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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: matter
Commit: 4d78daa384ee824200f297ed3035668a78c4da3e
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-26 22:23:18 -0400
Commit message:
Commit: 4d78daa384ee824200f297ed3035668a78c4da3e
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-26 22:23:18 -0400
Commit message:
v2.5.22 fix y-flipped images on non-macOS
Package: matter
Commit: 112256b1303cf113914ed5ff2ae8cd262fe5f88b
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-26 21:00:02 -0400
Commit message:
Commit: 112256b1303cf113914ed5ff2ae8cd262fe5f88b
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-26 21:00:02 -0400
Commit message:
v2.5.21
Package: matter
Commit: fd417593567e4397a1def5aa37f7f843e5ae4850
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-26 20:47:51 -0400
Commit message:
Commit: fd417593567e4397a1def5aa37f7f843e5ae4850
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-26 20:47:51 -0400
Commit message:
add rasterImages+rasterParams to plot_image()
Package: matter
Commit: e3f1198f2fc75d44da052ee82ddf126be8c6d199
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-26 17:39:48 -0400
Commit message:
Commit: e3f1198f2fc75d44da052ee82ddf126be8c6d199
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-26 17:39:48 -0400
Commit message:
add vizi_image; safely pass ... to plot_init()
Package: SFEData
Commit: 04867eed2989aac99cf9b514d6cd3a3e08b1ddca
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2024-04-26 16:26:26 -0700
Commit message:
Commit: 04867eed2989aac99cf9b514d6cd3a3e08b1ddca
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2024-04-26 16:26:26 -0700
Commit message:
Temporarily host data on Box
Package: SFEData
Commit: 321fd2eddac2993c45f221006d52d7082e54a815
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2024-04-26 15:54:37 -0700
Commit message:
Commit: 321fd2eddac2993c45f221006d52d7082e54a815
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2024-04-26 15:54:37 -0700
Commit message:
Added one more Seurat test dataset
Package: RBioFormats
Commit: b39291dd9623cb98cf8b6e315af5dda206d9e5e2
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-04-27 00:30:09 +0200
Commit message:
Commit: b39291dd9623cb98cf8b6e315af5dda206d9e5e2
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-04-27 00:30:09 +0200
Commit message:
Update to BioFormats 7.3.0
Package: RBioFormats
Commit: 1f36684a1d5ef764978545542033cf46b66f95c0
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-04-27 00:16:24 +0200
Commit message:
Commit: 1f36684a1d5ef764978545542033cf46b66f95c0
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-04-27 00:16:24 +0200
Commit message:
Update to BioFormats 7.2.0
Package: RBioFormats
Commit: 6f318f404d4f19d4593c01ecebed64abdbe636ea
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-04-27 00:12:43 +0200
Commit message:
Commit: 6f318f404d4f19d4593c01ecebed64abdbe636ea
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-04-27 00:12:43 +0200
Commit message:
Update to BioFormats 7.1.0
Package: RBioFormats
Commit: 48def1b78e025becc5745e7de1026b456efcea31
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-04-26 23:58:12 +0200
Commit message:
Commit: 48def1b78e025becc5745e7de1026b456efcea31
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-04-26 23:58:12 +0200
Commit message:
Update to BioFormats 7.0.1
Package: GenomicDistributions
Commit: d9c719385b60ce819dd30e4ab6b84d7c10815e24
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2024-04-26 17:51:28 -0400
Commit message:
Commit: d9c719385b60ce819dd30e4ab6b84d7c10815e24
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2024-04-26 17:51:28 -0400
Commit message:
update imports
Package: OUTRIDER
Commit: edd760b0656f6ac1828bd383f6c1ac2ec545ad5a
Author: Christian Mertes <mertes@in.tum.de>
Date: 2024-04-26 23:51:56 +0200
Commit message:
Commit: edd760b0656f6ac1828bd383f6c1ac2ec545ad5a
Author: Christian Mertes <mertes@in.tum.de>
Date: 2024-04-26 23:51:56 +0200
Commit message:
update version to new BioC RELEASE_3_20
Package: RBioFormats
Commit: 47a865f54f6846e9ca5da527359728fe0ba2b964
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-04-26 23:50:34 +0200
Commit message:
Commit: 47a865f54f6846e9ca5da527359728fe0ba2b964
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-04-26 23:50:34 +0200
Commit message:
Update to BioFormats 7.0.0
Package: OUTRIDER
Commit: e8d8a62c170bf55b5d24207a791ce9c9b1c578a7
Author: Christian Mertes <mertes@in.tum.de>
Date: 2024-04-26 22:18:44 +0200
Commit message:
Commit: e8d8a62c170bf55b5d24207a791ce9c9b1c578a7
Author: Christian Mertes <mertes@in.tum.de>
Date: 2024-04-26 22:18:44 +0200
Commit message:
Preparing new BioC RELEASE_3_20 This is a merge of branch 'master' into 'bioc_devel'
Package: OUTRIDER
Commit: dc995884b0fb75f9947ae8cda8c6e81285152d72
Author: Christian Mertes <mertes@in.tum.de>
Date: 2024-04-25 14:08:59 +0200
Commit message:
Commit: dc995884b0fb75f9947ae8cda8c6e81285152d72
Author: Christian Mertes <mertes@in.tum.de>
Date: 2024-04-25 14:08:59 +0200
Commit message:
Version Bump for Bioconductor 3.18 (#65) * bump x.y.z version to even y prior to creation of RELEASE_3_17 branch * bump x.y.z version to odd y following creation of RELEASE_3_17 branch * bump x.y.z version to even y prior to creation of RELEASE_3_18 branch * Bump version and NEWS file --------- Co-authored-by: J Wokaty <jwokaty@users.noreply.github.com> Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Package: OUTRIDER
Commit: 63ae890631e8bbe96bd5d0c4fbf6242b012ccc39
Author: AtaJadidAhari <atajadidahari@gmail.com>
Date: 2024-04-25 14:08:25 +0200
Commit message:
Commit: 63ae890631e8bbe96bd5d0c4fbf6242b012ccc39
Author: AtaJadidAhari <atajadidahari@gmail.com>
Date: 2024-04-25 14:08:25 +0200
Commit message:
fix gha cache address (#66)
Package: OUTRIDER
Commit: b17d86d1d9acbef7d64b2be44046c8d5a10f5b63
Author: Ines Scheller <56256384+ischeller@users.noreply.github.com>
Date: 2024-04-24 09:28:46 +0200
Commit message:
Commit: b17d86d1d9acbef7d64b2be44046c8d5a10f5b63
Author: Ines Scheller <56256384+ischeller@users.noreply.github.com>
Date: 2024-04-24 09:28:46 +0200
Commit message:
Update gha and update documentation (#63) * adapt github actions to use new BIOC versions and use always variables * document arg and fix import warnings --------- Co-authored-by: Christian Mertes <mertes@in.tum.de>
Package: OUTRIDER
Commit: 71f52c856c885dc0226072886d75d314cea4139a
Author: AtaJadidAhari <atajadidahari@gmail.com>
Date: 2024-04-15 16:25:57 +0200
Commit message:
Commit: 71f52c856c885dc0226072886d75d314cea4139a
Author: AtaJadidAhari <atajadidahari@gmail.com>
Date: 2024-04-15 16:25:57 +0200
Commit message:
Update check-bioc version (#62) * fix bioc-version * check-bioc version --------- Co-authored-by: Ata Jadid Ahari <ata.ahari@tum.de>
Package: OUTRIDER
Commit: 72066edca72de41e8a73aea309edcd6d8cdf83ed
Author: Vicente Yepez <30469316+vyepez88@users.noreply.github.com>
Date: 2024-04-09 15:47:20 +0200
Commit message:
Commit: 72066edca72de41e8a73aea309edcd6d8cdf83ed
Author: Vicente Yepez <30469316+vyepez88@users.noreply.github.com>
Date: 2024-04-09 15:47:20 +0200
Commit message:
Merge branch 'plot_fdr_results' into master
Package: OUTRIDER
Commit: c74d7243d4c98faf54dd103821f558957acf47a8
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-06-20 14:23:55 +0200
Commit message:
Commit: c74d7243d4c98faf54dd103821f558957acf47a8
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-06-20 14:23:55 +0200
Commit message:
small fix in manhattanPlot to highlight only the exact aberrant genes
Package: OUTRIDER
Commit: 067853af44effc99897a98bd3221baf7ea612e92
Author: Felix Brechtmann <37140213+brechtmann@users.noreply.github.com>
Date: 2023-05-10 13:47:23 +0200
Commit message:
Commit: 067853af44effc99897a98bd3221baf7ea612e92
Author: Felix Brechtmann <37140213+brechtmann@users.noreply.github.com>
Date: 2023-05-10 13:47:23 +0200
Commit message:
Update inputCheckerFunctions.R
Package: OUTRIDER
Commit: 0e33db91ca695d5df5521ebc5c3bff1afc034854
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-04-12 18:23:26 +0200
Commit message:
Commit: 0e33db91ca695d5df5521ebc5c3bff1afc034854
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-04-12 18:23:26 +0200
Commit message:
cleanup of labels in plots
Package: OUTRIDER
Commit: 4157afbdfefa370af01f0484d4c6edafe5fce330
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-04-12 15:14:41 +0200
Commit message:
Commit: 4157afbdfefa370af01f0484d4c6edafe5fce330
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-04-12 15:14:41 +0200
Commit message:
color aberrant status based on FDR subset results
Package: OUTRIDER
Commit: d41facdd5490df9591945315b2f2e40ef7caa38b
Author: Ines Scheller <56256384+ischeller@users.noreply.github.com>
Date: 2023-03-30 17:20:07 +0200
Commit message:
Commit: d41facdd5490df9591945315b2f2e40ef7caa38b
Author: Ines Scheller <56256384+ischeller@users.noreply.github.com>
Date: 2023-03-30 17:20:07 +0200
Commit message:
update version number
Package: OUTRIDER
Commit: dfe85ebe833f1039c9dd8bfae5e0f61c1765dd52
Author: Felix Brechtmann <37140213+brechtmann@users.noreply.github.com>
Date: 2023-03-30 16:15:30 +0200
Commit message:
Commit: dfe85ebe833f1039c9dd8bfae5e0f61c1765dd52
Author: Felix Brechtmann <37140213+brechtmann@users.noreply.github.com>
Date: 2023-03-30 16:15:30 +0200
Commit message:
Merge pull request #55 from gagneurlab/plot_function_update Plot function update
Package: OUTRIDER
Commit: bc16e60e1851ba7f949f226886dd99fc13dd2f6e
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-03-10 18:01:33 +0100
Commit message:
Commit: bc16e60e1851ba7f949f226886dd99fc13dd2f6e
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-03-10 18:01:33 +0100
Commit message:
fix manhattan plot for subset of chromosomes
Package: OUTRIDER
Commit: 2acf4d812a1b8622252edc402b614adb82fc726d
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-02-14 18:19:14 +0100
Commit message:
Commit: 2acf4d812a1b8622252edc402b614adb82fc726d
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-02-14 18:19:14 +0100
Commit message:
minor fix
Package: OUTRIDER
Commit: 3acdfd9fb96e12be114f39f9b3e0340dd9488bb4
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-02-14 17:28:29 +0100
Commit message:
Commit: 3acdfd9fb96e12be114f39f9b3e0340dd9488bb4
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-02-14 17:28:29 +0100
Commit message:
report FDR subset padj as separate col instead of row
Package: OUTRIDER
Commit: 45b6e8d29ec9b13caf7ad5d65d89920eb9657269
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-02-01 14:18:35 +0100
Commit message:
Commit: 45b6e8d29ec9b13caf7ad5d65d89920eb9657269
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-02-01 14:18:35 +0100
Commit message:
test new argument in plotting tests
Package: OUTRIDER
Commit: a9f197a5e652779ea8ad1bb10bee6dc6f236053f
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-02-01 13:35:55 +0100
Commit message:
Commit: a9f197a5e652779ea8ad1bb10bee6dc6f236053f
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-02-01 13:35:55 +0100
Commit message:
fix typo
Package: OUTRIDER
Commit: f7a731c98aad77a74a1fe0d469728eea951fa858
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-02-01 12:01:21 +0100
Commit message:
Commit: f7a731c98aad77a74a1fe0d469728eea951fa858
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-02-01 12:01:21 +0100
Commit message:
add test for new plot function
Package: OUTRIDER
Commit: d679d42a55290ccc7783186f669d46bba693c14f
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-01-31 14:49:24 +0100
Commit message:
Commit: d679d42a55290ccc7783186f669d46bba693c14f
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-01-31 14:49:24 +0100
Commit message:
update doc and imports for manhattan plot function
Package: OUTRIDER
Commit: 0d4a3f796e4a0570510525a3473c428fb7d6723b
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-01-31 13:36:42 +0100
Commit message:
Commit: 0d4a3f796e4a0570510525a3473c428fb7d6723b
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-01-31 13:36:42 +0100
Commit message:
add ggrepel package to imports
Package: OUTRIDER
Commit: c15c11b22b290ce4bfeb1d3837f61cb967ef1c90
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-01-31 13:05:37 +0100
Commit message:
Commit: c15c11b22b290ce4bfeb1d3837f61cb967ef1c90
Author: Ines Scheller <scheller@in.tum.de>
Date: 2023-01-31 13:05:37 +0100
Commit message:
add support of labelling genes/samples in plots, plus new manhattan plot function
Package: OUTRIDER
Commit: 5c6815a0b3c1506577aa2fa161c0cff12aa426b7
Author: Christian Mertes <mertes@in.tum.de>
Date: 2023-01-10 16:23:38 +0100
Commit message:
Commit: 5c6815a0b3c1506577aa2fa161c0cff12aa426b7
Author: Christian Mertes <mertes@in.tum.de>
Date: 2023-01-10 16:23:38 +0100
Commit message:
explain columns for results function in detail (#52) Closes #35 * explain columns for results function in detail fixes #35 * updating doc for p and z score computation * fix result column order * Added results documnetation to vignette * Removed code links * Update OUTRIDER.Rnw * log2 formatting * removed underscores Co-authored-by: Felix Brechtmann <37140213+brechtmann@users.noreply.github.com>
Package: OUTRIDER
Commit: 6140e72b2a00feb2bb13f4aa6dd63c61c4952a1c
Author: Christian Mertes <mertes@in.tum.de>
Date: 2023-01-08 23:08:19 +0100
Commit message:
Commit: 6140e72b2a00feb2bb13f4aa6dd63c61c4952a1c
Author: Christian Mertes <mertes@in.tum.de>
Date: 2023-01-08 23:08:19 +0100
Commit message:
add bpmapply to NAMESPACE
Package: RBioFormats
Commit: 4e78b8f6b91239d24cb20b05294332fd7373ba5e
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-04-26 23:22:41 +0200
Commit message:
Commit: 4e78b8f6b91239d24cb20b05294332fd7373ba5e
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-04-26 23:22:41 +0200
Commit message:
Update to BioFormats 6.14.0
Package: RBioFormats
Commit: 1d9274a631eefb01eeb09fcfc3f8a6f2fb46cccf
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-04-26 23:17:51 +0200
Commit message:
Commit: 1d9274a631eefb01eeb09fcfc3f8a6f2fb46cccf
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-04-26 23:17:51 +0200
Commit message:
Update to BioFormats 6.13.0
Package: MSstatsConvert
Commit: 7049452310a7c72115fde83d36fba14aca580d61
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2024-04-26 23:14:41 +0200
Commit message:
Commit: 7049452310a7c72115fde83d36fba14aca580d61
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2024-04-26 23:14:41 +0200
Commit message:
conflict fix
Package: MSstatsConvert
Commit: e5489bd253287e14f7749eb3520e3e2fc4660a50
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2024-04-26 23:13:38 +0200
Commit message:
Commit: e5489bd253287e14f7749eb3520e3e2fc4660a50
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2024-04-26 23:13:38 +0200
Commit message:
conflict fix
Package: MSstatsConvert
Commit: ace2b77447d9e15f1d249e8d80d41f7169342255
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2024-04-26 23:09:25 +0200
Commit message:
Commit: ace2b77447d9e15f1d249e8d80d41f7169342255
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2024-04-26 23:09:25 +0200
Commit message:
conflict fix
Package: MSstatsConvert
Commit: 4ce4061020de5cf187cd0bc54b829690fbf85a8f
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2024-04-26 23:08:41 +0200
Commit message:
Commit: 4ce4061020de5cf187cd0bc54b829690fbf85a8f
