Commit: 365ba307ad8de7fd63c2884c6e264d3f0e96228c
Author: Estella Yixing Dong <estelladong729@gmail.com>
Date: 2025-10-07 17:52:09 +0200
Commit message:

 Merge pull request #10 from estellad/vhdcell

Vhdcell
Package: OSTA
Commit: 33c20d075cf9d5e92852a9ea3e2c90cf8d6abf20
Author: estellad <estelladong729@gmail.com>
Date: 2025-10-07 17:50:00 +0200
Commit message:

 update plot title'
Package: OSTA
Commit: 58c1e56d42097ca46b116c0d04532e6c4b723c24
Author: estellad <estelladong729@gmail.com>
Date: 2025-10-07 17:48:27 +0200
Commit message:

 update VHD workflow and add link to workshop
Package: OSTA
Commit: 73cef1e81378e083ec5cc498cf48dddf7ea99a13
Author: estellad <estelladong729@gmail.com>
Date: 2025-10-07 11:53:20 +0200
Commit message:

 Merge branch 'sandbox' into vhdcell
updates from last night
Package: OSTA
Commit: e8a7b423b0bbdddf6ac82513eb33c0d2533c0f0f
Author: estellad <estelladong729@gmail.com>
Date: 2025-10-07 11:52:37 +0200
Commit message:

 resolve conflicts
Package: OSTA
Commit: f286822c59f388be220700e875aca31878ec9e5a
Author: estellad <estelladong729@gmail.com>
Date: 2025-10-07 11:40:39 +0200
Commit message:

 changes so far
Package: OSTA
Commit: 43cac8af41238863027a4786a417dbcfadf67a4b
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-06 11:17:25 +0200
Commit message:

 adressing HLC review
Package: OSTA
Commit: 85e4ec8cb754516ccca075de486cf3f76da516ba
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-03 15:35:49 +0200
Commit message:

 new version of spatialFDA
Package: OSTA
Commit: 2a9df5b2452ee755129718f57eb33e87208ec838
Author: estellad <estelladong729@gmail.com>
Date: 2025-07-20 18:33:27 +0200
Commit message:

 initiate PR for VHD cell
Package: SpiecEasi
Commit: a8c24b7c65114332bee0049b545112f961511681
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2025-10-16 13:41:51 -0400
Commit message:

 Bump version: 1.99.1 → 1.99.2
Package: AnnotationForge
Commit: d5a6cb0c621a5ccfddac6a8e8c3e368c00fc5cdc
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-16 10:30:44 -0400
Commit message:

 Update viableID for release
Package: MetaboAnnotation
Commit: 4df51a54c95b1cb5a9e43fa8fcdeffeb4aaa4928
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-10-16 14:26:18 +0200
Commit message:

 Merge pull request #127 from rformassspectrometry/jomain

docs: extend documentation for use of external similarity functions
Package: MetaboAnnotation
Commit: e54809a02debc21032e717155c6ee900a9f228b7
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-10-16 14:05:45 +0200
Commit message:

 docs: fix vignette
Package: MetaboAnnotation
Commit: 34c65dcb730e1214e4ab881f13f327d44b45c5a2
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-10-16 13:58:02 +0200
Commit message:

 docs: extend documentation for use of external similarity functions

- related to issue #126: expand the documentation of `CompareSpectraParam()` and
  add examples to the vignette describing how e.g. *msentropy* spectra
  similarity calculations can be used instead of the default.
Package: VariantAnnotation
Commit: af7ae49722281222e133cda7262aba4bfd6ade3f
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-10-16 09:31:22 -0400
Commit message:

 improving unit tests for 3.22
Package: Ibex
Commit: 45b94558e9ac03a08d3ae9faedee52762bef23eb
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-16 08:15:53 -0500
Commit message:

 Merge branch 'main' into devel
Fixing Herve deletion of data?
Package: Ibex
Commit: 189dde33623b385e0bb42c55a8c5715e2a38a3c1
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-16 08:15:33 -0500
Commit message:

 Update DESCRIPTION
Package: Ibex
Commit: f1e558327e22b6d218d0dca049816703a9365fba
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-13 09:11:53 -0500
Commit message:

 Update README.md
Package: Ibex
Commit: 778ab54efcb9df903834a9f60e3ef2e15bed1ae4
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-13 09:11:33 -0500
Commit message:

 Update README.md
Package: omicsGMF
Commit: 95d60268ff62e3f0029e33c6bc6ecffddc6ae5a4
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2025-10-16 15:07:41 +0200
Commit message:

 update vignette and testthat with smaller mock data
Package: Ibex
Commit: c225504fa63a61ecb6a950807c67c00bf64e4b13
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-16 07:58:43 -0500
Commit message:

 Update DESCRIPTION
Package: Ibex
Commit: 4701bfa1c040364bfb649efa32610a6bf008652c
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-16 07:57:27 -0500
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/Ibex into devel
Package: Ibex
Commit: e7730df19a3873598c8f66bd2674ca17dabc8f50
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-01 08:03:08 -0500
Commit message:

 Merge branch 'main' into devel

refining description
Package: Ibex
Commit: fa4c4461ff7658b4a47e80f25a2d9b50992ae0f7
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-01 08:02:14 -0500
Commit message:

 v1.0.0
Package: MsBackendSql
Commit: 7b77a0c2d57e3bdc9cd5808cd70c0826d990330e
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-10-16 13:59:26 +0200
Commit message:

 Merge pull request #30 from rformassspectrometry/jomain

Jomain
Package: MsBackendSql
Commit: 65743e58ac378d62d55fc4cf7887381ce4ded87b
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-10-16 10:18:18 +0200
Commit message:

 refactor: small performance improvements for longForm
Package: MsBackendSql
Commit: cec005c18e731619b33f445db7e6b301e24717a9
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-10-14 06:24:52 +0200
Commit message:

 refactor: small performance improvements for longForm
Package: epiregulon
Commit: bfee05dc0256715d2681815a4b3fb1515160d19f
Author: TomVuod <tomasz.wlodarczyk@contractors.roche.com>
Date: 2025-10-16 11:53:30 +0000
Commit message:

 v1.99.1
Package: epiregulon
Commit: d185d291ad993f96013836a6040acd143019f1e7
Author: TomVuod <tomasz.wlodarczyk@contractors.roche.com>
Date: 2025-10-16 10:21:05 +0000
Commit message:

 handle clusters being a list
Package: epiregulon
Commit: 68ed86a8f0ab0131e7c15549e4c889a1b294d57e
Author: TomVuod <tomasz.wlodarczyk@contractors.roche.com>
Date: 2025-10-16 10:20:27 +0000
Commit message:

 handle clusters NULL
Package: epiregulon
Commit: c9030479e5fee47eb472cdd69fe1264caffae4fe
Author: TomVuod <tomasz.wlodarczyk@contractors.roche.com>
Date: 2025-10-16 10:18:27 +0000
Commit message:

 fixing GitHub issue #44
Package: OrganismDbi
Commit: fb8673c5fd3e38dc457970bbef4b2b070b6a8b0b
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-10-16 07:44:02 -0400
Commit message:

 increased a length threshold for exon extraction test
Package: TFEA.ChIP
Commit: 9fb694f92ff74dedb264f66f7d7984b0f9d6ccd1
Author: yosra <yosraberrouayel@gmail.com>
Date: 2025-10-16 12:48:44 +0200
Commit message:

 fixed version number
Package: TFEA.ChIP
Commit: 91245df689ef6ffa5b586e750745f0e62d5344a3
Author: yosra <yosraberrouayel@gmail.com>
Date: 2025-10-14 15:16:14 +0200
Commit message:

 fixed preprocessing part2
Package: TFEA.ChIP
Commit: cb7ece631b61b4aaf2900706c8bc6a16ea1561dc
Author: yosra <yosraberrouayel@gmail.com>
Date: 2025-10-14 12:49:08 +0200
Commit message:

 fixed preprocessing
Package: epiregulon.extra
Commit: fd774546c8d4d825ade1037a44693ccb04ffee9c
Author: Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com>
Date: 2025-10-16 10:11:40 +0000
Commit message:

 v1.5.1
Package: epiregulon.extra
Commit: f67de745e39d567444301ddac96e8ff47cee6b91
Author: Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com>
Date: 2025-10-16 10:11:21 +0000
Commit message:

 removal of plot test and regulon update
Package: topdownr
Commit: 3cf1c5dbdce4669bae581824f7200b7d80a87797
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2025-10-16 11:52:36 +0200
Commit message:

 docs: fix download shield
Package: topdownrdata
Commit: ee1276a5f0dbde5adf178578fd5e494f85aee239
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2025-10-16 11:50:26 +0200
Commit message:

 chore: move to codeberg.org
Package: topdownr
Commit: 5f498e96bd4b3c9b31be4bf35e1cea3faa181a00
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2025-10-16 11:46:40 +0200
Commit message:

 chore: move to codeberg.org
Package: anndataR
Commit: a95ccf9a976ecc08f56ae50b5b918fba35f6ff10
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-10-16 10:51:29 +0200
Commit message:

 Address Bioconductor check issues (#371)

* Combine opts_chunks$set() on usage_python vignette

* Replace dontrun with donttest in man pages

* Fix format in AbstractAnnData-s3methods example

* Fix typo in example format

* Remove example from internal as_HDF5AnnData docs

* Update NEWS

* Bump devel version
Package: stPipe
Commit: c0b834c7e1106937ced402efe4d770119ae0cdae
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-10-16 18:23:29 +1100
Commit message:

 Remove exclude-lib in Makevars, update version.
Package: stPipe
Commit: bc4088b7a54f90e6b73ae38bdb1efea086272b0a
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-10-16 18:22:34 +1100
Commit message:

 Remove exclude-lib in Makevars
Package: MSstats
Commit: f3ab58f73f50f2416791b1e2f1b49d27afff2185
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2025-10-16 09:07:39 +0200
Commit message:

 version bump
Package: MSstats
Commit: ef3c81a3a11c562470d62240132c60da094f77fc
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2025-10-15 13:04:53 -0400
Commit message:

 Update NEWS.rd for version 4.18.0 release

Added new features and updates for version 4.18.0, including MSstats+ functionalities and updates to dataProcess and groupComparison functions.
Package: MSstats
Commit: 64058e37420316dfa62ce6db7fd752d1d4cd7326
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-09-30 09:48:54 -0400
Commit message:

 fix(dataProcessPlots, groupComparisonPlots): Migrate away from deprecated functions for ggplot (#175)
Package: MSstats
Commit: d71faa385bdc15d14460761ec8fa175ad394abcc
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2025-09-19 09:36:19 -0400
Commit message:

 Change license from MIT to Artistic License 2.0
Package: MSstats
Commit: f502591493eb693d5887ac5ea2364d0bb79d18a9
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2025-09-18 10:07:45 -0400
Commit message:

 Add MIT License to the project
Package: MSstats
Commit: fea8488ec232c32a166420edbf24f309645016fc
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2025-09-10 15:27:16 -0400
Commit message:

 Merge pull request #174 from Vitek-Lab/feature-model_weights

Feature model weights
Package: MSstats
Commit: 5b972e7529330cbd0394168c2b22a8a5c2d55426
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-09-10 15:26:26 -0400
Commit message:

 minor text edits to msstatsplus vignette
Package: MSstats
Commit: beecaaec8db429b8b00e396b3c3c437633e85d0d
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-09-09 12:59:57 -0400
Commit message:

 merge with changes in devel
Package: MSstats
Commit: dcdfd780a1c40430f83831ba0ba0042ff35ae116
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2025-09-09 15:39:32 +0200
Commit message:

 Merge pull request #173 from Vitek-Lab/tony-feature-model_weights

test(anomaly_scores): Add unit tests for dataProcess and groupComparison for anomaly score feature
Package: MSstats
Commit: 8479d2876832845237b542c7c3963a0811bbd254
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2025-09-09 15:38:03 +0200
Commit message:

 Merge pull request #169 from Vitek-Lab/feature-DataProcess_defaults

changed default to topN with 100 features
Package: MSstats
Commit: c1403628766ed6787880e3baaa6a94ee8f1fc540
Author: Tony Wu <wu.anthon@northeastern.edu>
Date: 2025-09-08 11:58:30 -0400
Commit message:

 Add more granular unit tests for data summarization subfunctions
Package: MSstats
Commit: c71c16c4aafedb8fef3f2b8fd57b3567cb53cc54
Author: Tony Wu <wu.anthon@northeastern.edu>
Date: 2025-09-05 15:57:32 -0400
Commit message:

 add defaults for aft_iterations parameter to prevent Shiny from breaking
Package: MSstats
Commit: 3a184ca590eed5bbd4fb27dd4391c200227697f3
Author: Tony Wu <wu.anthon@northeastern.edu>
Date: 2025-08-26 16:58:44 -0400
Commit message:

 test(anomaly_scores): Add unit tests for dataProcess and groupComparison for anomaly score feature
Package: MSstats
Commit: b42eaffcfe330bca9c39d3f91eb8a15a8fc76a67
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-08-26 15:07:05 -0400
Commit message:

 style(countMissingPercentage): Fix styling of arrows to equal signs (#172)
Package: MSstats
Commit: 8c137efe4630c459b4f9b5d9472f4ad41b736e4a
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-08-26 14:26:01 -0400
Commit message:

 fix(groupcomparison): Fix .countMissingPercentage for custom contrast matrices (#171)
Package: MSstats
Commit: e019a9a3c5cff10935ca546f649773fd69190628
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-08-05 08:59:53 -0400
Commit message:

 MSstatsBig example
Package: MSstats
Commit: 7ffce0f98beaeb7886b335c431b703c9d32d917c
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-07-28 09:47:39 -0400
Commit message:

 changed default to topN with 100 features
Package: MSstats
Commit: f7a957b66c45d021e7946ae61385382edcfb2cb7
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-07-25 11:40:53 -0400
Commit message:

 documentation bugs
Package: MSstats
Commit: be2a8d6c2b821e0d3fc2ce0b88f0f82e828edc32
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-07-25 11:40:16 -0400
Commit message:

 added manual converter example
Package: MSstats
Commit: aa3f5b0170d69bacf9e1fe76ea525f2fbc77704a
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-07-16 12:23:53 -0400
Commit message:

 MSstats+ vignette
Package: MSstats
Commit: 5aff1097827989a376a2825bdda2e8f48e98714e
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-07-15 09:12:35 -0400
Commit message:

 bug fix
Package: MSstats
Commit: 323a9bc6e00bd8a726115eb1d9dc3cf7ca0509f6
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-07-09 10:55:27 -0400
Commit message:

 lm model
Package: MSstats
Commit: 2978d1824eb86ebc96c03b235fe098d479d12ec6
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-07-09 10:54:35 -0400
Commit message:

 minor bug fixes
Package: MSstats
Commit: 8ee6fd58c671228b4395e0c7ad5bbddb71c689aa
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-05-13 08:42:19 -0400
Commit message:

 testing remove pca
Package: MSstats
Commit: e14d87196ecff73e5450b9a93a748bd37857d4ad
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-05-12 22:21:39 -0400
Commit message:

 bug fix
Package: MSstats
Commit: 1b3c60f0008cb599a0e6caa5b3f04a563504f793
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-05-09 10:34:00 -0400
Commit message:

 Merge branch 'feature-model_weights' of https://github.com/Vitek-Lab/MSstats into feature-model_weights
Package: MSstats
Commit: 4655736c4fa982a22d70bb55fe8481566ab79911
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-05-09 10:33:28 -0400
Commit message:

 anomaly score to column validator
Package: MSstats
Commit: 56dd6208ff391d843133970fd5c40fee851a8b6f
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-05-09 10:23:39 -0400
Commit message:

 imputation convergence bug
Package: MSstats
Commit: bb7ca0158826fc995fde59ce67e8decb2e52cdd5
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-04-29 17:47:25 -0400
Commit message:

 fixed anomaly bug
Package: MSstats
Commit: 1574fd93fbdb4b38e224b564e55fa1389d7da479
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-04-15 12:23:30 -0400
Commit message:

 anomaly scores into summaraization and model
Package: MSstats
Commit: 89c031ed2dacde6ff07d334c7146e5a035397f78
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-04-13 14:42:36 -0400
Commit message:

 anomaly weighted summarization
Package: MSstats
Commit: c0a8ac64cb3f1c5584e75a1137c091a02dd163e5
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-04-13 10:59:43 -0400
Commit message:

 adding anomaly scores to dataProcess
Package: MSstats
Commit: 35747e92db3277d245ee744503c2a6ecb81c5f9b
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2025-04-04 08:53:35 -0400
Commit message:

 added weights to groupComparison
Package: MAST
Commit: dc79813cf3cb0ff9116a90a5b1ce799c2ac47454
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2025-10-16 00:05:31 -0700
Commit message:

 bump version and update Authors@R
Package: miRspongeR
Commit: 5928b35f6b3517cc35c6e8b39abee57b18c1570e
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2025-10-16 12:30:26 +0800
Commit message:

 UPDATE
Package: miRspongeR
Commit: edd558bdb2f818e10a74107f2882e3527c8d4597
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2025-06-19 11:30:12 +0800
Commit message:

 Update
Package: gVenn
Commit: 50318aa884d853b54a716c51d1e09581fb4fbdb7
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-15 23:57:54 -0400
Commit message:

 feat: add color customization to plotUpSet()
Package: CBN2Path
Commit: ebd971d0b14fe6a4d923f7c38d8efc0f6d953f7c
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2025-10-15 22:41:46 -0500
Commit message:

 bump
Package: CBN2Path
Commit: 0f39a8c7a9cb0174db2ef684b038071741e2f733
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2025-10-15 22:41:00 -0500
Commit message:

 faster example cases
Package: CBN2Path
Commit: 6e01abdbd3653f4d18c37eb7080702d6bc1fea2d
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2025-10-15 21:00:56 -0500
Commit message:

 fix issue with doc
Package: CBN2Path
Commit: 71b4f21fc0d97cd7b538aad8068e1e39b4120168
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2025-10-15 20:56:22 -0500
Commit message:

 just bump
Package: CBN2Path
Commit: a80d286bd181514ac50b94f11c4e1c3fe339429c
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2025-10-15 20:46:47 -0500
Commit message:

 trying to fix issues
Package: CBN2Path
Commit: b47efd3ee1bb00b9a1e305513454f10febff4856
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2025-10-15 20:36:26 -0500
Commit message:

 still trying to reduce example times and small fix to imports
Package: CAGEr
Commit: 679bef9fe755f3ac305674b5c97f4d17bda02ff9
Author: Charles Plessy <charles.plessy@oist.jp>
Date: 2025-10-14 18:35:27 +0900
Commit message:

 Merge pull request #136 from charles-plessy/prepare_2.16.0

Prepare the 2.16.0 release.
Package: CAGEr
Commit: 569c9c7efcb81234b0d7c517f1b1b52f1d8248c5
Author: Charles Plessy <charles.plessy@oist.jp>
Date: 2025-10-14 09:28:53 +0900
Commit message:

 Better document where the alpha value is saved.
Package: CAGEr
Commit: af9fca14ca0a94b28f5877f926a3f939b41b83d8
Author: Charles Plessy <charles.plessy@oist.jp>
Date: 2025-10-14 09:28:18 +0900
Commit message:

 Add Katalin to the contributors