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2024-04-26 23:08:41 +0200
Commit message:
conflict fix
Package: MSstatsConvert
Commit: 584b78b7e9c0843acef1af6fb4c674714d7340aa
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2024-04-26 23:06:33 +0200
Commit message:
Commit: 584b78b7e9c0843acef1af6fb4c674714d7340aa
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2024-04-26 23:06:33 +0200
Commit message:
conflict resolved
Package: MSstatsConvert
Commit: aca951e22891075019e3d8ebf64b3f5833eef6a1
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-04-17 10:45:37 -0400
Commit message:
Commit: aca951e22891075019e3d8ebf64b3f5833eef6a1
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-04-17 10:45:37 -0400
Commit message:
version bump
Package: MSstatsConvert
Commit: 4752b7508fd0222d91126758a56461608f07c4ae
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-04-17 10:44:56 -0400
Commit message:
Commit: 4752b7508fd0222d91126758a56461608f07c4ae
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-04-17 10:44:56 -0400
Commit message:
fix(diann-converter): Allow for quantification column to be determined by client (#92)
Package: MSstatsConvert
Commit: 867115b68adee2ca78f4f84c140dfbb865875c3d
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-04-09 12:28:09 -0400
Commit message:
Commit: 867115b68adee2ca78f4f84c140dfbb865875c3d
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-04-09 12:28:09 -0400
Commit message:
version bump
Package: MSstatsConvert
Commit: 6bae8482acbeb614a2cd8899b0a43143187b80ca
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-04-09 12:27:33 -0400
Commit message:
Commit: 6bae8482acbeb614a2cd8899b0a43143187b80ca
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-04-09 12:27:33 -0400
Commit message:
refactor(converter): Migrate core MSstats converter functions into MSstatsConvert (#91) * refactor(converter): Migrate core MSstats converter classes into MSstatsConvert * Add annotation files to MSstatsConvert package for pd, os, diau
Package: MSstatsConvert
Commit: d8ca32a96e3cb1e79d9054a8aaf7eeac8a6e0412
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-03-19 14:09:08 -0400
Commit message:
Commit: d8ca32a96e3cb1e79d9054a8aaf7eeac8a6e0412
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-03-19 14:09:08 -0400
Commit message:
version bump
Package: MSstatsConvert
Commit: f5a5f6c28c87dbb039db2ac86252ca1a3c012b7f
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-03-19 14:08:37 -0400
Commit message:
Commit: f5a5f6c28c87dbb039db2ac86252ca1a3c012b7f
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-03-19 14:08:37 -0400
Commit message:
fix(skyline): Modified error message for Skyline outlining that MSstats only analyzes MS1 or MS2 but not both (#89) * fix(workflows): Modify workflows to perform dry run build upon PRs on devel branch * docs(pr-template): Modified PR template wording * fix(skyline): Modified error message for Skyline outlining that MSstats only analyzes MS1 or MS2 but not both
Package: MSstatsConvert
Commit: 21cb3161c524a1d6e5893edff140303351a88aa5
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-02-15 14:40:50 -0500
Commit message:
Commit: 21cb3161c524a1d6e5893edff140303351a88aa5
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-02-15 14:40:50 -0500
Commit message:
version bump
Package: MSstatsConvert
Commit: 13127c914a8739dbcb250329958785ef1ccefe6c
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-02-15 13:43:34 -0500
Commit message:
Commit: 13127c914a8739dbcb250329958785ef1ccefe6c
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-02-15 13:43:34 -0500
Commit message:
refactor(proteome-discoverer): Add validation for input columns (#87) * refactor(proteome-discoverer): Add validation for input columns * Allow PD to MSstatsTMT converter to handle both old and new column names for # Proteins and # Protein Groups
Package: MSstatsConvert
Commit: 462d3a514e5963ae4d1c323dd4412771e2562720
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-02-07 11:24:05 -0500
Commit message:
Commit: 462d3a514e5963ae4d1c323dd4412771e2562720
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-02-07 11:24:05 -0500
Commit message:
version bump
Package: MSstatsConvert
Commit: 62030e448c61d0b7daa82b021535b086268bdfff
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-02-07 11:23:11 -0500
Commit message:
Commit: 62030e448c61d0b7daa82b021535b086268bdfff
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-02-07 11:23:11 -0500
Commit message:
feat(metamorpheus): Create converter from Metamorpheus to core MSstats (#85)
Package: MSstatsConvert
Commit: 9e88fb5be5dec6a5b0689b280dfdecbbf4ac48c2
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-01-23 12:08:21 -0500
Commit message:
Commit: 9e88fb5be5dec6a5b0689b280dfdecbbf4ac48c2
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-01-23 12:08:21 -0500
Commit message:
version bump
Package: MSstatsConvert
Commit: 846d692b0d8d255d1fd1f77a9b4786927df67d94
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-01-23 12:07:36 -0500
Commit message:
Commit: 846d692b0d8d255d1fd1f77a9b4786927df67d94
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-01-23 12:07:36 -0500
Commit message:
docs(warnings): Remove warnings related to documentation (#86)
Package: MSstatsConvert
Commit: 2d7dd3e942854ee199fe16b82154ee5d86384a0b
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-01-17 10:19:49 -0500
Commit message:
Commit: 2d7dd3e942854ee199fe16b82154ee5d86384a0b
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-01-17 10:19:49 -0500
Commit message:
version bump
Package: MSstatsConvert
Commit: 94bdd783d6d43dc0a9d7adeb61b0fdafd8534a7b
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-01-17 10:19:08 -0500
Commit message:
Commit: 94bdd783d6d43dc0a9d7adeb61b0fdafd8534a7b
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-01-17 10:19:08 -0500
Commit message:
feat(metamorpheus-converter): Add clean functionality of metamorpheus converter (#83) * feat(metamorpheus-converter): Add clean functionality of metamorpheus converter * Modified metamorpheus annotation filename and removed techRep column from annotation file * Modify RDS filename to MSstatsMetamorpheusFilesObject for unit testing * create processed_data folder for testing
Package: MSstatsConvert
Commit: 71ca31c3aa2c4118c607e6d2c9fb4e7180cb4a71
Author: Tony Wu <ant.wu@northeastern.edu>
Date: 2024-01-16 15:58:29 -0500
Commit message:
Commit: 71ca31c3aa2c4118c607e6d2c9fb4e7180cb4a71
Author: Tony Wu <ant.wu@northeastern.edu>
Date: 2024-01-16 15:58:29 -0500
Commit message:
version bump
Package: MSstatsConvert
Commit: eb5a221fdab8ba821fd7000d78577e82c5e3f983
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-01-16 15:47:50 -0500
Commit message:
Commit: eb5a221fdab8ba821fd7000d78577e82c5e3f983
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-01-16 15:47:50 -0500
Commit message:
docs(pr-template): Add a pull request template (#84)
Package: MSstatsConvert
Commit: 3131312bcb07db8b018f55010b51b06191e56572
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2024-01-09 23:13:54 +0100
Commit message:
Commit: 3131312bcb07db8b018f55010b51b06191e56572
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2024-01-09 23:13:54 +0100
Commit message:
version bump
Package: MSstatsConvert
Commit: 522613828f8a91b2794bf3e2fb0afe4042f73fe5
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2024-01-09 17:13:19 -0500
Commit message:
Commit: 522613828f8a91b2794bf3e2fb0afe4042f73fe5
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2024-01-09 17:13:19 -0500
Commit message:
feat(metamorpheus): Set up MSstatsMetamorpheusFiles class for metamorpheus (#81) * feat(metamorpheus): Set up MSstatsMetamorpheusFiles class for metamorpheus converter * update input data file to be from metamorpheus vignette * Modify input metamorpheus file to have more proteins and bioreplicates
Package: MSstatsConvert
Commit: 780ffb749ec95488647133ae20cff970453f870a
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2024-01-09 17:11:14 -0500
Commit message:
Commit: 780ffb749ec95488647133ae20cff970453f870a
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2024-01-09 17:11:14 -0500
Commit message:
refactor(github-actions): Add github actions workflow to perform dry run build upon pull request (#82) * refactor(github-actions): Add github actions workflow to perform dry run build upon pull request * change bioc-version to release * Checking out repo prior to running build * install dependencies in actions * remove bad test * switch to version 4 for checkout * version bump --------- Co-authored-by: Mateusz Staniak <mtst@mstaniak.pl>
Package: gemma.R
Commit: 01133031414a89ff622d839826274332c1ac7fe5
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-26 14:11:59 -0700
Commit message:
Commit: 01133031414a89ff622d839826274332c1ac7fe5
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-26 14:11:59 -0700
Commit message:
status 500 fix
Package: MSstats
Commit: db8297ee13e0f0dfa730404e202444753b55c0be
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2024-04-26 16:58:55 -0400
Commit message:
Commit: db8297ee13e0f0dfa730404e202444753b55c0be
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2024-04-26 16:58:55 -0400
Commit message:
Merge pull request #121 from Vitek-Lab/fix-design-sample-plotly plotly for design sample
Package: MSstats
Commit: 959715cce4ac5c6eefe30e08d234f91313875fd7
Author: deril2605 <derilraju@gmail.com>
Date: 2024-04-26 14:07:00 -0400
Commit message:
Commit: 959715cce4ac5c6eefe30e08d234f91313875fd7
Author: deril2605 <derilraju@gmail.com>
Date: 2024-04-26 14:07:00 -0400
Commit message:
fix layout
Package: MSstats
Commit: 1393c7900cb7008f62e5289286b5ea4591c348aa
Author: deril2605 <derilraju@gmail.com>
Date: 2024-04-26 13:58:26 -0400
Commit message:
Commit: 1393c7900cb7008f62e5289286b5ea4591c348aa
Author: deril2605 <derilraju@gmail.com>
Date: 2024-04-26 13:58:26 -0400
Commit message:
fix plotly layout conflicts
Package: MSstats
Commit: 123af6e8752c22949bf51e9b5b85ef5d656800eb
Author: deril2605 <derilraju@gmail.com>
Date: 2024-04-24 21:35:02 -0400
Commit message:
Commit: 123af6e8752c22949bf51e9b5b85ef5d656800eb
Author: deril2605 <derilraju@gmail.com>
Date: 2024-04-24 21:35:02 -0400
Commit message:
fixes
Package: MSstats
Commit: 186407e3134e367c0a80b44cb310f0a2f7b4e239
Author: deril2605 <derilraju@gmail.com>
Date: 2024-04-24 21:33:22 -0400
Commit message:
Commit: 186407e3134e367c0a80b44cb310f0a2f7b4e239
Author: deril2605 <derilraju@gmail.com>
Date: 2024-04-24 21:33:22 -0400
Commit message:
remove warnings and fix pipes
Package: MSstats
Commit: 7862798bc63b0b775a3adac130139a9fa776a41e
Author: deril2605 <derilraju@gmail.com>
Date: 2024-04-18 20:48:52 -0400
Commit message:
Commit: 7862798bc63b0b775a3adac130139a9fa776a41e
Author: deril2605 <derilraju@gmail.com>
Date: 2024-04-18 20:48:52 -0400
Commit message:
plotly for design sample
Package: rtracklayer
Commit: ead4d7441abfb7bcd3b536ad7c83384beeb79b2e
Author: Michael Lawrence <michafla@gene.com>
Date: 2024-04-26 13:12:00 -0700
Commit message:
Commit: ead4d7441abfb7bcd3b536ad7c83384beeb79b2e
Author: Michael Lawrence <michafla@gene.com>
Date: 2024-04-26 13:12:00 -0700
Commit message:
Merge pull request #115 from sanchit-saini/arm_fix Apply patch to fix compilation issue on ARM submitted by @kalibera
Package: rtracklayer
Commit: 339dbdea7605a27ca1bcbe26f0cacd353dd1f71a
Author: Sanchit Saini <sanchitsaini14@gmail.com>
Date: 2024-03-22 20:59:58 +0530
Commit message:
Commit: 339dbdea7605a27ca1bcbe26f0cacd353dd1f71a
Author: Sanchit Saini <sanchitsaini14@gmail.com>
Date: 2024-03-22 20:59:58 +0530
Commit message:
Apply patch to fix compilation issue on ARM submitted by @kalibera
Package: gINTomics
Commit: 664ba56bc38ccc4f21e9efb8264a295d382ad169
Author: angeve96 <angeve89@gmail.com>
Date: 2024-04-26 20:43:14 +0200
Commit message:
Commit: 664ba56bc38ccc4f21e9efb8264a295d382ad169
Author: angeve96 <angeve89@gmail.com>
Date: 2024-04-26 20:43:14 +0200
Commit message:
minor
Package: gINTomics
Commit: ba9f5126aa4601d5d0e3233739b6e4292e676db0
Author: angeve96 <angeve89@gmail.com>
Date: 2024-04-26 20:42:54 +0200
Commit message:
Commit: ba9f5126aa4601d5d0e3233739b6e4292e676db0
Author: angeve96 <angeve89@gmail.com>
Date: 2024-04-26 20:42:54 +0200
Commit message:
version bump
Package: MSstatsPTM
Commit: bc427a626be80aa19c688d63016ccb19c8c1d0bc
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2024-04-26 14:43:22 -0400
Commit message:
Commit: bc427a626be80aa19c688d63016ccb19c8c1d0bc
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2024-04-26 14:43:22 -0400
Commit message:
version bump
Package: MSstatsPTM
Commit: 0c8c74dfc5dcfc7b54c7a80b4816d8367e2672ce
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2024-04-26 14:42:58 -0400
Commit message:
Commit: 0c8c74dfc5dcfc7b54c7a80b4816d8367e2672ce
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2024-04-26 14:42:58 -0400
Commit message:
swapped converter imports to msstatsconvert
Package: SomaScan.db
Commit: 7eac7312a74f75e3a28b4a10f79c24d16ffa6739
Author: Amanda Hiser <ahiser@somalogic.com>
Date: 2024-04-26 08:28:59 -0700
Commit message:
Commit: 7eac7312a74f75e3a28b4a10f79c24d16ffa6739
Author: Amanda Hiser <ahiser@somalogic.com>
Date: 2024-04-26 08:28:59 -0700
Commit message:
Update NEWS to describe new 11k content
Package: GSVA
Commit: d67be67932783749ffc94a6b3c2a00edae1cd6d6
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-04-26 18:29:39 +0200
Commit message:
Commit: d67be67932783749ffc94a6b3c2a00edae1cd6d6
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-04-26 18:29:39 +0200
Commit message:
Updated NEWS file, added a missing export
Package: GSVA
Commit: 75ae6fa34d47e2f71e82befa32bb3259cfdc6e26
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-04-26 17:35:56 +0200
Commit message:
Commit: 75ae6fa34d47e2f71e82befa32bb3259cfdc6e26
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-04-26 17:35:56 +0200
Commit message:
Merge pull request #164 from rcastelo/71-speed-up-ssgsea-and-reduce-memory-by-moving-fastrndwalk-to-c++ Optimization in R code of .fastRndWalk()
Package: GSVA
Commit: a48d5bdff8c528828ae1aa4ffefe372ac659c747
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-04-26 17:29:50 +0200
Commit message:
Commit: a48d5bdff8c528828ae1aa4ffefe372ac659c747
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-04-26 17:29:50 +0200
Commit message:
Optimization in R code after discussion in https://github.com/rcastelo/GSVA/issues/71
Package: HicAggR
Commit: b8e4452254ba4de972958e9e85f64e5ddf3b9e48
Author: RobTesf <rob.tesf@gmail.com>
Date: 2024-04-26 17:27:52 +0200
Commit message:
Commit: b8e4452254ba4de972958e9e85f64e5ddf3b9e48
Author: RobTesf <rob.tesf@gmail.com>
Date: 2024-04-26 17:27:52 +0200
Commit message:
version bump
Package: GSVA
Commit: aee5f6781151625d71b99ef7162379dcd15c87da
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-04-26 17:09:15 +0200
Commit message:
Commit: aee5f6781151625d71b99ef7162379dcd15c87da
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-04-26 17:09:15 +0200
Commit message:
Bugfix on a rare combination of GSVA parameters
Package: multiGSEA
Commit: fb6d8be9073eae7a36bc511c4f7a3c1ff2bbf7fa
Author: Sebastian Canzler <sebastian.canzler@ufz.de>
Date: 2024-04-26 16:26:57 +0200
Commit message:
Commit: fb6d8be9073eae7a36bc511c4f7a3c1ff2bbf7fa
Author: Sebastian Canzler <sebastian.canzler@ufz.de>
Date: 2024-04-26 16:26:57 +0200
Commit message:
Update NEWS file.
Package: AnVIL
Commit: 365d17dadf1d2be4ca306691be175e65ea9eeedd
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-26 10:10:07 -0400
Commit message:
Commit: 365d17dadf1d2be4ca306691be175e65ea9eeedd
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-26 10:10:07 -0400
Commit message:
version bump 1.15.13
Package: AnVIL
Commit: f4676fb4c00892f8f395e1a4f43b7de9cea7bc67
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-26 10:09:53 -0400
Commit message:
Commit: f4676fb4c00892f8f395e1a4f43b7de9cea7bc67
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-26 10:09:53 -0400
Commit message:
update NEWS file
Package: mia
Commit: 1b6f55b40e54fd2c043ba904c7f3a212a4d72906
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-04-26 17:07:24 +0300
Commit message:
Commit: 1b6f55b40e54fd2c043ba904c7f3a212a4d72906
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-04-26 17:07:24 +0300
Commit message:
Update manual pages (#537)
Package: mia
Commit: 47378e3968a1b4af96ffe886664c782227d2b134
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-04-26 17:04:30 +0300
Commit message:
Commit: 47378e3968a1b4af96ffe886664c782227d2b134
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-04-26 17:04:30 +0300
Commit message:
Add explanation for agglomerateByPrevalence (#509)
Package: mia
Commit: a537731c8da142ed5a0864af5caec52a03288cb4
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-04-25 10:16:05 +0300
Commit message:
Commit: a537731c8da142ed5a0864af5caec52a03288cb4
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-04-25 10:16:05 +0300
Commit message:
Rename estimateDivergence to addDivergence (#531) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Package: mia
Commit: 1adf43c1e8de53ef0185ec6dfe307fe545df7a74
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-04-24 18:21:36 +0300
Commit message:
Commit: 1adf43c1e8de53ef0185ec6dfe307fe545df7a74
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-04-24 18:21:36 +0300
Commit message:
deprecate plotNMDS (#517) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Package: HicAggR
Commit: e0fb221bd0206c4e88ad72f21cebaaece8a5a42a
Author: RobTesf <rob.tesf@gmail.com>
Date: 2024-04-26 15:12:52 +0200
Commit message:
Commit: e0fb221bd0206c4e88ad72f21cebaaece8a5a42a
Author: RobTesf <rob.tesf@gmail.com>
Date: 2024-04-26 15:12:52 +0200
Commit message:
BioFileCache as imported package: vignette building failing
Package: HicAggR
Commit: 001bc5b7bf663289ced7632eda7594d2879cd295
Author: RobTesf <rob.tesf@gmail.com>
Date: 2024-04-26 14:42:25 +0200
Commit message:
Commit: 001bc5b7bf663289ced7632eda7594d2879cd295
Author: RobTesf <rob.tesf@gmail.com>
Date: 2024-04-26 14:42:25 +0200
Commit message:
minor vignette 4
Package: HicAggR
Commit: 5caf91848b72bf9ee2265a0c21b4c5b9843dc8b3
Author: RobTesf <rob.tesf@gmail.com>
Date: 2024-04-26 14:41:26 +0200
Commit message:
Commit: 5caf91848b72bf9ee2265a0c21b4c5b9843dc8b3
Author: RobTesf <rob.tesf@gmail.com>
Date: 2024-04-26 14:41:26 +0200
Commit message:
minor bug corrections 3
Package: HicAggR
Commit: 97f85061bd03e0119dec3605e7b39d879cf3c385
Author: RobTesf <rob.tesf@gmail.com>
Date: 2024-04-26 11:12:20 +0200
Commit message:
Commit: 97f85061bd03e0119dec3605e7b39d879cf3c385
Author: RobTesf <rob.tesf@gmail.com>
Date: 2024-04-26 11:12:20 +0200
Commit message:
minor bugs 2
Package: HicAggR
Commit: a06522d97b6cba9139fe8a5f934a3ccca9fd88b2
Author: RobTesf <rob.tesf@gmail.com>
Date: 2024-04-26 10:26:45 +0200
Commit message:
Commit: a06522d97b6cba9139fe8a5f934a3ccca9fd88b2
Author: RobTesf <rob.tesf@gmail.com>
Date: 2024-04-26 10:26:45 +0200
Commit message:
to version 0.99.6 minor bugs
Package: HicAggR
Commit: 5fb867a4caa305b15068c2d0c98a14fa8cac735f
Author: RobTesf <rob.tesf@gmail.com>
Date: 2024-04-25 19:29:22 +0200
Commit message:
Commit: 5fb867a4caa305b15068c2d0c98a14fa8cac735f
Author: RobTesf <rob.tesf@gmail.com>
Date: 2024-04-25 19:29:22 +0200
Commit message:
to version 0.99.6
Package: RNAseq123
Commit: d4c672f4ded8616cd80bff2861baeced81b38bd8
Author: Matthew Ritchie <mritchie@wehi.edu.au>
Date: 2024-04-26 22:43:44 +1000
Commit message:
Commit: d4c672f4ded8616cd80bff2861baeced81b38bd8
Author: Matthew Ritchie <mritchie@wehi.edu.au>
Date: 2024-04-26 22:43:44 +1000
Commit message:
Add design matrix F1000Res publication to CITATION file
Package: limpca
Commit: 5a42813752ad2480bae2f3a7e22a5280152f33b9
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-04-26 14:09:57 +0200
Commit message:
Commit: 5a42813752ad2480bae2f3a7e22a5280152f33b9
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-04-26 14:09:57 +0200
Commit message:
adapted intro of vignettes
Package: msa
Commit: 5d2e1a8f5b92306c84103ea89f6992d59f9cee25
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-26 13:52:48 +0200
Commit message:
Commit: 5d2e1a8f5b92306c84103ea89f6992d59f9cee25
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-26 13:52:48 +0200
Commit message:
Update of help pages; version number bumped to 1.35.5
Package: Pirat
Commit: 20328da36f8d7f7efc7ede8d088fdb1dbbb99711
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-04-26 13:19:35 +0200
Commit message:
Commit: 20328da36f8d7f7efc7ede8d088fdb1dbbb99711
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-04-26 13:19:35 +0200
Commit message:
Fix some reviewer remarks
Package: limpca
Commit: 141cd517570ba0966dbc0f0cc6aa3fbcb82e813b
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-04-26 13:03:52 +0200
Commit message:
Commit: 141cd517570ba0966dbc0f0cc6aa3fbcb82e813b
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-04-26 13:03:52 +0200
Commit message:
adapted intro of vignettes
Package: qPLEXanalyzer
Commit: fab20cc1f8ff9e194d4dcfa35ddf4d2dd81024ed
Author: Ashley Sawle <ads2202cu@gmail.com>
Date: 2024-04-26 11:54:49 +0100
Commit message:
Commit: fab20cc1f8ff9e194d4dcfa35ddf4d2dd81024ed
Author: Ashley Sawle <ads2202cu@gmail.com>
Date: 2024-04-26 11:54:49 +0100
Commit message:
Update DESCRIPTION
Package: qPLEXanalyzer
Commit: 4d3a0bdb40cda927e46f574c3c7f876bcaa3c150
Author: Ashley Sawle <ads2202cu@gmail.com>
Date: 2024-04-26 11:35:13 +0100
Commit message:
Commit: 4d3a0bdb40cda927e46f574c3c7f876bcaa3c150
Author: Ashley Sawle <ads2202cu@gmail.com>
Date: 2024-04-26 11:35:13 +0100
Commit message:
Update NEWS and version bump
Package: qPLEXanalyzer
Commit: 340e4be4de566b1b4f5e7af96ba4e0e12f8763ee
Author: kamalfartiyal84 <kamal.fartiyal84@gmail.com>
Date: 2023-10-18 16:27:47 +0100
Commit message:
Commit: 340e4be4de566b1b4f5e7af96ba4e0e12f8763ee
Author: kamalfartiyal84 <kamal.fartiyal84@gmail.com>
Date: 2023-10-18 16:27:47 +0100
Commit message:
coefVar.R
Package: qPLEXanalyzer
Commit: 5bc331f16286f1c86d62bb8afaa3c9df526cc7c3
Author: kamalfartiyal84 <kamal.fartiyal84@gmail.com>
Date: 2023-10-18 14:29:03 +0100
Commit message:
Commit: 5bc331f16286f1c86d62bb8afaa3c9df526cc7c3
Author: kamalfartiyal84 <kamal.fartiyal84@gmail.com>
Date: 2023-10-18 14:29:03 +0100
Commit message:
qPLEXanalyzer-package
Package: qPLEXanalyzer
Commit: 719f4a787c47b30f8689a9cb533192ae8dd61cf7
Author: kamalfartiyal84 <kamal.fartiyal84@gmail.com>
Date: 2023-10-18 14:28:32 +0100
Commit message:
Commit: 719f4a787c47b30f8689a9cb533192ae8dd61cf7
Author: kamalfartiyal84 <kamal.fartiyal84@gmail.com>
Date: 2023-10-18 14:28:32 +0100
Commit message:
coefVar new function to compute coffiecient of variation
Package: tripr
Commit: 113732215e742f4ef83df5a74b931b91480903be
Author: KonstantinosKardamiliotis <k.kardamiliotis@gmail.com>
Date: 2024-04-26 13:18:32 +0300
Commit message:
Commit: 113732215e742f4ef83df5a74b931b91480903be
Author: KonstantinosKardamiliotis <k.kardamiliotis@gmail.com>
Date: 2024-04-26 13:18:32 +0300
Commit message:
Bioconductor_April_release_final_commit
Package: fenr
Commit: 4cfaf71a990efc31051fba3702ea89327eeb712f
Author: Marek Gierlinski <Marek.Gierlinski@gmail.com>
Date: 2024-04-26 10:47:47 +0100
Commit message:
Commit: 4cfaf71a990efc31051fba3702ea89327eeb712f
Author: Marek Gierlinski <Marek.Gierlinski@gmail.com>
Date: 2024-04-26 10:47:47 +0100
Commit message:
Quick patch - fixing a mixup in the vignette
Package: autonomics
Commit: 91dc187ff443ad1bc36e6c8625ce7d7b22660155
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-04-26 11:41:07 +0200
Commit message:
Commit: 91dc187ff443ad1bc36e6c8625ce7d7b22660155
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-04-26 11:41:07 +0200
Commit message:
1.11.110 : billing19 internalization, `Protein group IDs` colclass, obsolete functions
Package: fenr
Commit: 39d97805476bfb410df64e87f86f614e0f9c2c9c
Author: Marek Gierlinski <Marek.Gierlinski@gmail.com>
Date: 2024-04-26 10:37:48 +0100
Commit message:
Commit: 39d97805476bfb410df64e87f86f614e0f9c2c9c
Author: Marek Gierlinski <Marek.Gierlinski@gmail.com>
Date: 2024-04-26 10:37:48 +0100
Commit message:
Version 1.1.10
Package: epiregulon
Commit: af381a58f1365826dd9684e25adba10b906868f7
Author: TomVuod <tomwlo@gmail.com>
Date: 2024-04-26 02:06:46 -0700
Commit message:
Commit: af381a58f1365826dd9684e25adba10b906868f7
Author: TomVuod <tomwlo@gmail.com>
Date: 2024-04-26 02:06:46 -0700
Commit message:
v0.99.23
Package: epiregulon
Commit: 09f1c74ea90a7d456f1aa4bc38a5929be9a27b16
Author: TomVuod <tomwlo@gmail.com>
Date: 2024-04-26 00:48:13 -0700
Commit message:
Commit: 09f1c74ea90a7d456f1aa4bc38a5929be9a27b16
Author: TomVuod <tomwlo@gmail.com>
Date: 2024-04-26 00:48:13 -0700
Commit message:
Improve input validation and remove unnecessary code
Package: epiregulon
Commit: 6696298e3ac79e46be851e3ebcb8e838c8f6b77c
Author: TomVuod <tomwlo@gmail.com>
Date: 2024-04-25 11:46:04 -0700
Commit message:
Commit: 6696298e3ac79e46be851e3ebcb8e838c8f6b77c
Author: TomVuod <tomwlo@gmail.com>
Date: 2024-04-25 11:46:04 -0700
Commit message:
v0.99.22
Package: epiregulon
Commit: 40ad5127a6cc5e33ad6dbd80ba9dbc41d8dfb114
Author: TomVuod <tomwlo@gmail.com>
Date: 2024-04-25 07:38:00 -0700
Commit message:
Commit: 40ad5127a6cc5e33ad6dbd80ba9dbc41d8dfb114
Author: TomVuod <tomwlo@gmail.com>
Date: 2024-04-25 07:38:00 -0700
Commit message:
handle 1-dim arrays nested in DataFrame
Package: epiregulon
Commit: 03a244a5fc522ed9fbb407c736e057040f3121ce
Author: TomVuod <tomwlo@gmail.com>
Date: 2024-04-25 03:50:01 -0700
Commit message:
Commit: 03a244a5fc522ed9fbb407c736e057040f3121ce
Author: TomVuod <tomwlo@gmail.com>
Date: 2024-04-25 03:50:01 -0700
Commit message:
sanity check
Package: epiregulon
Commit: b3681ed0d7250f11181175250085fbe95e10d523
Author: TomVuod <tomwlo@gmail.com>
Date: 2024-04-25 03:49:38 -0700
Commit message:
Commit: b3681ed0d7250f11181175250085fbe95e10d523
Author: TomVuod <tomwlo@gmail.com>
Date: 2024-04-25 03:49:38 -0700
Commit message:
initialize objects after if statement
Package: tripr
Commit: ed7681aaef816abc2d2a94cabdc66561f0c80704
Author: KonstantinosKardamiliotis <k.kardamiliotis@gmail.com>
Date: 2024-04-26 12:07:12 +0300
Commit message:
Commit: ed7681aaef816abc2d2a94cabdc66561f0c80704
Author: KonstantinosKardamiliotis <k.kardamiliotis@gmail.com>
Date: 2024-04-26 12:07:12 +0300
Commit message:
Bioconductor April release commit
Package: ZygosityPredictor
Commit: 2e68a72bfd4044b704b38576c5478f37e8cbd77f
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-04-26 10:50:14 +0200
Commit message:
Commit: 2e68a72bfd4044b704b38576c5478f37e8cbd77f
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-04-26 10:50:14 +0200
Commit message:
included CITATION file
Package: MAGAR
Commit: 581fa366831bf4e171fb1436a733ea5e86db8abc
Author: Michael Scherer <s9mlscer@gmail.com>
Date: 2024-04-26 09:05:46 +0200
Commit message:
Commit: 581fa366831bf4e171fb1436a733ea5e86db8abc
Author: Michael Scherer <s9mlscer@gmail.com>
Date: 2024-04-26 09:05:46 +0200
Commit message:
Included RnBeads.hg38 as dependency
Package: gemma.R
Commit: e4fed2f3d2b76659625c753e150de0765a99502d
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-25 23:41:35 -0700
Commit message:
Commit: e4fed2f3d2b76659625c753e150de0765a99502d
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-25 23:41:35 -0700
Commit message:
version bump
Package: gemma.R
Commit: dc2abda6ba0a7f1b0103082e25324bcd26fa41d5
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-25 23:38:59 -0700
Commit message:
Commit: dc2abda6ba0a7f1b0103082e25324bcd26fa41d5
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-25 23:38:59 -0700
Commit message:
return zero rowed data.tables for empty outputs
Package: Pirat
Commit: de36aca85fe33ac0a6a3124241bec50d4a845f97
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-04-26 08:56:02 +0200
Commit message:
Commit: de36aca85fe33ac0a6a3124241bec50d4a845f97
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-04-26 08:56:02 +0200
Commit message:
Fix some reviewer remarks
Package: gemma.R
Commit: 4d964e4e526fcc7641c3f543bd4510dc58db8d6f
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-25 22:05:39 -0700
Commit message:
Commit: 4d964e4e526fcc7641c3f543bd4510dc58db8d6f
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-25 22:05:39 -0700
Commit message:
version bump
Package: gemma.R
Commit: 631bce8add01a8fcfa9c289d02428f2027ef938d
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-25 22:05:12 -0700
Commit message:
Commit: 631bce8add01a8fcfa9c289d02428f2027ef938d
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-25 22:05:12 -0700
Commit message:
get_child_terms fixed for the childless
Package: gemma.R
Commit: d6630b7f47ea7123efba0b53c01c70864550a29c
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-24 23:50:00 -0700
Commit message:
Commit: d6630b7f47ea7123efba0b53c01c70864550a29c
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-24 23:50:00 -0700
Commit message:
update base vignette
Package: gemma.R
Commit: 458eecb065df78966ef8e9caac811bd094f94e4b
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-23 17:18:01 -0700
Commit message:
Commit: 458eecb065df78966ef8e9caac811bd094f94e4b
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-23 17:18:01 -0700
Commit message:
query details for all endpoints
Package: BioNAR
Commit: 654bfb71081dfd2f61433199d5994fd80d97b958
Author: Anatoly Sorokin <lptolik@gmail.com>
Date: 2024-04-26 14:04:01 +0900
Commit message:
Commit: 654bfb71081dfd2f61433199d5994fd80d97b958
Author: Anatoly Sorokin <lptolik@gmail.com>
Date: 2024-04-26 14:04:01 +0900
Commit message:
remove fixtures introduced due to error in org.Hs.eg.db
Package: Cardinal
Commit: 5a88b9c62df9778682f142e94e8e7c7c26d21edc
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-26 00:59:17 -0400
Commit message:
Commit: 5a88b9c62df9778682f142e94e8e7c7c26d21edc
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-26 00:59:17 -0400
Commit message:
v3.5.6 update slice()
Package: CytoML
Commit: c641bff8922191667a4361f8e4fbf6a5cf42579d
Author: mikejiang <mike@ozette.ai>
Date: 2024-04-25 21:32:30 -0700
Commit message:
Commit: c641bff8922191667a4361f8e4fbf6a5cf42579d
Author: mikejiang <mike@ozette.ai>
Date: 2024-04-25 21:32:30 -0700
Commit message:
bump
Package: cytolib
Commit: 4f42d8550fe80c52dbc08b45c7c454feee036a33
Author: mikejiang <mike@ozette.ai>
Date: 2024-04-25 21:25:53 -0700
Commit message:
Commit: 4f42d8550fe80c52dbc08b45c7c454feee036a33
Author: mikejiang <mike@ozette.ai>
Date: 2024-04-25 21:25:53 -0700
Commit message:
bump
Package: cytolib
Commit: 59a7348e6fb2e83089086d4059158a0183839c66
Author: Mike Jiang <mike@ozette.com>
Date: 2024-04-25 18:44:54 -0700
Commit message:
Commit: 59a7348e6fb2e83089086d4059158a0183839c66
Author: Mike Jiang <mike@ozette.com>
Date: 2024-04-25 18:44:54 -0700
Commit message:
Merge pull request #58 from RGLab/warning-fcs3.2 give warning instead of the exception on FCS3.2
Package: cytolib
Commit: f054881d445d430fd70b643d3d38216b59e1fcf8
Author: mikejiang <mike@ozette.ai>
Date: 2024-04-25 17:30:18 -0700
Commit message:
Commit: f054881d445d430fd70b643d3d38216b59e1fcf8
Author: mikejiang <mike@ozette.ai>
Date: 2024-04-25 17:30:18 -0700
Commit message:
give warning instead of the exception on FCS3.2
Package: matter
Commit: 1c694430f6548506e72d70d56a0438cfc4bbd255
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-26 00:17:47 -0400
Commit message:
Commit: 1c694430f6548506e72d70d56a0438cfc4bbd255
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-26 00:17:47 -0400
Commit message:
v2.5.20 update trans2d() and warp2_trans()
Package: Cardinal
Commit: 775d4c182f579795f2a493d9c0cf7ed197b94c04
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-25 23:23:24 -0400
Commit message:
Commit: 775d4c182f579795f2a493d9c0cf7ed197b94c04
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-25 23:23:24 -0400
Commit message:
v3.5.5
Package: cliqueMS
Commit: c4a967390b289b1abc1c272ffc8a1746b8c06045
Author: osenan <oriol.senan@praenoscere.com>
Date: 2024-04-26 05:17:55 +0200
Commit message:
Commit: c4a967390b289b1abc1c272ffc8a1746b8c06045
Author: osenan <oriol.senan@praenoscere.com>
Date: 2024-04-26 05:17:55 +0200
Commit message:
version bump
Package: cliqueMS
Commit: dcb1cff1bfa9317a780733b21803b03ba3cf382e
Author: osenan <oriol.senan@praenoscere.com>
Date: 2024-04-26 05:16:49 +0200
Commit message:
Commit: dcb1cff1bfa9317a780733b21803b03ba3cf382e
Author: osenan <oriol.senan@praenoscere.com>
Date: 2024-04-26 05:16:49 +0200
Commit message:
Merge branch 'devel' of git.bioconductor.org:packages/cliqueMS into devel
Package: cliqueMS
Commit: 51c1377876ad5efff961d4ae491e2047e9356a6d
Author: osenan <oriol@praenoscere.com>
Date: 2024-04-26 00:05:42 -0300
Commit message:
Commit: 51c1377876ad5efff961d4ae491e2047e9356a6d
Author: osenan <oriol@praenoscere.com>
Date: 2024-04-26 00:05:42 -0300
Commit message:
chore: version bump
Package: cliqueMS
Commit: 764e4885b94ded6a70d81ce7a7603a839dddd80b
Author: osenan <oriol@praenoscere.com>
Date: 2024-04-26 00:04:30 -0300
Commit message:
Commit: 764e4885b94ded6a70d81ce7a7603a839dddd80b
Author: osenan <oriol@praenoscere.com>
Date: 2024-04-26 00:04:30 -0300
Commit message:
docs: update documentation
Package: cliqueMS
Commit: 704b94f84176ba85aceb17fcecf69a05681310ed
Author: osenan <oriol.senan@praenoscere.com>
Date: 2024-04-26 03:50:10 +0200
Commit message:
Commit: 704b94f84176ba85aceb17fcecf69a05681310ed
Author: osenan <oriol.senan@praenoscere.com>
Date: 2024-04-26 03:50:10 +0200
Commit message:
fix: change dependency qlcMatrix
Package: Pirat
Commit: 8ca19194aec9a05713bd22b051616e3e83f759bc
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-04-26 05:14:08 +0200
Commit message:
Commit: 8ca19194aec9a05713bd22b051616e3e83f759bc
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-04-26 05:14:08 +0200
Commit message:
fixing reviewer s remarks
Package: matter
Commit: e2e24b1581c3983b03202d544f025a1391ceb93b
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-25 23:12:01 -0400
Commit message:
Commit: e2e24b1581c3983b03202d544f025a1391ceb93b
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-25 23:12:01 -0400
Commit message:
v2.5.19
Package: celldex
Commit: 350e3a20300336b3b6ea7c0034d80c12678e3be0
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-04-25 17:15:06 -0700
Commit message:
Commit: 350e3a20300336b3b6ea7c0034d80c12678e3be0
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-04-25 17:15:06 -0700
Commit message:
Switch to the new formatObjectMetadata function for takane metadata.
Package: celldex
Commit: 151be9d25877ee67adfbb30175f145fe2ad4f271
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-03-14 16:49:46 -0700
Commit message:
Commit: 151be9d25877ee67adfbb30175f145fe2ad4f271
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-03-14 16:49:46 -0700
Commit message:
Clarified maintainer instructions for handling new submissions.
Package: scRNAseq
Commit: c2eebaf5ac3bdcd620c7bccb5c869993efba6b80
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-04-25 17:11:00 -0700
Commit message:
Commit: c2eebaf5ac3bdcd620c7bccb5c869993efba6b80
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-04-25 17:11:00 -0700
Commit message:
Switch to the new formatObjectMetadata function when saving datasets.
Package: gypsum
Commit: eec9122451bb876ba29eecdeb25ec393ee351aa2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-04-25 17:07:31 -0700
Commit message:
Commit: eec9122451bb876ba29eecdeb25ec393ee351aa2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-04-25 17:07:31 -0700
Commit message:
Added helper function for creating takane-related metadata. Strictly speaking, this doesn't really belong here as gypsum doesn't deal with the actual content of the files. However, there's no better place to put it right now, so we'll just stick it in here and do some voodoo to avoid roping in excessive dependencies.
Package: gypsum
Commit: 1ac95a5a25fc2d23e943e7290db824bfc3b61b6a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-04-22 13:55:14 -0700
Commit message:
Commit: 1ac95a5a25fc2d23e943e7290db824bfc3b61b6a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-04-22 13:55:14 -0700
Commit message:
Mention the ancestor list in the manifest docs.
Package: gypsum
Commit: eec9122451bb876ba29eecdeb25ec393ee351aa2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-04-25 17:07:31 -0700
Commit message:
Commit: eec9122451bb876ba29eecdeb25ec393ee351aa2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-04-25 17:07:31 -0700
Commit message:
Added helper function for creating takane-related metadata. Strictly speaking, this doesn't really belong here as gypsum doesn't deal with the actual content of the files. However, there's no better place to put it right now, so we'll just stick it in here and do some voodoo to avoid roping in excessive dependencies.
Package: scp
Commit: bf3d91f237b7cdaab7899911b3746183d0d6dfeb
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2024-04-25 23:59:17 +0200
Commit message:
Commit: bf3d91f237b7cdaab7899911b3746183d0d6dfeb
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2024-04-25 23:59:17 +0200
Commit message:
bump version
Package: scp
Commit: 352c5e31d8432d5e2d029d1964b3e2bc8f6dc83d
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2024-04-24 18:01:04 +0200
Commit message:
Commit: 352c5e31d8432d5e2d029d1964b3e2bc8f6dc83d
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2024-04-24 18:01:04 +0200
Commit message:
fix: fixed small error in degrees of freedom
Package: scp
Commit: 6a39bb38256668a6af7704d033194c94c8179cae
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2024-04-17 07:35:56 +0200
Commit message:
Commit: 6a39bb38256668a6af7704d033194c94c8179cae
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2024-04-17 07:35:56 +0200
Commit message:
fix: break workflow upon infinite values
Package: scp
Commit: 5d6d7e786c4be8c9c2c59d3d0ac4825ef42b2c1a
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2024-04-15 10:57:18 +0200
Commit message:
Commit: 5d6d7e786c4be8c9c2c59d3d0ac4825ef42b2c1a
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2024-04-15 10:57:18 +0200
Commit message:
bump version
Package: autonomics
Commit: 40d68c2b71d213c9fa6d25040cdafc6f7c3f1057
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-04-25 23:08:25 +0200
Commit message:
Commit: 40d68c2b71d213c9fa6d25040cdafc6f7c3f1057
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-04-25 23:08:25 +0200
Commit message:
1.11.109 : Add (downsized) billing19 to extdata
Package: GenomicPlot
Commit: c90786d16696274a20802fd5a8cd7c4be5a3a0f1
Author: Shuye Pu <shuye2009@gmail.com>
Date: 2024-04-25 16:55:33 -0400
Commit message:
Commit: c90786d16696274a20802fd5a8cd7c4be5a3a0f1
Author: Shuye Pu <shuye2009@gmail.com>
Date: 2024-04-25 16:55:33 -0400
Commit message:
handle NCBI style of seqlevels
Package: BiocPkgTools
Commit: 42a2516ecb7d95a9b91093c4afca67fb7b1d1434
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 16:00:12 -0400
Commit message:
Commit: 42a2516ecb7d95a9b91093c4afca67fb7b1d1434
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 16:00:12 -0400
Commit message:
version bump 1.21.11
Package: BiocPkgTools
Commit: fce572662610dff0d514b3abf69d4b0bf75d7fef
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 16:00:05 -0400
Commit message:
Commit: fce572662610dff0d514b3abf69d4b0bf75d7fef
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 16:00:05 -0400
Commit message:
bug fix: condition length > 1
Package: BiocPkgTools
Commit: 35893f48f60c4df81f5443cf6f5c8311508b1aef
Author: Sean Davis <seandavi@gmail.com>
Date: 2024-04-25 15:25:50 -0400
Commit message:
Commit: 35893f48f60c4df81f5443cf6f5c8311508b1aef
Author: Sean Davis <seandavi@gmail.com>
Date: 2024-04-25 15:25:50 -0400
Commit message:
Merge pull request #72 from jwokaty/new-test-prefix Replace old test prefix with new test prefix
Package: BiocPkgTools
Commit: 98322694bf9414c11ec52ed4cc4b6282db2a206c
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2024-03-29 14:15:09 -0400
Commit message:
Commit: 98322694bf9414c11ec52ed4cc4b6282db2a206c
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2024-03-29 14:15:09 -0400
Commit message:
Replace old prefix for new test repository
Package: KEGGREST
Commit: fdec6a44852fb99f162f0fd76c12621c8d85d768
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-25 12:50:08 -0700
Commit message:
Commit: fdec6a44852fb99f162f0fd76c12621c8d85d768
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-25 12:50:08 -0700
Commit message:
Clarify usage restriction, add a bunch of contributors
Package: GSVA
Commit: c0f8a0f1a9920fada6a00cc86cc3e4cdef990152
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-04-25 21:26:00 +0200
Commit message:
Commit: c0f8a0f1a9920fada6a00cc86cc3e4cdef990152
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-04-25 21:26:00 +0200
Commit message:
Add missing export to readGMT()
Package: GSVA
Commit: b67ed2355ad07660736df48bdac50f0256f6fc5b
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2024-04-25 20:41:38 +0200
Commit message:
Commit: b67ed2355ad07660736df48bdac50f0256f6fc5b
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2024-04-25 20:41:38 +0200
Commit message:
Merge pull request #163 from rcastelo/158-load-gmt-files-dealing-duplicated-gene-sets 158 load gmt files dealing duplicated gene sets
Package: GSVA
Commit: b47c509f73ee7a9a3e23bbdfa6494caa0b516d0f
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2024-04-25 19:29:43 +0200
Commit message:
Commit: b47c509f73ee7a9a3e23bbdfa6494caa0b516d0f
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2024-04-25 19:29:43 +0200
Commit message:
fix minor documentation typo in ?readGMT
Package: GSVA
Commit: 2164828bcae562169d0f2fc6c935fd6215dcced5
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2024-04-25 19:15:53 +0200
Commit message:
Commit: 2164828bcae562169d0f2fc6c935fd6215dcced5
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2024-04-25 19:15:53 +0200
Commit message:
add functions readGMT() and deduplicateGeneSets()
Package: clusterExperiment
Commit: c9fb563f1688d2f1644c53b8915e68940218fcf6
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2024-04-25 11:39:43 -0700
Commit message:
Commit: c9fb563f1688d2f1644c53b8915e68940218fcf6
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2024-04-25 11:39:43 -0700
Commit message:
fix .3
Package: clusterExperiment
Commit: 73dd89027ed53867b64b512ec9c758ebc58a155b
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2024-04-25 11:38:38 -0700
Commit message:
Commit: 73dd89027ed53867b64b512ec9c758ebc58a155b
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2024-04-25 11:38:38 -0700
Commit message:
fix .3
Package: clusterExperiment
Commit: 80a07ce198ed779c298e74b0b65ce7922cd77d3e
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2024-04-25 11:33:19 -0700
Commit message:
Commit: 80a07ce198ed779c298e74b0b65ce7922cd77d3e
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2024-04-25 11:33:19 -0700
Commit message:
fix
Package: procoil
Commit: b5515c5fc234ae94cc62065d6bf643b99353eee5
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 19:58:39 +0200
Commit message:
Commit: b5515c5fc234ae94cc62065d6bf643b99353eee5
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 19:58:39 +0200
Commit message:
Change of maintainer's e-mail address and package website; corresponding changes in documentation; version number bumped to 2.31.1
Package: DECIPHER
Commit: 531d0a2821e49df6fe5cd697ea930b321b4756f0
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-25 10:32:50 -0700
Commit message:
Commit: 531d0a2821e49df6fe5cd697ea930b321b4756f0
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-25 10:32:50 -0700
Commit message:
Import pairwiseAlignment only from pwalign instead of everything
Package: SynExtend
Commit: f5bd271c064d02a8ce916b571ad4825a6b18db05
Author: npcooley <npcooley@gmail.com>
Date: 2024-04-25 13:01:33 -0400
Commit message:
Commit: f5bd271c064d02a8ce916b571ad4825a6b18db05
Author: npcooley <npcooley@gmail.com>
Date: 2024-04-25 13:01:33 -0400
Commit message:
Merge branch 'devel' of https://github.com/npcooley/SynExtend into devel
Package: SynExtend
Commit: 70378d92716f6d227c54c6290e3052870c071bb2
Author: npcooley <npcooley@gmail.com>
Date: 2024-04-25 12:56:35 -0400
Commit message:
Commit: 70378d92716f6d227c54c6290e3052870c071bb2
Author: npcooley <npcooley@gmail.com>
Date: 2024-04-25 12:56:35 -0400
Commit message:
adjusted pipeline
Package: SynExtend
Commit: b455adcc7a300bc5e77c6cb33d703c78f8e1e7f6
Author: Nicholas Cooley <39340402+npcooley@users.noreply.github.com>
Date: 2024-04-24 10:30:15 -0400
Commit message:
Commit: b455adcc7a300bc5e77c6cb33d703c78f8e1e7f6
Author: Nicholas Cooley <39340402+npcooley@users.noreply.github.com>
Date: 2024-04-24 10:30:15 -0400
Commit message:
Merge pull request #46 from ahl27/master fix: optimzations to ~~ShoalFinder~~ ExoLabel
Package: SynExtend
Commit: 3692807c11a9fac65bd90b2c1a487435f817444a
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-23 13:55:35 -0400
Commit message:
Commit: 3692807c11a9fac65bd90b2c1a487435f817444a
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-23 13:55:35 -0400
Commit message:
update naming
Package: SynExtend
Commit: 7a718de8e5628fd9ae03d37587bf0c3f6203f939
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-23 12:08:27 -0400
Commit message:
Commit: 7a718de8e5628fd9ae03d37587bf0c3f6203f939
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-23 12:08:27 -0400
Commit message:
fix missing argument in man page
Package: SynExtend
Commit: 856fedf19514c854f5f5fa0f5b4ea1ac2855c816
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-04-23 12:04:08 -0400
Commit message:
Commit: 856fedf19514c854f5f5fa0f5b4ea1ac2855c816
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-04-23 12:04:08 -0400
Commit message:
remove file added by mistake
Package: SynExtend
Commit: ff931d13b4e9b2a03ca421bc4a2fe9cddbb1a92c
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-04-23 12:01:26 -0400
Commit message:
Commit: ff931d13b4e9b2a03ca421bc4a2fe9cddbb1a92c
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-04-23 12:01:26 -0400
Commit message:
Merge branch 'npcooley:devel' into master
Package: SynExtend
Commit: e9c1bdc4538224bff33d890b129d3aa0c0e536af
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-23 12:00:40 -0400
Commit message:
Commit: e9c1bdc4538224bff33d890b129d3aa0c0e536af
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-23 12:00:40 -0400
Commit message:
minor optimzations to runtime and memory usage'
Package: SynExtend
Commit: 19306297d5d86287e741127ee4ba3bc9c78131ee
Author: Nicholas Cooley <39340402+npcooley@users.noreply.github.com>
Date: 2024-04-23 09:55:09 -0400
Commit message:
Commit: 19306297d5d86287e741127ee4ba3bc9c78131ee
Author: Nicholas Cooley <39340402+npcooley@users.noreply.github.com>
Date: 2024-04-23 09:55:09 -0400
Commit message:
Merge pull request #45 from ahl27/master feat: OOM label propagation
Package: SynExtend
Commit: c4d308134a11153badc1be974ce97f370d412fc3
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-04-22 18:10:58 -0400
Commit message:
Commit: c4d308134a11153badc1be974ce97f370d412fc3
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-04-22 18:10:58 -0400
Commit message:
Remove files following merge sort to reduce disk usage
Package: SynExtend
Commit: 3e146a8a4bcb74475961e3490984eba53b1223b1
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-22 11:28:31 -0400
Commit message:
Commit: 3e146a8a4bcb74475961e3490984eba53b1223b1
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-22 11:28:31 -0400
Commit message:
Add estimate shoal rd file
Package: SynExtend
Commit: 3a48f791941c6e5ea96aa124fd5fb55657d92ad8
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-22 11:28:19 -0400
Commit message:
Commit: 3a48f791941c6e5ea96aa124fd5fb55657d92ad8
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-22 11:28:19 -0400
Commit message:
add note to documentation
Package: SynExtend
Commit: 2b8f6c85f4d37a0a9b2b25273e40cbf9b31bfc7d
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-22 11:19:15 -0400
Commit message:
Commit: 2b8f6c85f4d37a0a9b2b25273e40cbf9b31bfc7d
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-22 11:19:15 -0400
Commit message:
fixes bug in memory estimation
Package: SynExtend
Commit: c78f5ea373f2e5f4f0fd37bdf9d95bc10c0a34de
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-22 11:09:56 -0400
Commit message:
Commit: c78f5ea373f2e5f4f0fd37bdf9d95bc10c0a34de
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-22 11:09:56 -0400
Commit message:
rename to ShoalFinder, adds EstimateShoal function
Package: SynExtend
Commit: f5aec3c9eac9b17df3e9ab337a930d2a5df61944
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-20 12:48:58 -0400
Commit message:
Commit: f5aec3c9eac9b17df3e9ab337a930d2a5df61944
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-20 12:48:58 -0400
Commit message:
re-adding cleanup_files argument to FLOOM
Package: SynExtend
Commit: 1fdf2d675975c9b4b3bd4661d8c43cc702b5d400
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-20 12:44:27 -0400
Commit message:
Commit: 1fdf2d675975c9b4b3bd4661d8c43cc702b5d400
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-20 12:44:27 -0400
Commit message:
removes a 1: usage in evoweaver predictor
Package: SynExtend
Commit: ac895cb1eb370ccfaca34686d125c94369cf37af
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-20 12:38:13 -0400
Commit message:
Commit: ac895cb1eb370ccfaca34686d125c94369cf37af
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-20 12:38:13 -0400
Commit message:
fix man page
Package: SynExtend
Commit: 059c0d65f8367d987894124ce72a7bb55a27bfd1
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-04-20 12:37:43 -0400
Commit message:
Commit: 059c0d65f8367d987894124ce72a7bb55a27bfd1
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-04-20 12:37:43 -0400
Commit message:
Update rpkgchecks.yml
Package: SynExtend
Commit: f4c4c0d1cdfac4f9ebc8fae134983afb08577fb4
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-04-20 12:31:09 -0400
Commit message:
Commit: f4c4c0d1cdfac4f9ebc8fae134983afb08577fb4
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-04-20 12:31:09 -0400
Commit message:
Update DESCRIPTION
Package: SynExtend
Commit: 93223e9dec8d0ada69b3ecc062043eb461411c80
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-04-20 12:30:05 -0400
Commit message:
Commit: 93223e9dec8d0ada69b3ecc062043eb461411c80
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-04-20 12:30:05 -0400
Commit message:
Update rpkgchecks.yml (#16)
Package: SynExtend
Commit: b2d3147bf3de3b5543e5577294305977ade2d252
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-04-20 12:19:18 -0400
Commit message:
Commit: b2d3147bf3de3b5543e5577294305977ade2d252
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-04-20 12:19:18 -0400
Commit message:
Merge branch 'devel' into master
Package: SynExtend
Commit: 49256e78495884e481a6a3988c3c944f1691d44f
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-20 12:17:07 -0400
Commit message:
Commit: 49256e78495884e481a6a3988c3c944f1691d44f
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-20 12:17:07 -0400
Commit message:
update news and description
Package: SynExtend
Commit: da678e36c59995a4177fbcff48c3b87b8cf48934
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-20 12:10:11 -0400
Commit message:
Commit: da678e36c59995a4177fbcff48c3b87b8cf48934
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-20 12:10:11 -0400
Commit message:
Updates naming, removes a potentially problematic example
Package: SynExtend
Commit: 6e13f098993e70d569d34371c503dcbc7d8e3d9f
Author: npcooley <npcooley@gmail.com>
Date: 2024-02-28 16:10:12 -0500
Commit message:
Commit: 6e13f098993e70d569d34371c503dcbc7d8e3d9f
Author: npcooley <npcooley@gmail.com>
Date: 2024-02-28 16:10:12 -0500
Commit message:
new functions, dependency updates
Package: SynExtend
Commit: 05f43f2aa447b6275e614a42fceaaf7ac20be345
Author: npcooley <npcooley@gmail.com>
Date: 2023-12-05 08:57:31 -0500
Commit message:
Commit: 05f43f2aa447b6275e614a42fceaaf7ac20be345
Author: npcooley <npcooley@gmail.com>
Date: 2023-12-05 08:57:31 -0500
Commit message:
cosmetic fixes
Package: SynExtend
Commit: 165845578326614e3a4fba9ba4cffd4ae35e2896
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-20 12:10:11 -0400
Commit message:
Commit: 165845578326614e3a4fba9ba4cffd4ae35e2896
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-20 12:10:11 -0400
Commit message:
Updates naming, removes a potentially problematic example
Package: SynExtend
Commit: ff195e52080cc385a60400d9bb79a6ae325cfaf2
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-20 11:59:22 -0400
Commit message:
Commit: ff195e52080cc385a60400d9bb79a6ae325cfaf2
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-04-20 11:59:22 -0400
Commit message:
small bugfixes to EvoWeaver, adds OOM FLP algorithm
Package: GenomicDataCommons
Commit: c75e5c8d4bdb88356ca6959f9ae3e3fb0ef30db9
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 13:01:32 -0400
Commit message:
Commit: c75e5c8d4bdb88356ca6959f9ae3e3fb0ef30db9
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 13:01:32 -0400
Commit message:
version bump 1.27.2
Package: GenomicDataCommons
Commit: b8dba8fe0e9aca2e89730c9b5e6518b84754418b
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 13:01:28 -0400
Commit message:
Commit: b8dba8fe0e9aca2e89730c9b5e6518b84754418b
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 13:01:28 -0400
Commit message:
update NEWS file
Package: gg4way
Commit: 91d0f1c46fc962ea0f201c7bc8b2d9c19d064a0f
Author: Ben Laufer <laufer.benjamin@gene.com>
Date: 2024-04-25 09:57:56 -0700
Commit message:
Commit: 91d0f1c46fc962ea0f201c7bc8b2d9c19d064a0f
Author: Ben Laufer <laufer.benjamin@gene.com>
Date: 2024-04-25 09:57:56 -0700
Commit message:
Legend improvements
Package: kebabs
Commit: a784e0da81a793e6479da01d4bc72cf2016b4c8c
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 18:56:04 +0200
Commit message:
Commit: a784e0da81a793e6479da01d4bc72cf2016b4c8c
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 18:56:04 +0200
Commit message:
fix of README.md
Package: kebabs
Commit: f467fabec1e64f3fb39396e87d06650948089306
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 18:54:31 +0200
Commit message:
Commit: f467fabec1e64f3fb39396e87d06650948089306
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 18:54:31 +0200
Commit message:
fix of README.md
Package: kebabs
Commit: 890c61799879cd493ee5a332e9f0475f026a2369
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 18:53:03 +0200
Commit message:
Commit: 890c61799879cd493ee5a332e9f0475f026a2369
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 18:53:03 +0200
Commit message:
Change of maintainer e-mail address and website; change of format of vignette; version number bumped to 1.37.2
Package: BiocPkgTools
Commit: d1e962c21d275401143aa17074217a0ecafc8369
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 12:17:59 -0400
Commit message:
Commit: d1e962c21d275401143aa17074217a0ecafc8369
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 12:17:59 -0400
Commit message:
version bump 1.21.10
Package: BiocPkgTools
Commit: 6add75beb5c1bd5b17a15bf62ae72942c1e5b9a5
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 12:10:28 -0400
Commit message:
Commit: 6add75beb5c1bd5b17a15bf62ae72942c1e5b9a5
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 12:10:28 -0400
Commit message:
update item lists in docs
Package: BiocPkgTools
Commit: 31c5bfcf0c4017caddf1b5334c8ac1fcea44ae41
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 11:07:16 -0400
Commit message:
Commit: 31c5bfcf0c4017caddf1b5334c8ac1fcea44ae41
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 11:07:16 -0400
Commit message:
version bump 1.21.9
Package: BiocPkgTools
Commit: fbeac26121d92ef652e6b1d79dccd9532f6ea5e4
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 11:03:33 -0400
Commit message:
Commit: fbeac26121d92ef652e6b1d79dccd9532f6ea5e4
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 11:03:33 -0400
Commit message:
update NEWS file
Package: STexampleData
Commit: a87a0e6c65ec990b3426d5de0c9d38de0b1d757e
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-04-25 12:03:14 -0400
Commit message:
Commit: a87a0e6c65ec990b3426d5de0c9d38de0b1d757e
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-04-25 12:03:14 -0400
Commit message:
update version
Package: STexampleData
Commit: b7a5c0a59c6b7e2d757bab12210d2fac062e3e1d
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-04-25 12:02:58 -0400
Commit message:
Commit: b7a5c0a59c6b7e2d757bab12210d2fac062e3e1d
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-04-25 12:02:58 -0400
Commit message:
update version in news
Package: STexampleData
Commit: f087030bf4e94419864233283c33e5ef475713b3
Author: estellad <estelladong729@gmail.com>
Date: 2024-04-25 17:57:41 +0200
Commit message:
Commit: f087030bf4e94419864233283c33e5ef475713b3
Author: estellad <estelladong729@gmail.com>
Date: 2024-04-25 17:57:41 +0200
Commit message:
update typo in xenium make data files
Package: STexampleData
Commit: d1bc182fa444001192e0d351e1033eaa2bb1ccf2
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-04-25 11:43:52 -0400
Commit message:
Commit: d1bc182fa444001192e0d351e1033eaa2bb1ccf2
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-04-25 11:43:52 -0400
Commit message:
version
Package: STexampleData
Commit: aa3df54157d9c2fbbfff8106fbede81871af245e
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-04-25 11:43:41 -0400
Commit message:
Commit: aa3df54157d9c2fbbfff8106fbede81871af245e
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-04-25 11:43:41 -0400
Commit message:
store files in subdirectories
Package: STexampleData
Commit: 953689b595305e0aa5308ea713e28885ed131924
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-04-25 11:38:44 -0400
Commit message:
Commit: 953689b595305e0aa5308ea713e28885ed131924
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-04-25 11:38:44 -0400
Commit message:
update NEWS
Package: STexampleData
Commit: ca8bc58371e1b92ec73fe01752f8200a5ee7fa99
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-04-25 11:37:47 -0400
Commit message:
Commit: ca8bc58371e1b92ec73fe01752f8200a5ee7fa99
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-04-25 11:37:47 -0400
Commit message:
select correct replicate
Package: scRNAseq
Commit: 140f6461e4bf168e8d7a9918123ebec15429af65
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-04-25 07:58:22 -0700
Commit message:
Commit: 140f6461e4bf168e8d7a9918123ebec15429af65
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-04-25 07:58:22 -0700
Commit message:
Fixed G2 phase assignments in the Leng ESC column data.
Package: VariantFiltering
Commit: d2456b1a93cedbd0e66bbbb153e6bebea2506666
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-04-25 16:55:24 +0200
Commit message:
Commit: d2456b1a93cedbd0e66bbbb153e6bebea2506666
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-04-25 16:55:24 +0200
Commit message:
Fixed warning in C code triggered by -Wformat-security
Package: BiocIO
Commit: a3a35dd9941c4880750282f30f00feb850be5b7f
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:55:43 -0400
Commit message:
Commit: a3a35dd9941c4880750282f30f00feb850be5b7f
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:55:43 -0400
Commit message:
version bump 1.13.1
Package: BiocIO
Commit: 3ce6ac41e3569df0ac7d8bdba2ca45f624e2d45a
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:55:36 -0400
Commit message:
Commit: 3ce6ac41e3569df0ac7d8bdba2ca45f624e2d45a
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:55:36 -0400
Commit message:
update NEWS files
Package: BiocIO
Commit: 5a9c33647bfc6264d6f0c7ae74937157345008cb
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:53:25 -0400
Commit message:
Commit: 5a9c33647bfc6264d6f0c7ae74937157345008cb
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:53:25 -0400
Commit message:
roxygen updates
Package: BiocIO
Commit: d608f17ab94e2ea8249ec2defe2cc0749113cf5c
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:53:16 -0400
Commit message:
Commit: d608f17ab94e2ea8249ec2defe2cc0749113cf5c
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:53:16 -0400
Commit message:
use exportClass tags
Package: UniProt.ws
Commit: 4f56e292cf574bf64189283788346a00a0f170c4
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:45:00 -0400
Commit message:
Commit: 4f56e292cf574bf64189283788346a00a0f170c4
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:45:00 -0400
Commit message:
version bump 2.43.1
Package: UniProt.ws
Commit: a340d0f0c63e0cdbd900cd2fb29ea608c21ad519
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:44:58 -0400
Commit message:
Commit: a340d0f0c63e0cdbd900cd2fb29ea608c21ad519
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:44:58 -0400
Commit message:
update NEWS file
Package: UniProt.ws
Commit: b92d749fb94f67b73da9f690878133e880ed2d65
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:43:08 -0400
Commit message:
Commit: b92d749fb94f67b73da9f690878133e880ed2d65
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:43:08 -0400
Commit message:
minor updates to DESCRIPTION
Package: BiocCheck
Commit: 2be4310a713e6fa05dd78f6f01b01f2dc1fa3286
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:37:13 -0400
Commit message:
Commit: 2be4310a713e6fa05dd78f6f01b01f2dc1fa3286
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:37:13 -0400
Commit message:
version bump 1.39.35
Package: BiocCheck
Commit: b21718441535cddf2ca0c7e63fa9a3aa352854b1
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:37:08 -0400
Commit message:
Commit: b21718441535cddf2ca0c7e63fa9a3aa352854b1
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:37:08 -0400
Commit message:
update NEWS file
Package: BiocCheck
Commit: be393761dd2095588c40a628f00c94332af03322
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:35:11 -0400
Commit message:
Commit: be393761dd2095588c40a628f00c94332af03322
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-25 09:35:11 -0400
Commit message:
clean up code after removal of redundant check
Package: UPDhmm
Commit: 28cb88a93f6b66655e40768492fbfe9962b7f70f
Author: martasevill <martasevillaporras@gmail.com>
Date: 2024-04-25 15:26:46 +0200
Commit message:
Commit: 28cb88a93f6b66655e40768492fbfe9962b7f70f
Author: martasevill <martasevillaporras@gmail.com>
Date: 2024-04-25 15:26:46 +0200
Commit message:
Changing vignette text
Package: msqrob2
Commit: 7b2399da99e81c40ec74e1b9b5a78b55f2e6c5ab
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 10:02:41 +0200
Commit message:
Commit: 7b2399da99e81c40ec74e1b9b5a78b55f2e6c5ab
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 10:02:41 +0200
Commit message:
Merge pull request #57 from StijnVandenbulcke/master Updating News and Description files
Package: msqrob2
Commit: ebcf2e326b8fde40fe1df636b19a74f14afecb5c
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 10:01:54 +0200
Commit message:
Commit: ebcf2e326b8fde40fe1df636b19a74f14afecb5c
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 10:01:54 +0200
Commit message:
Update DESCRIPTION
Package: msqrob2
Commit: 2484c917edd8d03baaa6a041a858474841bf60ff
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 10:01:44 +0200
Commit message:
Commit: 2484c917edd8d03baaa6a041a858474841bf60ff
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 10:01:44 +0200
Commit message:
Update NEWS.md
Package: msqrob2
Commit: adb3d405e420372b29f47c6e4ef019fec6bb00cb
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 09:59:25 +0200
Commit message:
Commit: adb3d405e420372b29f47c6e4ef019fec6bb00cb
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 09:59:25 +0200
Commit message:
Update msqrob.R Added a drop = FALSE argument, preventing possible issues
Package: msqrob2
Commit: a367242aa4e2df85e6799bfe7a7177c950907bb2
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 00:15:03 +0200
Commit message:
Commit: a367242aa4e2df85e6799bfe7a7177c950907bb2
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 00:15:03 +0200
Commit message:
Merge pull request #56 from StijnVandenbulcke/master Fixed Issues
Package: msqrob2
Commit: eba0dacdbd57285e6e1b96ad6cba5384a18cf51f
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 00:11:31 +0200
Commit message:
Commit: eba0dacdbd57285e6e1b96ad6cba5384a18cf51f
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-25 00:11:31 +0200
Commit message:
Update msqrob.R Fixed issue where model matrix was subsetted incorrectly
Package: msqrob2
Commit: f8cbcc614626d455916d1815d04369117f2cb0bc
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-24 23:08:57 +0200
Commit message:
Commit: f8cbcc614626d455916d1815d04369117f2cb0bc
Author: StijnVandenbulcke <57996469+StijnVandenbulcke@users.noreply.github.com>
Date: 2024-04-24 23:08:57 +0200
Commit message:
Update msqrob.R Fixed bug related to ordering of levels when using ridge regression
Package: fenr
Commit: 65bdf0dec710a63e6c897b47ee97beec8ed38d7a
Author: Marek Gierlinski <Marek.Gierlinski@gmail.com>
Date: 2024-04-25 10:59:00 +0100
Commit message:
Commit: 65bdf0dec710a63e6c897b47ee97beec8ed38d7a
Author: Marek Gierlinski <Marek.Gierlinski@gmail.com>
Date: 2024-04-25 10:59:00 +0100
Commit message:
Version 1.0.9
Package: fenr
Commit: 1800e36dc4b37c32b416827b8b0d1d93b5546416
Author: Marek Gierlinski <Marek.Gierlinski@gmail.com>
Date: 2024-04-25 10:38:57 +0100
Commit message:
Commit: 1800e36dc4b37c32b416827b8b0d1d93b5546416
Author: Marek Gierlinski <Marek.Gierlinski@gmail.com>
Date: 2024-04-25 10:38:57 +0100
Commit message:
Increased default timeout
Package: fenr
Commit: 6c8200475f68415a5fa6f5538d9a570026827410
Author: Marek Gierlinski <Marek.Gierlinski@gmail.com>
Date: 2024-04-25 10:27:28 +0100
Commit message:
Commit: 6c8200475f68415a5fa6f5538d9a570026827410
Author: Marek Gierlinski <Marek.Gierlinski@gmail.com>
Date: 2024-04-25 10:27:28 +0100
Commit message:
Increased default timeout
Package: msa
Commit: 84c8ed5da8a54629d13a0318e4a5b9dec6f7e428
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-25 01:04:18 -0700
Commit message:
Commit: 84c8ed5da8a54629d13a0318e4a5b9dec6f7e428
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-25 01:04:18 -0700
Commit message:
fix link to BLOSUM62
Package: msa
Commit: 0e98500b59f80e7bb1429f601ec07235be7252b7
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-25 00:50:13 -0700
Commit message:
Commit: 0e98500b59f80e7bb1429f601ec07235be7252b7
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-25 00:50:13 -0700
Commit message:
one more tweak
Package: rawDiag
Commit: 5e50e8651ae024b4e2525cdab6504fa6f30746af
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:46:45 +0200
Commit message:
Commit: 5e50e8651ae024b4e2525cdab6504fa6f30746af
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:46:45 +0200
Commit message:
doc: reran roxygen2::roxygenize()
Package: rawDiag
Commit: b787c763f9d9e4fc7e7fb9391bb2e3eedf982263
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:46:18 +0200
Commit message:
Commit: b787c763f9d9e4fc7e7fb9391bb2e3eedf982263
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:46:18 +0200
Commit message:
build: add shiny
Package: rawDiag
Commit: 880250c2d90a9c8d6b362a70ecaf9a8fb211b9b7
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:44:50 +0200
Commit message:
Commit: 880250c2d90a9c8d6b362a70ecaf9a8fb211b9b7
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:44:50 +0200
Commit message:
doc: bump version 0.99.34
Package: rawDiag
Commit: 5873904b12bd8c22abebc371e0d1c6da23357d17
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:41:37 +0200
Commit message:
Commit: 5873904b12bd8c22abebc371e0d1c6da23357d17
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:41:37 +0200
Commit message:
fix: handle case having no 'Ms' scans E.g., caused by using an SRM method as a result there is no TIC and BPC available (at least acc. to our def. of BCP and TIC).
Package: rawDiag
Commit: 70a1e6598dcb4aa32304b305f8e81b8744097102
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:18:54 +0200
Commit message:
Commit: 70a1e6598dcb4aa32304b305f8e81b8744097102
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-04-25 09:18:54 +0200
Commit message:
doc: add install notes for installing missing pkgs
Package: msa
Commit: 06c35ab3d6ce5d1991fc0dfbd2b82f02fd1f0e28
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:40:57 +0200
Commit message:
Commit: 06c35ab3d6ce5d1991fc0dfbd2b82f02fd1f0e28
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:40:57 +0200
Commit message:
Fixes to account for move of matrices to the 'pwalign' package
Package: msa
Commit: 2b74e88cb76c88d51c1ce8e4e91ac34770573756
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:38:50 +0200
Commit message:
Commit: 2b74e88cb76c88d51c1ce8e4e91ac34770573756
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:38:50 +0200
Commit message:
Fix of help page for msaConservationScore() to account for move of matrices to the 'pwalign' package
Package: MAGAR
Commit: 3c3e5ae93afdd9e7972e80cc8b5e806193eefab2
Author: Michael Scherer <s9mlscer@gmail.com>
Date: 2024-04-25 09:33:33 +0200
Commit message:
Commit: 3c3e5ae93afdd9e7972e80cc8b5e806193eefab2
Author: Michael Scherer <s9mlscer@gmail.com>
Date: 2024-04-25 09:33:33 +0200
Commit message:
Updated DESCRIPTION
Package: msa
Commit: 6fa77c8d54acbebc9232156a4b881fd0c8fc718a
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:32:44 +0200
Commit message:
Commit: 6fa77c8d54acbebc9232156a4b881fd0c8fc718a
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:32:44 +0200
Commit message:
Merge remote-tracking branch 'refs/remotes/origin/master'
Package: msa
Commit: bf997e3b91ca667baad6cff24ebb0fc91604df8a
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:30:37 +0200
Commit message:
Commit: bf997e3b91ca667baad6cff24ebb0fc91604df8a
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:30:37 +0200
Commit message:
Fix of typo in vignette source
Package: msa
Commit: b5bbad83331efbd1ae975c0bb76b884c8375770c
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:30:37 +0200
Commit message:
Commit: b5bbad83331efbd1ae975c0bb76b884c8375770c
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-04-25 09:30:37 +0200
Commit message:
Fix of typo in vignette source
Package: msa
Commit: c480f764f7dc9cdb498586c1b33b1a94409b691f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-25 00:23:53 -0700
Commit message:
Commit: c480f764f7dc9cdb498586c1b33b1a94409b691f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-25 00:23:53 -0700
Commit message:
The BLOSUM matrices have moved from Biostrings to pwalign
Package: MatrixQCvis
Commit: 9b2c8c52aba722ed156b644d7e3456f7c16e640f
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2024-04-25 09:10:57 +0200
Commit message:
Commit: 9b2c8c52aba722ed156b644d7e3456f7c16e640f
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2024-04-25 09:10:57 +0200
Commit message:
bump version to 1.11.7
Package: MatrixQCvis
Commit: 4c5ff15c25b0aa999bc474b5b6ae3d228fb6d96f
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2024-04-23 16:06:44 +0200
Commit message:
Commit: 4c5ff15c25b0aa999bc474b5b6ae3d228fb6d96f
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2024-04-23 16:06:44 +0200
Commit message:
add dplyr:: in front of pull in vignette
Package: iPAC
Commit: c24b078859fba09c37df812505d03cde00ca5607
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 23:34:27 -0700
Commit message:
Commit: c24b078859fba09c37df812505d03cde00ca5607
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 23:34:27 -0700
Commit message:
Small tweak to NAMESPACE Import selectively from Biostrings to avoid the following load-time warning: replacing previous import ‘Biostrings::pairwiseAlignment’ by ‘pwalign::pairwiseAlignment’ when loading ‘iPAC’
Package: scanMiRApp
Commit: 9e75eafa09eed5986877b705a45f852593c8030b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 23:08:02 -0700
Commit message:
Commit: 9e75eafa09eed5986877b705a45f852593c8030b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 23:08:02 -0700
Commit message:
makeTxDbFromGRanges() has moved from GenomicFeatures to txdbmaker
Package: sangeranalyseR
Commit: 204e6de7e1175ea8daf09a61b39b89074ff8f803
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 22:51:33 -0700
Commit message:
Commit: 204e6de7e1175ea8daf09a61b39b89074ff8f803
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 22:51:33 -0700
Commit message:
compareStrings() has moved from Biostrings to pwalign
Package: crisprShiny
Commit: f27faf49fa866d24de50ad99ef5a497564b7b098
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 22:39:11 -0700
Commit message:
Commit: f27faf49fa866d24de50ad99ef5a497564b7b098
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 22:39:11 -0700
Commit message:
compareStrings() has moved from Biostrings to pwalign
Package: ClustIRR
Commit: 533da03929c24996ff75a48a6c1469090e3459c5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 22:27:12 -0700
Commit message:
Commit: 533da03929c24996ff75a48a6c1469090e3459c5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 22:27:12 -0700
Commit message:
stringDist() and the BLOSUM matrices have moved from Biostrings to pwalign
Package: openPrimeR
Commit: 4217da8ccf83fa00012b3de3527b77dd30ca100c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 22:10:17 -0700
Commit message:
Commit: 4217da8ccf83fa00012b3de3527b77dd30ca100c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 22:10:17 -0700
Commit message:
pairwiseAlignment() and related have moved from Biostrings to pwalign IMPORTANT NOTE to the maintainer of openPrimeR: Running roxygen2::roxygenize() on the package generates 300+ man pages that are not in git. Please roxygenize() the package and don't forget to add the new man pages to git (with 'git add man/*') before you commit and push. Thanks!
Package: hiReadsProcessor
Commit: 5ee9d977981b151228ea1b8a23fdf3137f178062
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 21:39:29 -0700
Commit message:
Commit: 5ee9d977981b151228ea1b8a23fdf3137f178062
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 21:39:29 -0700
Commit message:
pairwiseAlignment() has moved from Biostrings to pwalign - Make necessary adjustments to DESCRIPTION and imports to account for pairwiseAlignment() being now in pwalign instead of Biostrings. - Also remove Tutorial.R, Tutorial.html, and Tutorial.md from the vignettes/ folder. Only Tutorial.Rmd belongs to git. The other files get automatically generated and added to the resulting package source tarball by 'R CMD build', and so should not be added to git.
Package: scanMiR
Commit: f2b3ece1a58789acea1341059b2592acf7d81d19
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 21:09:06 -0700
Commit message:
Commit: f2b3ece1a58789acea1341059b2592acf7d81d19
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 21:09:06 -0700
Commit message:
pairwiseAlignment() and related have moved from Biostrings to pwalign
Package: kmcut
Commit: d777f9a6564f24f110ba4c02e90c377cdd6f404b
Author: unknown <ikuznetsov@albany.edu>
Date: 2024-04-24 23:51:19 -0400
Commit message:
Commit: d777f9a6564f24f110ba4c02e90c377cdd6f404b
Author: unknown <ikuznetsov@albany.edu>
Date: 2024-04-24 23:51:19 -0400
Commit message:
This is completely updated version of the package that addresses all the changes. Detail responses are below. COMMENT: The vignette contains the following line: Introduction to the KMCUT package * but the name of the package is kmcut (all lower-case). R in general, and package names in particular, are case-sensitive. RESPONSE: The package name was changed to lower-case letters. COMMENT: * Man pages have very long titles, each of them made of several sentences that repeat exactly the content of the Description section. Good man page titles should be short (a few words only). RESPONSE: Titles of man pages were shortened. COMMENT: * You seem to misunderstand the purpose of importing other packages in your package. The examples in most man pages start with many library() calls e.g. in kmoptpermcut: library(survival) library(stringr) library(data.table) library(tools) library(pracma) library(foreach) library(doParallel) library(parallel) library(kmcut) * Please note that packages that are imported are automatically available to the code inside your package so there's no need to put the extra burden to manually load each of them on the user. For loading the kmcut package itself, a widely accepted convention is to not pollute the examples in the man pages of a given package (say foo) with explicit calls to library(foo). The reason for this convention is that it is considered reasonable to assume that the package is already loaded when the user is looking at its man pages. RESPONSE: All library() calls in examples were removed. COMMENT: * Please minimize the dependencies of your package and only import what you actually need to import. For example, the package does not seem to use anything from the stringr package so that dependency is not needed. Please re-evaluate all the other dependencies and make sure to drop those that you don't need. RESPONSE: The dependencies onand other unnecessary packages were removed. COMMENT: * Also please re-evaluate the need for all the library() calls at the beginning of the vignette (although keeping library(kmcut) is fine there and is actually needed). RESPONSE: All library() calls at the beginning of the vignette were removed, except for library(kmcut) COMMENT: * Bioconductor recommend against the use of flatcase style for your function names (e.g. kmoptpermcut, transposetable, kmqcut, kmucut, etc...), as it makes the names hard to read and/or remember. Please use snake_case or camelCase instead. RESPONSE: All function names were changed to include underscores (as in snake_case ) COMMENT: * About the file with gene expression-like features. The vignette says: "The first column must contain sample identifiers and and the first row must contain gene identifiers." Isn't it the otherway around? RESPONSE: You are correct. This error was fixed. COMMENT: * The kmoptpermcut() function is extremely slow, to a point that seems to make it almost unsuitable for real-world data. For example, calling it on the example_genes_295.txt file provided in the package takes 89 sec on my laptop when n_iter is set to 1000. However, the file only contains 2 rows (i.e. 2 genes) and the man page for kmoptpermcut() recommends to set n_iter to 10,000. This means that using the recommended n_iter on a file with 100 genes will take more than 10 hours! RESPONSE: Unfortunately, km_opt_pcut() cannot be made much faster. It estimates the unknown sampling distribution of the test statistics by applying the permutation test, which is very slow. It is recommended that kmoptpermcut be run on at least 16 CPUs (this can be achieved on a low/midrange desktop or high-end laptop). This function is meant to be applied to a relatively small subset of candidate genes identified by the km_opt_scut function. The recommendation regarding application of km_opt_pcut() to a relatively small subset of genes identified by km_opt_scut() was added to the vignette. The size of the package's built-in example dataset was reduced to better reflect the number of samples in a real life dataset. COMMENT: * How useful is the kmoptpermcut() function when called with wpdf=FALSE? In this case, the function will display a series of plot, one after the other, the next one replacing the previous one at a possibly fast pace, with barely enough time for the user to look at them! RESPONSE: When km_opt_pcut() is used with wpdf=FALSE from RStudio or R GUI, after the execution is over, the user can go back and forth through the plots by clicking left and right arrows. The main reason why this option was added is to provide a functionality to embed the graphs during the vignette compilation. COMMENT: * If the goal is to make it as simple as possible for clinical oncologists or other scientists without strong programming skills to use the package, then some improvements on how errors are handled would be welcome. For example, I doubt that the targeted audience will be able to make sense of an error message like this one: > kmoptscut(fname="survival_data_295.txt", sfname="example_genes_295b.txt") Error in order(sdat$sample_id) : argument 1 is not a vector RESPONSE: The check of file existence and other argument checks were added to all functions. COMMENT: Documenting a function argument like this: fname: character vector that specifies the name of the file etc... * without specifying that the character vector must be of length 1 suggests that the character vector could be of arbitrary length. Note that many functions in R that work on character data are vectorized and can handle a character vector of arbitrary length (e.g. tolower() or grepl()) but that doesn't seem to be the case here. Please disambiguate. RESPONSE: This was clarified in the updated version, all man pages now state that file name must be a character vector of length one. COMMENT: * Finally note that coordinating right-censored survival data and gene expression-like features, and keeping them aligned when subsetting the data, is exactly what the SummarizedExperiment container is for. In your case, the SummarizedExperiment object would have the feature ids as rownames and the sample ids as colnames, and the right-censored survival time data would be stored in the colData component of the object. All you would need to do is implement a function that loads the input data in a SummarizedExperiment object e.g. load_kmcut_input(). The function would essentially do something like this: load_kmcut_input <- function(epath, spath) { edat <- read.delim(epath, header = TRUE, stringsAsFactors = FALSE) sdat <- read.delim(spath, header = TRUE, row.names = 1) ... ... some sanity checks about 'edat' and 'sdat' ... assay <- as.matrix(edat[ , -1]) rownames(assay) <- edat[ , 1] coldata <- DataFrame(sdat) SummarizedExperiment(list(expr=assay), colData=coldata) } Typical use: epath <- system.file("extdata", "example_genes_295.txt", package = "kmcut") spath <- system.file("extdata", "survival_data_295.txt", package = "kmcut") kmcut_se <- load_kmcut_input(epath, spath) kmcut_se 12. Then all functions in the package would take such object as input instead of fname and sfname, making them slightly easier to use and avoiding the need to load the same data from disk again and again. Furthermore, the user can now subset the data at will by doing things like kmcut_se["MYH2", c("SEQC_NB002", "SEQC_NB003")] with the guarantee that the right-censored survival data and the gene expression-like data remain aligned at all time, hence avoiding the need of utility functions like extractrows() or extractcolumns(). Every Bioconductor user knows how to perform such basic subsetting operation. This is the true Bioconductor way and it has proven to be a very valuable approach to software design. RESPONSE: All core function were changed to take a SummarizedExperiment object as input. A function that creates SummarizedExperiment objects from two input files, create_se_object(), was also added. </pre> </div> Package: CardinalWorkflows
Commit: b1bfb8147012177dcb3013c82c3b6b30f63c09d7
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 23:48:45 -0400
Commit message:
v1.35.5Package: CardinalWorkflows
Commit: 9592e29305454c76bb2ead990cc1905fda0a1875
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 12:19:16 -0400
Commit message:
add startup messagePackage: svaNUMT
Commit: 03c48947a951f4e594b991eb78bdf46d09e82dcb
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 20:48:02 -0700
Commit message:
pairwiseAlignment() and related have moved from Biostrings to pwalignPackage: GenomicFeatures
Commit: 755b3dfc8347b279be5986a14a9aed8e0b83da1f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 20:34:48 -0700
Commit message:
minor cosmeticPackage: BSgenome
Commit: a1925b59a6ddb038c2e0e9fb101ab1ef6506c48d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 20:33:23 -0700
Commit message:
minor cosmeticPackage: Biostrings
Commit: d9cc6dbe7b5d69998fb9ef404f781bae23942bfa
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 20:31:05 -0700
Commit message:
minor cosmeticPackage: Cardinal
Commit: 6a2edd3b33fdec8212c59ce9bc5d886a8d54cb91
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 23:26:35 -0400
Commit message:
v3.5.4Package: Cardinal
Commit: 897a331f948583e196f348a8727943dde3fc647a
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 22:27:04 -0400
Commit message:
add image3D back againPackage: Cardinal
Commit: f764446047b2b4b707d0bef2035c6fd2d2cc9e0d
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 18:11:04 -0400
Commit message:
add check arg to readMSIData(), add is3D method againPackage: Cardinal
Commit: 016548d5552e447f8e42d63f5df485b91fada283
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 14:33:23 -0400
Commit message:
fix removing position columns with coord()<-Package: Cardinal
Commit: c65c45fb518ffc1e7c085d24f89b90a28a87542c
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 14:08:18 -0400
Commit message:
fix deprecated functionality for iData()Package: Cardinal
Commit: cda4f817b69f240d259c1c1b822a8aa5ffae9ea7
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 13:59:45 -0400
Commit message:
export vizi_style() + vizi_engine(); rearrange some docsPackage: Cardinal
Commit: 0e732ecac6bbcb6bc2261d11e157da85c156297a
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-23 20:59:43 -0400
Commit message:
fix pls coef plotting; update gitignorePackage: LinTInd
Commit: c6348376cdd8db9c0147c29c82ef8db90758768d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 20:22:08 -0700
Commit message:
pairwiseAlignment() and related have moved from Biostrings to pwalignPackage: matter
Commit: e56f72cc327446ce750bfa43910284577c7be61e
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 23:00:15 -0400
Commit message:
v2.5.18Package: matter
Commit: faab5e97b9ce2a7d71c8be911aa03e7322f4e6a8
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 22:26:33 -0400
Commit message:
fix plotly error on non-gridded voxelsPackage: matter
Commit: be1e2dc4db28c825c9471df3eef2ca7995097360
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 20:47:20 -0400
Commit message:
update NEWS w/ plot_image 3d supportPackage: matter
Commit: 5347ef8429f5290e508dfa043d3526153de4d14e
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 20:42:00 -0400
Commit message:
add 3d support to plot_image()Package: matter
Commit: e5f8fb00e30f5fe10e060ef28690d86501155bd2
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 18:34:06 -0400
Commit message:
change parse_formula eval defaultPackage: matter
Commit: 842476fb74ef07f956b9cedd7b80ef6e3f70852c
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 18:24:34 -0400
Commit message:
update NEWS re: parse_formula()Package: matter
Commit: 55dcb6a99bdc192779b66118e99c11c12dbd2ed0
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 18:22:45 -0400
Commit message:
export parse_formula()Package: matter
Commit: aaf2cb7d77d9bd80f8997742bd5bf41069c9846c
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 12:51:41 -0400
Commit message:
add vizi_engine()Package: matter
Commit: 8bec4ea2bdd2853d0b651df5b62ba23e2f00d089
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-23 23:33:17 -0400
Commit message:
cleanup aspect ratioPackage: matter
Commit: 9869773e4d2a682104319be799980471ae257919
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-23 23:08:54 -0400
Commit message:
cleanup plot_init and friends; fix free facet axes for plotlyPackage: matter
Commit: 81597937e13be62f95ad8c1c07b1d793a82fe6dc
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-23 22:36:22 -0400
Commit message:
fix aspect ratio for plotlyPackage: matter
Commit: 41180b91ca64995e69d9bc17876a6aedc115eac4
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-23 22:13:42 -0400
Commit message:
fix facet plot initialization for plotlyPackage: matter
Commit: 20c71cc6f40f63c05942f6db6f66f20fc2180132
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-23 21:49:38 -0400
Commit message:
fix reversed axes for plotlyPackage: matter
Commit: b1056cd19130802fe9690664294b5d89305778b7
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-23 21:23:43 -0400
Commit message:
fix bug in flooring x-axis for mark=peakPackage: matter
Commit: 7fa4599b09cb84f81e875cd81802dd567d862c63
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-23 20:51:35 -0400
Commit message:
fix bugs in pixels channelsPackage: matter
Commit: 3210959700cc66cdf819511251df694abc558497
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-23 20:37:39 -0400
Commit message:
cleanup NAMESPACEPackage: matter
Commit: ac8343d7c579348fe5e1ed727b2ac1ab2caeccee
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-23 20:34:39 -0400
Commit message:
finish up 1st draft plotly supportPackage: matter
Commit: 8f87381e3cb1d14234defd949327abc4ec6aa3d7
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-23 17:32:13 -0400
Commit message:
update plotly support for legendsPackage: matter
Commit: bdca4767e1dd6aaea46197e87273aca810d22dc5
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-22 17:43:15 -0400
Commit message:
added mark vizi_barsPackage: matter
Commit: ca2e8eeae2f5502ffc1a91aff9cd26e6637eb994
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-21 16:53:08 -0400
Commit message:
add vizi engine=plotly supportPackage: IsoformSwitchAnalyzeR
Commit: bd680e93c87f1778af432ac250d8c4b7e16860b9
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 19:22:58 -0700
Commit message:
Add 2 missing symbols to NAMESPACE Many many more are missing as reported by 'R CMD check' under "Undefined global functions or variables". See for example CHECK result on Bioconductor daily report: https://bioconductor.org/checkResults/3.19/bioc-LATEST/IsoformSwitchAnalyzeR Note that this is unrelated to the move of pairwiseAlignment() to the new pwalign package (previous commit).Package: SCArray.sat
Commit: e3c68e5ff4ccd85d5fcb786b22924ea8c5ace72e
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2024-04-24 21:27:47 -0500
Commit message:
update for Seurat v5Package: IsoformSwitchAnalyzeR
Commit: 4c35fe8431c65942402f6494d60a0ca8493c3319
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 19:11:45 -0700
Commit message:
pairwiseAlignment() has moved from Biostrings to pwalignPackage: SPLINTER
Commit: 2aade96cb831ce64901e9d6bc1a9a79602fc6c3c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-24 16:05:00 -0700
Commit message:
pairwiseAlignment() and related have moved from Biostrings to pwalignPackage: RTCGAToolbox
Commit: 4420e7ae0852afd3b3722730c11c54f1293e3152
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 19:05:47 -0400
Commit message:
version bump 2.33.3Package: RTCGAToolbox
Commit: 185354d884067ec75aaa004b17e93ddea8e254ec
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 19:05:45 -0400
Commit message:
update NEWS filePackage: BiocHubsShiny
Commit: a2353e2b2139bd2ba223422c5e57c851f8dbc1e2
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 17:56:10 -0400
Commit message:
version bump 1.3.1Package: BiocHubsShiny
Commit: e788b358db99ec4015200ce8afd900f8eec876e4
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 17:56:03 -0400
Commit message:
update NEWS filePackage: TENxIO
Commit: 30b79e52886101801e12939ae2261654a9509276
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 17:51:10 -0400
Commit message:
version bump 1.5.4Package: TENxIO
Commit: feb03d484960a651d71de8ddce7d327bc5256552
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 17:51:09 -0400
Commit message:
update NEWS filePackage: pwalign
Commit: b6da850610afe7c8201131a3738fabbd0b8277d2
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-22 22:22:07 -0700
Commit message:
small tweaksPackage: BiocBaseUtils
Commit: c5278d3d8b6ea63e96ce86b9fcf5588b46fc9b80
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 17:38:39 -0400
Commit message:
version bump 1.5.2Package: BiocBaseUtils
Commit: 75e7a008dad940354493f6bc37d4043c1002c1e9
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 17:38:31 -0400
Commit message:
update NEWSPackage: BiocBaseUtils
Commit: 9d877ee6e7cde9d8c612f83c1651a4bfd62e0ada
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 17:28:26 -0400
Commit message:
add checkInstalled functionPackage: CardinalIO
Commit: 6f5fbb25ec9513600a9d8bc0f150aa8caea545f9
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-04-24 17:25:31 -0400
Commit message:
v1.1.6 fix error if extraArrays not foundPackage: OmnipathR
Commit: 442b9cf43368e72c6915878654bd9b80be2f0141
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-24 23:18:30 +0200
Commit message:
Bump version: 3.11.13 → 3.11.14Package: OmnipathR
Commit: 6e8f2ce899b9ed5767af40580896f0e7f36a57b8
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-24 23:18:25 +0200
Commit message:
namespace updatePackage: OmnipathR
Commit: e05841c293e7b12956757b52f97605ffcf29dc85
Author: deeenes <turei.denes@gmail.com>
Date: 2024-01-16 13:34:04 +0100
Commit message:
`misc`: some more operator and formatting routinesPackage: OmnipathR
Commit: 38893e92422297e74395e0afc27214d4b6a92afc
Author: deeenes <turei.denes@gmail.com>
Date: 2024-01-24 02:12:11 +0100
Commit message:
`for_organism`: fixed: custom mapping erased the resultPackage: OmnipathR
Commit: b25bd513fbf8c98d35d3a6908432f0b35729a745
Author: deeenes <turei.denes@gmail.com>
Date: 2024-01-19 12:53:53 +0100
Commit message:
`misc`: `maybe_call`, `maybe_get`: clean wrappers around `get` optionally calling a funcPackage: OmnipathR
Commit: 8efe882a3bcc58444ad9b6611fcdc172fd36ef7b
Author: deeenes <turei.denes@gmail.com>
Date: 2024-01-19 12:52:43 +0100
Commit message:
read built-in organism support data into pkg env on loadPackage: OmnipathR
Commit: 22dafedc289105917a65a1f8f636daa939ca963d
Author: deeenes <turei.denes@gmail.com>
Date: 2024-01-18 01:19:19 +0100
Commit message:
use `read_yaml` instead of `yaml.load_file`Package: OmnipathR
Commit: e35ff45eab2ef61e4d248ad9e8f4efac776c523e
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-24 23:15:32 +0200
Commit message:
namespace update with `organism_for`Package: OmnipathR
Commit: 53ef0c5f024b4f7a1149db1792183d74d5529e8c
Author: deeenes <turei.denes@gmail.com>
Date: 2024-01-18 01:18:31 +0100
Commit message:
`taxonomy`: `organism_for` - access organism support of resourcesPackage: OmnipathR
Commit: 6d0a0ced5356b17c8924da652f2a54b1d9cfc3f5
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-24 23:08:36 +0200
Commit message:
`oma`: URL encode ID types for query stringPackage: OmnipathR
Commit: 444b78d5f1bc8dcc7c9fd5d8f5ba5696dc20755f
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-24 23:08:16 +0200
Commit message:
`oma`: error handling for incorrect ID types in query string (that results less columns than expected)Package: OmnipathR
Commit: 83f2cf1ab1c1f418ab2df911f6bf023c0b8e2541
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-24 23:07:11 +0200
Commit message:
`oma`: updated reader parameters for new TSV layoutPackage: OmnipathR
Commit: 76b66ab93810b1e1a5b262804631f56bcedb5f42
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-24 23:06:22 +0200
Commit message:
`oma`: `oma_pairwise_translated`: generic function for all ID types that OMA does not providePackage: OmnipathR
Commit: 59358703ab6e8308adbe095f1e7cea589f9a428a
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-24 23:04:03 +0200
Commit message:
`oma`: use `organism_for`Package: OmnipathR
Commit: 78faa6ba2ebcacb7b6ef8b15b39ab9d74af8d98e
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-24 23:02:00 +0200
Commit message:
`oma`: organism configPackage: OmnipathR
Commit: d2d8874aae758294b146f4697f5745534c52b867
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-24 23:00:09 +0200
Commit message:
`oma`: updated API URLPackage: OmnipathR
Commit: 29f02990a335082f6e1841a4c8a5e15c26e7f983
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-24 22:47:05 +0200
Commit message:
`oma`: fixed ID type codesPackage: OmnipathR
Commit: ba8fab39f56c1a6c72c9f295b9a8e1b3e9dc79a7
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-24 22:39:34 +0200
Commit message:
`oma`: function to list all the OMA organism codesPackage: OmnipathR
Commit: 83cb658b2b7cc120a7933c0b18b406c732b8b728
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-13 11:44:04 +0200
Commit message:
docs updatePackage: OmnipathR
Commit: c379027ed9f494a24e6b3d28b653f1b4b919d4ce
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-13 11:39:12 +0200
Commit message:
pkgdown site rebuildPackage: OmnipathR
Commit: 440e99037a97bafbd2562e17b586010acebd82aa
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-12 03:49:06 +0200
Commit message:
Bump version: 3.11.12 → 3.11.13Package: OmnipathR
Commit: b75ed2297e70bbe9a465337470b7a8e10c80a305
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-12 03:48:59 +0200
Commit message:
docs rebuildPackage: OmnipathR
Commit: de31b50f3dc8741a60c40d27881ade6f2b51a973
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-12 03:48:05 +0200
Commit message:
function for resource name matching (primary, secondary)Package: OmnipathR
Commit: e1dbcee625ca0ae4690a0b2bd65e3d4468e8b398
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-12 03:47:32 +0200
Commit message:
`only_from`: fixed: do not insert resource prefix in case of zero referencesPackage: OmnipathR
Commit: 94a40e6b619757d0c6e388ff7f286424a3f1a678
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-12 03:46:45 +0200
Commit message:
`from_evidences`: function for resource name constructionPackage: OmnipathR
Commit: b9a3402285343c1f67f3170fbcc38a0fd126521f
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-12 01:21:11 +0200
Commit message:
`only_from`: remove records that remained without any evidence after filtering (no idea how this happened before bc I have not encountered such records until now)Package: OmnipathR
Commit: c61403ac5408fa92715b007374fcfd6d77dd39c8
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-12 01:18:04 +0200
Commit message:
`exclude` and `.keep` parameters for `only_from` (`filter_evidences`): exclude certain resources; keep and update the "evidences" columnsPackage: OmnipathR
Commit: 6ffb09fd26b4631b1598dafa9718e7c99eb35522
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-12 01:14:31 +0200
Commit message:
`evidences_from`: updating "evidences" column in `only_for`Package: OmnipathR
Commit: f802029810dbd0268be57b44155e2b00fe11cb16
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-12 01:12:32 +0200
Commit message:
`match_evidence`: moved evidence matching into function (for evidence filtering)Package: OmnipathR
Commit: bec3d0b930056fbcc6f231e26af03954217dc99b
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-10 13:53:03 +0200
Commit message:
Bump version: 3.11.11 → 3.11.12Package: OmnipathR
Commit: 308e9e9e9519fec433ffb108a56b09a6decd2227
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-10 13:52:55 +0200
Commit message:
docs+pkgdown rebuildPackage: OmnipathR
Commit: 7189357b363345e36153267b34464551da8c2670
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-10 13:52:17 +0200
Commit message:
missing importPackage: OmnipathR
Commit: dd31d1a714e2dfad3dcb78034d496d5325487ff3
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-10 13:51:53 +0200
Commit message:
`resources_in`: collect resources from a data frame columnPackage: OmnipathR
Commit: c7d361426fea6de02c9b48a4d7225f8b6607d899
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-10 13:48:36 +0200
Commit message:
`misc`: new helper function to unlist, unique and sort anythingPackage: OmnipathR
Commit: 6305befd5585771a594c11e8b6f333cd606a2cca
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-09 18:14:16 +0200
Commit message:
Bump version: 3.11.10 → 3.11.11Package: OmnipathR
Commit: 9437af175889ecefdd0ad093917aca664e08e4d9
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-09 18:08:28 +0200
Commit message:
`omnipath`: added `keep_evidences` to known parametersPackage: OmnipathR
Commit: 0b864ba3b1a603adb84243fd104b9d69de1b8d37
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-09 17:51:40 +0200
Commit message:
`evidences`: new arg `.keep` for `unnest_evidences` & `only_from`: keep the "evidences" columnPackage: OmnipathR
Commit: 27c39acf65f8ae79ceb605b513a9a29d0d801cbe
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-09 17:49:20 +0200
Commit message:
little style correctionsPackage: OmnipathR
Commit: 1b222ae2eb5ccced71a6e76f66fe26f5659397c3
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-09 17:48:57 +0200
Commit message:
`check_param/post_download`: `keep_evidences` if the evidences field was requested in the callPackage: OmnipathR
Commit: 71a0e9dac75aef2da17bc60a2e25a58109e4de49
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-09 15:57:03 +0200
Commit message:
pkgdown site: missing fontsPackage: OmnipathR
Commit: b95b7f9f7fdcf8fea5c97343a713dd05a1cd7469
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-09 15:54:30 +0200
Commit message:
pkgdown site: missing `font.css`Package: OmnipathR
Commit: d1302c6913045b2b045abbb04e59a21477e146c0
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-09 15:48:53 +0200
Commit message:
pkgdown site bootstrap version updatePackage: OmnipathR
Commit: 5a8e99657c0ff8ab85ff5b213fac960a28728bc0
Author: deeenes <turei.denes@gmail.com>
Date: 2024-04-07 18:00:44 +0200
Commit message:
pkgdown site rebuildPackage: SingleCellMultiModal
Commit: 3156f1ec6757c2e72cb7b8c25b05367acd1799fd
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 16:31:48 -0400
Commit message:
version bump 1.15.1Package: SingleCellMultiModal
Commit: 47da2f18039f78125d35618885a9eb37542121dd
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 16:31:44 -0400
Commit message:
update NEWSPackage: TCGAutils
Commit: 3c6f903569c91a1231394b863bcdd10185091a8a
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 16:28:59 -0400
Commit message:
version bump 1.23.5Package: TCGAutils
Commit: d40070f096a3607944fe39461231fd25ae99903e
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 16:28:56 -0400
Commit message:
update NEWSPackage: RaggedExperiment
Commit: 33a664778997a89406ebd260d3c43503394fe0b4
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 16:08:42 -0400
Commit message:
version bump 1.27.2Package: RaggedExperiment
Commit: 32cc4590a3555cc026c371b3e0bbcb34984bec2d
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 16:08:37 -0400
Commit message:
update NEWS filePackage: PureCN
Commit: e2de63642828324c6261b798de89e813e91f2e08
Author: Markus Riester <markus.riester@novartis.com>
Date: 2024-04-24 15:17:15 -0400
Commit message:
Version bump.Package: PureCN
Commit: 0edcd4dda56a384400e656a33e7916ee792d0e2a
Author: Markus Riester <markus.riester@novartis.com>
Date: 2024-04-24 15:15:01 -0400
Commit message:
Merge pull request #366 from lima1/issue_40 Issue 40Package: PureCN
Commit: 354413cc04eac7854b4ad4e8da0682203f6ce9aa
Author: Markus Riester <markus.riester@novartis.com>
Date: 2024-04-24 15:13:23 -0400
Commit message:
Merge pull request #365 from lima1/issue_363 Issue 363Package: PureCN
Commit: 37f0097a34030cd46a9c98d484a9700d57ce4a24
Author: Markus Riester <markus.riester@novartis.com>
Date: 2024-04-24 14:47:05 -0400
Commit message:
Attempt in fixing #363.Package: PureCN
Commit: 822e4df325df61cf5bdd67478e660455ab385fa1
Author: Markus Riester <markus.riester@novartis.com>
Date: 2024-04-24 14:43:56 -0400
Commit message:
Attempt in fixing #363.Package: PureCN
Commit: 5ec2226363f7e29b5886a87a5a32deb2a51fba88
Author: Markus Riester <markus.riester@novartis.com>
Date: 2024-04-01 11:39:12 -0400
Commit message:
Changed default of min.ratio to cleaner -8.Package: PureCN
Commit: daf175bf1f3df9f06274d98a9e8c9e7b627826be
Author: Markus Riester <markus.riester@novartis.com>
Date: 2024-03-31 17:02:36 -0400
Commit message:
Fix broken test.Package: PureCN
Commit: 5169999d03b10c9715039bd842b42bea73cef526
Author: Markus Riester <markus.riester@novartis.com>
Date: 2024-03-31 16:38:37 -0400
Commit message:
Attempt in a resolution for #40.Package: cBioPortalData
Commit: 5838dd37d0dbd87f933ff2d5254aa4a9718a92ae
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 15:58:07 -0400
Commit message:
version bump 2.15.5Package: cBioPortalData
Commit: 18136ee61e72096a277215df73325addbcac712b
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 15:58:02 -0400
Commit message:
update NEWS filePackage: MSstatsPTM
Commit: 804a856c6b5acac4db6842beb7826462704ee0fc
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2024-04-24 15:57:43 -0400
Commit message:
version bumpPackage: MSstatsPTM
Commit: 03c79cc7c829366fea418a672a47dd59b2ba9c37
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-04-17 16:05:52 -0400
Commit message:
version bumpPackage: MSstatsPTM
Commit: 529334959fb0e8f7039c322f9d7d4bac7480a248
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-04-17 16:04:14 -0400
Commit message:
feat(metamorpheus): Add global profiling feature to Metamorpheus PTM converter (#87) * feat(metamorpheus): Add global profiling feature to Metamorpheus PTM converter * add news on metamorpheus converter * added more unit testsPackage: MSstatsPTM
Commit: ad8cc8095d4702df3b844f983e171d44402a60a2
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-03-04 09:58:50 -0500
Commit message:
version bumpPackage: MSstatsPTM
Commit: 7ff61cd341c98863345a84babd7f7cc6ca00c5c6
Author: tonywu1999 <ant.wu@northeastern.edu>
Date: 2024-03-04 09:58:20 -0500
Commit message:
feat(metamorpheus-converter): Create converter for Metamorpheus to MSstatsPTM format (#86) * feat(metamorpheus-converter): Create converter for Metamorpheus to MSstatsPTM format * fix: For ptm_input, filter out rows without targeted ptmPackage: MSstatsPTM
Commit: fc90cfadb4170f7433a6297ea7867862154efdc1
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2024-02-14 15:00:51 -0500
Commit message:
Merge pull request #85 from Vitek-Lab/devel bug fixPackage: MSstatsPTM
Commit: 81da1b02f773a3b2b471c874bb53c81c80ea0ba7
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2024-02-14 14:59:13 -0500
Commit message:
bug fixPackage: MSstatsPTM
Commit: 1c871e05ea28a844358775c3caca1428ccd48868
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2024-02-13 09:05:17 -0500
Commit message:
Merge branch 'RELEASE_3_18' into masterPackage: MSstatsPTM
Commit: 8378cced13cbb48c9e24d2535dbbb580c0984cc6
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2024-02-13 09:04:41 -0500
Commit message:
Merge pull request #83 from Vitek-Lab/devel DevelPackage: MSstatsPTM
Commit: 3e423f0dec1439aa86cd25b12e911d1eecac1653
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2024-02-04 11:26:17 +0200
Commit message:
version bumpPackage: MSstatsPTM
Commit: d6277b3dd9a233620169602bc97b118812faaeed
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2024-02-04 11:26:00 +0200
Commit message:
version bumpPackage: MSstatsPTM
Commit: a89750191ab0d44904be3170d8207dfddfcfc1ed
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2024-02-04 04:25:01 -0500
Commit message:
Merge pull request #82 from Vitek-Lab/master PD bug fixPackage: MSstatsPTM
Commit: f65db0aaf3cf59587a5105fa66fab2733b63a7e2
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2024-01-31 14:43:13 -0500
Commit message:
remove model filePackage: MSstatsPTM
Commit: 9678ad1b046ea04b305dbe06e0182f63e0deece6
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2024-01-31 14:40:58 -0500
Commit message:
version bumpPackage: MSstatsPTM
Commit: b16eea1632d4ad0966b09894d6c937c15da67d11
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2024-01-31 14:40:34 -0500
Commit message:
Merge pull request #80 from Vitek-Lab/master skyline bugPackage: cBioPortalData
Commit: a6fba305b31b5c86b8ed728672a37ec762ce37e2
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 15:56:28 -0400
Commit message:
version bump 2.15.4Package: cBioPortalData
Commit: 01fe589283a614b1e538e771a7addfa763455732
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 15:56:18 -0400
Commit message:
use package name in CITATIONPackage: cBioPortalData
Commit: 1356109249899cbabdc0c5812bdc92745e3b14cb
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 15:52:32 -0400
Commit message:
update roxygenPackage: cBioPortalData
Commit: f4b327179a11761637ef5d09fd65c5c20f3ac2cc
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 15:52:22 -0400
Commit message:
avoid partial arg match warningPackage: MultiAssayExperiment
Commit: 8ed6e47ba6602df656fe8084a45df41f111863eb
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 15:41:54 -0400
Commit message:
version bump 1.29.2Package: MultiAssayExperiment
Commit: cbec5787d0d1a52357b1dcde71c80806755b9bf4
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 15:40:17 -0400
Commit message:
update NEWS filePackage: MultiAssayExperiment
Commit: dbe61a1dcb972be3e4c81b0efa6e16d68785a098
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-04-24 15:40:02 -0400
Commit message:
update formatting in inst/REFERENCES.bibPackage: MSstatsTMT
Commit: 5c8b9e79093e9555a191b34505b4b2e7be390de2
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2024-04-24 15:32:13 -0400
Commit message:
fix news filePackage: MSstatsTMT
Commit: cb5070d5b21b1af43301e5b4cf689a8f5344a2ef
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2024-04-24 15:30:56 -0400
Commit message:
removed dup news filePackage: MSstatsTMT
Commit: d811d000e740cc472e9473cbfbf0eee9b549af24
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2024-04-24 15:30:21 -0400
Commit message:
Delete inst/NEWS.rdPackage: rtracklayer
Commit: 843c950c4f6c1ae09d022dbb16e0b488bc8f37c7
Author: Michael Lawrence <michafla@gene.com>
Date: 2024-04-24 11:45:34 -0700
Commit message:
Merge pull request #118 from hpages/master Fix linking error on Windows/Rtools44Package: rtracklayer
Commit: f70856a67e3e77ce2ee5189f76b59b922f58cd6b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-21 10:45:40 -0700
Commit message:
Fix linking error on Windows/Rtools44Package: extraChIPs
Commit: b317aa9500d182d00cf7acca7889e72b0d5049f6
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-04-25 02:30:06 +0930
Commit message:
Bugfix in mergeByHMPPackage: epiregulon
Commit: e8b6e4e55b75c34ee4ca4eca5de9f2bc9f4987b4
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2024-04-24 09:34:49 -0700
Commit message:
0.99.21Package: epiregulon.extra
Commit: 1aa00b24a4c3334fe2bcddfcdb56b40a4179c7f4
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2024-04-24 08:31:07 -0700
Commit message:
0.99.17Package: epiregulon.extra
Commit: c46c43cdfcda64af94305b0d6b41ae0498b27ad6
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2024-04-24 08:26:01 -0700
Commit message:
0.99.17Package: epiregulon.extra
Commit: 049e0d0d2299c7e5d26d459944c635cdae6688e1
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2024-04-24 08:25:15 -0700
Commit message:
update newsPackage: epiregulon.extra
Commit: 77bedde1dcdc7d9d4bdc81475490c002a43f488e
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2024-04-24 08:19:05 -0700
Commit message:
0.99.16Package: epiregulon.extra
Commit: 556bc30332cf28683570092d4c15ef5598117cfd
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2024-04-24 08:18:37 -0700
Commit message:
BioC second view update news and NAMESPACEPackage: epiregulon.extra
Commit: bbee48b9bd542cf4a238df3a6e3d30fb4fc201ef
Author: Tomasz Wlodarczyk <tomwlo@gmail.com>
Date: 2024-04-24 08:28:14 -0700
Commit message:
v0.99.16Package: epiregulon.extra
Commit: de31ff1b88ab37d559a63129ac610275b242c0f5
Author: Tomasz Wlodarczyk <tomwlo@gmail.com>
Date: 2024-04-24 07:42:04 -0700
Commit message:
Merge branch 'devel' of git.bioconductor.org:packages/epiregulon.extra into develPackage: epiregulon.extra
Commit: fef941f9ce43fd014e29f0c837bf888d940e2bca
Author: Tomasz Wlodarczyk <tomwlo@gmail.com>
Date: 2024-04-24 07:41:10 -0700
Commit message:
v0.99.15Package: epiregulon.extra
Commit: f74a20256bbb431002f81a489b9d80437533d4ec
Author: Tomasz Wlodarczyk <tomwlo@gmail.com>
Date: 2024-04-24 07:40:42 -0700
Commit message:
NEWS updatePackage: autonomics
Commit: 092dbef5a333a39e16aa6457bde4d172d795dd79
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-04-24 16:40:12 +0200
Commit message:
1.11.108 : create `fix_xlgenes`Package: ENmix
Commit: b71062e45764d4bccc297ce7f2a53f4f9762c082
Author: Zongli Xu <xuz@niehs.nih.gov>
Date: 2024-04-24 10:40:27 -0400
Commit message:
bugfix Signed-off-by: Zongli Xu <xuz@niehs.nih.gov>Package: zitools
Commit: 5f45d497ccbf72259c0d37c386d7035b17000471
Author: cmeyring <122982530+cmeyring@users.noreply.github.com>
Date: 2024-04-24 16:21:43 +0200
Commit message:
Merge pull request #2 from kreutz-lab/devel DevelPackage: zitools
Commit: 33975f77ad062af7941c0154dcc9282cad181eb1
Author: cmeyring <122982530+cmeyring@users.noreply.github.com>
Date: 2024-04-24 16:19:37 +0200
Commit message:
Merge branch 'main' into develPackage: zitools
Commit: d3dcc636f73541f8a90d527f34be3a832fb358bc
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-24 16:13:37 +0200
Commit message:
Merge branch 'devel' of https://github.com/kreutz-lab/zitools into develPackage: zitools
Commit: 0375ab1fb80a57300ceb18b54d6ab9327c9618f3
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-24 16:13:20 +0200
Commit message:
Updated README.mdPackage: MungeSumstats
Commit: 16afb54bd60847003b45235287999200b40a272d
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2024-04-24 15:17:29 +0100
Commit message:
enable local chain filesPackage: mia
Commit: 9c1902ee4c712f6a136ed41ff72bc89687af39a1
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-04-24 16:46:20 +0300
Commit message:
importMetaphlan: bugfixes (#530)Package: mia
Commit: 88947bba18ceba799589faa3d9870b7675ca952d
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-04-24 16:20:40 +0300
Commit message:
Deprecate functions *_join (#515)Package: mia
Commit: 1ab099804e92c7a41f8dfabc7c2f2a4c4cbbe2c9
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-04-24 15:59:25 +0300
Commit message:
correct typo 'importBiom' to 'importBIOM' (#525) Co-authored-by: Leo Lahti <leo.lahti@iki.fi>Package: mia
Commit: 1b84bc52016b62041c275a24127d78219fc73a30
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-04-19 16:36:57 +0300
Commit message:
deprecate subset* functions (#518)Package: mia
Commit: 58cc49bd118ff2b75d12b2eca006cfd48c307933
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-04-18 10:30:43 +0300
Commit message:
Revert "Issue 334 estimate diversity" (#516)Package: mia
Commit: c96a4e5d31362e3aa8abbb359110f7f099cff7dd
Author: nmdegunst <74536546+Insaynoah@users.noreply.github.com>
Date: 2024-04-17 10:19:22 +0300
Commit message:
Issue 334 estimate diversity (#514)Package: mia
Commit: f0d3436b7df37cddd1193967644ede26cdd19f76
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-04-16 15:47:51 +0300
Commit message:
Explain difference between phylogenetic and hierarchy trees (#510)Package: mia
Commit: b7dd1c27318731d5cc5042695d35ae657816d086
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-04-15 15:05:40 +0300
Commit message:
rename importers to standardize "import" terminology (#505) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>Package: epiregulon
Commit: be942f92d7e1e446f0f09c56d8aa3faf86d1b637
Author: TomVuod <tomwlo@gmail.com>
Date: 2024-04-24 06:31:01 -0700
Commit message:
news updatePackage: epiregulon
Commit: bcef194ccc0d242cf4fc9e62aa4d051eca2cc58e
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2024-04-22 21:25:50 -0700
Commit message:
edit vignettePackage: scaeData
Commit: 064c3c76baa5da2f4b9843386ea6ec4ab5f43bcf
Author: Ahmad Al Ajami <ahmad.alajami@kgu.de>
Date: 2024-04-24 15:08:00 +0200
Commit message:
fixed a typo in the lookup table of pbmc 5k dataset; version bump triggeredPackage: methodical
Commit: 5e6d3a23270abdfbb9a725184713e5b39d7dfae7
Author: richardheery <richardheery@gmail.com>
Date: 2024-04-24 14:44:31 +0200
Commit message:
Bumped versionPackage: atena
Commit: e814a13d541840de228930a6dcdb8cd154cced5e
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-04-24 13:54:58 +0200
Commit message:
Reduced execution time in some of the examplesPackage: zitools
Commit: 859a17096bdc3bcecef4ebe296b4a845ae6ffc32
Author: cmeyring <122982530+cmeyring@users.noreply.github.com>
Date: 2024-04-24 13:25:37 +0200
Commit message:
Update DESCRIPTIONPackage: zitools
Commit: 02a2cc453a567b253307b95d25c4014c0cbb0b03
Author: cmeyring <122982530+cmeyring@users.noreply.github.com>
Date: 2024-04-24 13:21:27 +0200
Commit message:
Merge pull request #1 from kreutz-lab/devel DevelPackage: zitools
Commit: 0d3ac13d07890743ee28a81a1f6a56e6f68ee675
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-24 12:56:47 +0200
Commit message:
update DESCRIPTION and Version NumberPackage: MungeSumstats
Commit: bf83eaacc908c0913dbb945cfc42055156d11206
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2024-04-24 11:21:11 +0100
Commit message:
drop miss dat select colsPackage: MungeSumstats
Commit: 588a898fd64cf3e3ae4134c7729667c960038b25
Author: Alan Murphy <62257358+Al-Murphy@users.noreply.github.com>
Date: 2024-04-24 10:19:49 +0100
Commit message:
Merge pull request #182 from rmgpanw/dev_check_missing_data_cols add `drop_na_cols` parameter to `format_sumstats()`Package: MungeSumstats
Commit: b88a70dcf44378c267972c238bf63f1c9012e18e
Author: rmgpanw <alasdair.warwick06@gmail.com>
Date: 2024-04-22 22:47:32 +0100
Commit message:
add `drop_na_cols` parameter to `format_sumstats()` and `check_miss_data()`Package: tripr
Commit: df7ee2395eb83e3ff432372a7f20769adaafb1bc
Author: KonstantinosKardamiliotis <k.kardamiliotis@gmail.com>
Date: 2024-04-24 11:38:57 +0300
Commit message:
Bioconductor 3.19 release commitPackage: fenr
Commit: 104b0d4ae30e83255a4be0355b46d1d425e6b26e
Author: Marek Gierlinski <Marek.Gierlinski@gmail.com>
Date: 2024-04-24 09:15:02 +0100
Commit message:
Version 1.0.8. Improving error handlingPackage: cleaver
Commit: a85947b60d7b846a5ca95f3979908b5439fa7ae6
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2024-04-24 10:15:30 +0200
Commit message:
ci: upgrade to biocthis::use_bioc_github_action('devel')Package: cleaver
Commit: 5f02afa33a2b2aabb0cc1998d11abe861a202021
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2024-04-24 09:57:59 +0200
Commit message:
chore: bump versionPackage: cleaver
Commit: c5b3b798847bb58b269da49fb7850fe93e3a288c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2024-04-24 09:57:48 +0200
Commit message:
fix: use along.with instead of along to avoid partial matchingPackage: cleaver
Commit: c2db5c2776ae4e82b29f049b6b754b0a430979de
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2024-04-24 09:56:55 +0200
Commit message:
feat: add trypsin-{high,low,simple}Package: SFEData
Commit: 63324c09ad8c6393fe382b197013d2c1117782f9
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2024-04-24 01:07:53 -0700
Commit message:
Added note on raw bytes in XeniumOutputPackage: SFEData
Commit: cf613beee8aaac7a72a228838be94e3805debd9e
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2024-04-24 01:04:22 -0700
Commit message:
Made XOA v2 data subset. Cropping the multi file OME-TIFF was the worst pain in the ass.Package: SFEData
Commit: 9bf639c9154186bdfc1ad178f805b0f8d31830c9
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2024-04-23 18:10:25 -0700
Commit message:
Added Seurat test dataPackage: zitools
Commit: eec747685335757efb0281bfc130aa7dff38b81f
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-24 09:44:49 +0200
Commit message:
Update News FilePackage: zitools
Commit: 0e1aa28728d066775c8cc1692d6fe7211c478417
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-24 09:18:59 +0200
Commit message:
Update NEWS FilePackage: atena
Commit: ad226bc0b12ec6b4aa938aa3a59bad03ba2ba614
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-04-24 09:12:58 +0200
Commit message:
Updated vignette, added progress reporting messagesPackage: dar
Commit: d86de14543ad38aa8fcbe749ae0fe9a11ab020ef
Author: xec-cm <fcatala@irsicaixa.es>
Date: 2024-04-24 08:28:11 +0200
Commit message:
bumpPackage: dar
Commit: 29a3d4adc846ef559a3d41aefd3d2053219a3e2a
Author: xec-cm <fcatala@irsicaixa.es>
Date: 2024-04-24 08:26:53 +0200
Commit message:
Update data_import.RmdPackage: amplican
Commit: b6cdef124c10cdb9b1eca5baebcc5fbccdbf14d5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 22:40:12 -0700
Commit message:
import coverage from IRangesPackage: amplican
Commit: 1389265bbdd6362fe075efa9ec2358bc73fbb995
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 22:34:34 -0700
Commit message:
pairwiseAlignment() and related have moved from Biostring to pwalignPackage: ClassifyR
Commit: beae92285cd98ea487eb5337f71356d4b83ad4b2
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2024-04-24 15:25:36 +1000
Commit message:
- News file updated in preparation for next Bioconductor release.Package: Rcpi
Commit: 6bd4a59c378da46c1e9c6ce59ca3b0ed16b49838
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 21:59:03 -0700
Commit message:
pairwiseAlignment() has moved from Biostrings to pwalignPackage: QuartPAC
Commit: ab5838bf15eeb726a428c2b89afc07f3587aa2ef
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 21:45:33 -0700
Commit message:
pairwiseAlignment() has moved from Biostrings to pwalignPackage: GUIDEseq
Commit: 27314e39213fb51ed312f31cb7d26523224bfe4b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 21:08:55 -0700
Commit message:
pairwiseAlignment() and related have moved from Biostrings to pwalignPackage: girafe
Commit: 7fd255495078c36e9b6a1a5c8c8fcef491c3fd9a
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 20:46:26 -0700
Commit message:
pairwiseAlignment() has moved from Biostrings to pwalignPackage: IMMAN
Commit: 298baab116ffae96e3963dd501ceddd68f9a45bf
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 19:51:55 -0700
Commit message:
pairwiseAlignment() has moved from Biostrings to pwalignPackage: QSutils
Commit: a2ba66be100df1a2dd8a52d422bb1ca1c32d221c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 19:45:18 -0700
Commit message:
pairwiseAlignment() has moved from Biostrings to pwalignPackage: methylscaper
Commit: e3b95d38d37d250607520b951734e275b886d344
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 19:34:25 -0700
Commit message:
pairwiseAlignment() and related have moved from Biostrings to pwalignPackage: DMRcate
Commit: 3bfb7c55412ff594c79f38ab78af7028261bfed1
Author: timpet <t.peters@garvan.org.au>
Date: 2024-04-24 12:25:00 +1000
Commit message:
DMRcate_2.99.6Package: sangerseqR
Commit: a3fbf6b28fdf531b774a2b42dda6c0285d05063c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 19:22:11 -0700
Commit message:
pairwiseAlignment() has moved from Biostrings to pwalignPackage: BioNAR
Commit: 14ae53f85bada21668274b55bdb779e45cb10e3a
Author: Anatoly Sorokin <lptolik@gmail.com>
Date: 2024-04-24 11:12:43 +0900
Commit message:
version bumps upPackage: BioNAR
Commit: ed15467d3de2d5558769fbd297714cd33a3e2316
Author: Anatoly Sorokin <lptolik@gmail.com>
Date: 2024-04-24 11:12:31 +0900
Commit message:
add GRPEL1 name to all invocation of annotateGeneNamePackage: BioNAR
Commit: d8c789c47b655fdbf8e77cb4c21920bb8430dbb4
Author: Anatoly Sorokin <lptolik@gmail.com>
Date: 2024-04-24 11:11:38 +0900
Commit message:
review the plot snapshotsPackage: R453Plus1Toolbox
Commit: aede3c3dde6a95b6adc8cca2ed6deead4464e127
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 19:07:18 -0700
Commit message:
pairwiseAlignment() and related have moved from Biostrings to pwalignPackage: edgeR
Commit: 992f8dc3e8d8dfb33be933a24c0aa230c4770e9e
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2024-04-24 11:52:05 +1000
Commit message:
edgeR 4.1.26 - Seurat2PB() now checks for Seurat version. - Allow AveLogCPM to be NULL in .computePriorS2(). - Edit description of `design` argument in roast.DGEGLM().Package: epiregulon.extra
Commit: aec704abd39f6fe6fdb9fab5ecf233c2fd051618
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2024-04-23 18:51:24 -0700
Commit message:
0.99.15 BioC reviewPackage: epiregulon.extra
Commit: 58c84936f9a92e7edfb36b4bc94fcfaef63be464
Author: Tomasz Wlodarczyk <tomwlo@gmail.com>
Date: 2024-04-23 14:05:54 -0700
Commit message:
typoPackage: epiregulon.extra
Commit: 1ccf0570017e32fa9c426132328dcc4aeb9887e0
Author: Tomasz Wlodarczyk <tomwlo@gmail.com>
Date: 2024-04-23 11:50:25 -0700
Commit message:
Changes after BioC reviewPackage: MSA2dist
Commit: e0d3b1e9106bd4d133deeccf70af028dc5ff0216
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 18:50:22 -0700
Commit message:
Substitution matrices BLOSUM* and PAM* have moved from Biostrings to pwalignPackage: MSA2dist
Commit: dbfa5346e8c60cd5f17906e25fb340de6b55387b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 18:45:02 -0700
Commit message:
pairwiseAlignment() has moved from Biostrings to pwalignPackage: SeqArray
Commit: 9c6161626b8744bedf251c8ef8fc79d00a1a8c4c
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2024-04-23 20:17:46 -0500
Commit message:
update seqApply()Package: StructuralVariantAnnotation
Commit: ecffeacf00477ca87ee47250f9aa77eba3326ed4
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 18:14:47 -0700
Commit message:
pairwiseAlignment() and related have moved from Biostrings to pwalignPackage: DominoEffect
Commit: 834c920f724087ab52dc0f43d36863777dd6a1c3
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 17:51:12 -0700
Commit message:
pairwiseAlignment() and pid() have moved from Biostrings to pwalignPackage: HTSeqGenie
Commit: a5c0bdda1546ce65830aa5ac992fcc305d3bd9b8
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 17:33:48 -0700
Commit message:
pairwiseAlignment() has moved from Biostrings to pwalignPackage: XNAString
Commit: 638859d4b089458bec9a43dd145cc6d99f80518a
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 17:20:33 -0700
Commit message:
nucleotideSubstitutionMatrix() and pairwiseAlignment() have moved from Biostrings to pwalignPackage: clusterExperiment
Commit: ff4b21f8ed5b588395a50d5874b74acc1ad1ba04
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2024-04-23 16:54:06 -0700
Commit message:
passes testsPackage: motifbreakR
Commit: 227e6df5ea6b780c51f9db103ed07d495752cef0
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 16:41:48 -0700
Commit message:
pairwiseAlignment() has moved from Biostrings to pwalignPackage: idpr
Commit: 3cd821c30b0d66a9723301a1e09c5a6183981b5e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 16:28:08 -0700
Commit message:
pairwiseAlignment() has moved from Biostrings to pwalignPackage: ShortRead
Commit: 4699244596409a99845cf573d84af5cf083e8239
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 16:01:33 -0700
Commit message:
Import selectively from Biostrings rather than in bulk This is to avoid load-time warning: replacing previous import ‘Biostrings::pairwiseAlignment’ by ‘pwalign::pairwiseAlignment’ when loading ‘ShortRead’Package: gemma.R
Commit: 9a1b28df08d41ac56e06ce88b4d62ebfeaea8c95
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-23 15:59:00 -0700
Commit message:
version bumpPackage: gemma.R
Commit: 465edd3aa0825b710b9623cd724db8ec91ea9810
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-23 15:58:37 -0700
Commit message:
fix titlePackage: gemma.R
Commit: 6468a31dd2f6311aad7ba3cb5151abb8f0b727e7
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-12 16:45:03 -0700
Commit message:
add news of 3.0Package: gemma.R
Commit: 1fca17b04cb1d6a6c0c195d119164e2d8a43a1f3
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-12 16:29:46 -0700
Commit message:
few things to ignorePackage: gemma.R
Commit: b3345a26f8094785439a7599e4bee2e8aa048aa8
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-04-12 16:28:50 -0700
Commit message:
delete htmlPackage: RSVSim
Commit: edfc0c7ad251f66e1e51623b507dc7cf37f48947
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-23 15:35:06 -0700
Commit message:
Add pwalign to Suggests compareSVs() uses nucleotideSubstitutionMatrix() and pairwiseAlignment() internally which have moved from Biostrings to pwalign.Package: MSstats
Commit: 5a5c036ee37decb13298ba428d93d95290a5c428
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2024-04-24 00:26:27 +0200
Commit message:
removed error logPackage: BioCor
Commit: 8233e6a4579fe99d451faabc9f350b5da3f8be73
Author: Lluís <lluis.revilla@gmail.com>
Date: 2024-04-23 23:39:15 +0200
Commit message:
Prepare NEWS so that it matches in the releasePackage: MSstats
Commit: 3cecb354760bb869d4dbe0756135f9ce37bb37c4
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2024-04-23 22:53:42 +0200
Commit message:
removed error logPackage: gDRcore
Commit: 968d74c797c5655a33637485e0be9c70d823acf3
Author: gDR team <gdr-support-d@gene.com>
Date: 2024-04-23 20:34:40 +0000
Commit message:
Merge branch 'main' into develPackage: gDRcore
Commit: b1d4e3adbeef4169dba69c7ee8c9aec8344e7dde
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2024-04-23 22:34:25 +0200
Commit message:
Merge pull request #147 from gdrplatform/GDR-2506 Gdr 2506Package: gDRcore
Commit: b4dfef4cf61af317187c76847241e86560aca64e
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-04-23 20:42:17 +0200
Commit message:
ci: resolve conflictPackage: gDRcore
Commit: ced2cfd0b1ca4e00ee34182619fdcae9093dfc7b
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-04-23 11:13:18 +0200
Commit message:
doc: update as per review (II)Package: gDRcore
Commit: 637043f92915cb1decdc7c36bee032e5a9cfa4d7
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-04-23 10:41:42 +0200
Commit message:
doc: udpate as per reviewPackage: gDRcore
Commit: aa450c6e8cd7d8735e8d9810ce07ecca45bd9504
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-04-22 17:16:53 +0200
Commit message:
chore: bump version and update NEWS.mdPackage: gDRcore
Commit: 403afffebaca199aad415b702a7f269151769d1a
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-04-22 17:16:08 +0200
Commit message:
doc: add vignette for data annotationPackage: zitools
Commit: cf2da098373546c4ee561431b769c49870af6221
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-23 15:18:48 +0200
Commit message:
Update Version NumberPackage: zitools
Commit: 2900c7888d3ce7049f04aee7b11c61bb20e19cb9
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-22 10:40:22 +0200
Commit message:
change Vignette HeaderPackage: zitools
Commit: 91fef13c2b202e8d947e0b84c50781efc2305fdc
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-08 15:32:05 +0200
Commit message:
Update R DependencyPackage: zitools
Commit: 82af89d9ebbd644b03d9d59ee0e307f6e5bb1c27
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-08 15:14:13 +0200
Commit message:
address Bioconductor CommentsPackage: zitools
Commit: b71f50f56212e6c83098b4f6e935bbdfd64e4b32
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-06 09:02:24 +0200
Commit message:
Adress Bioconductor commentsPackage: zitools
Commit: 5bfef97c2689fc06244924eff33d46b923884ed8
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-06 08:11:35 +0200
Commit message:
adress Bioconductor commentsPackage: zitools
Commit: 233dc44cb97ce618c8e35bb2a5833e501e7ae90f
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-06 08:10:06 +0200
Commit message:
adress Bioconductor commentsPackage: zitools
Commit: 1e306eaf2b8306c1432ac79c162c252597f3dfc7
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-05 00:28:56 +0200
Commit message:
minor changesPackage: zitools
Commit: aa81a2e8e8f0abdb7a672a99fabb0fb2483a80ab
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-04 15:20:46 +0200
Commit message:
minor changesPackage: zitools
Commit: fd12869c8374daa68b5a322fc92314c1a3fe03f2
Author: cmeyring <carlotta-meyring@web.de>
Date: 2024-04-04 12:39:33 +0200
Commit message:
Merge branch 'main' of https://github.com/kreutz-lab/zitools
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