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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: ORFik
Commit: d2c3b496bac9fca3c3625ea46d211b85878719da
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-27 21:01:01 +0100
Commit message:
Commit: d2c3b496bac9fca3c3625ea46d211b85878719da
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-27 21:01:01 +0100
Commit message:
Fix for new config old path
Package: ORFik
Commit: 9ab66ab9e7c9a24af467423319c4d883c926d6a6
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-26 19:54:57 +0100
Commit message:
Commit: 9ab66ab9e7c9a24af467423319c4d883c926d6a6
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-26 19:54:57 +0100
Commit message:
All txdbmaker in single function
Package: ORFik
Commit: 0c6480f4af4a4e27b4ebf0bd05600222c34976c6
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-26 19:29:53 +0100
Commit message:
Commit: 0c6480f4af4a4e27b4ebf0bd05600222c34976c6
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-26 19:29:53 +0100
Commit message:
Wrapped all txdbmaker calls to single function
Package: ORFik
Commit: 084462baa832054e869aa9001c41e51455960fc7
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-26 19:12:20 +0100
Commit message:
Commit: 084462baa832054e869aa9001c41e51455960fc7
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-26 19:12:20 +0100
Commit message:
Cleaned up txdbmaker calls
Package: ORFik
Commit: c8b888be8da80ccbaadcf60dbce22ae21f6ff913
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-21 16:49:57 +0100
Commit message:
Commit: c8b888be8da80ccbaadcf60dbce22ae21f6ff913
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-21 16:49:57 +0100
Commit message:
Cleaned up docs for txdb methods
Package: edge
Commit: 7c6682a81580f0cfc9a633bf78f1dd3bce6a7bca
Author: Andy Bass <ajb359@gmail.com>
Date: 2024-03-27 19:45:58 +0000
Commit message:
Commit: 7c6682a81580f0cfc9a633bf78f1dd3bce6a7bca
Author: Andy Bass <ajb359@gmail.com>
Date: 2024-03-27 19:45:58 +0000
Commit message:
removed snm
Package: GeDi
Commit: fe08eaa68cd6cd0fd99a66ed916d76dec151db57
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 20:41:11 +0100
Commit message:
Commit: fe08eaa68cd6cd0fd99a66ed916d76dec151db57
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 20:41:11 +0100
Commit message:
bump to 0.99.2 to check if the retrieval of PPI/annotation really does take that long as experienced in 0.99.1
Package: GeDi
Commit: 4b91380dbda18a9fc30ed3f94038eb3c52deb7ed
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 19:25:47 +0100
Commit message:
Commit: 4b91380dbda18a9fc30ed3f94038eb3c52deb7ed
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 19:25:47 +0100
Commit message:
Merge pull request #18 from AnnekathrinSilvia/bpparam_calculations Bpparam calculations
Package: GeDi
Commit: b3734f163d0cf37ae3ad161c6caacc8d80c1e89a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 19:11:15 +0100
Commit message:
Commit: b3734f163d0cf37ae3ad161c6caacc8d80c1e89a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 19:11:15 +0100
Commit message:
updated news
Package: GeDi
Commit: d0a2b7905735d5ef186bbf9e9b43b2311d89687c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 19:11:08 +0100
Commit message:
Commit: d0a2b7905735d5ef186bbf9e9b43b2311d89687c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 19:11:08 +0100
Commit message:
Bumping version to 0.99.1
Package: GeDi
Commit: a146f6ecaf1144a3f129243847bca2374e9f7e6a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 18:32:52 +0100
Commit message:
Commit: a146f6ecaf1144a3f129243847bca2374e9f7e6a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 18:32:52 +0100
Commit message:
re-rendered manpages
Package: GeDi
Commit: 391701223477f3d4f187605de72c8172622e39ee
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 18:32:43 +0100
Commit message:
Commit: 391701223477f3d4f187605de72c8172622e39ee
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 18:32:43 +0100
Commit message:
homogenizing the content of the BPPARAM entry, cleanup of commented code
Package: GeDi
Commit: 422ec80b28ee2d26773912ed9f6074585b1ccce7
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 18:32:21 +0100
Commit message:
Commit: 422ec80b28ee2d26773912ed9f6074585b1ccce7
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 18:32:21 +0100
Commit message:
fixing the tests to match the new API
Package: GeDi
Commit: 97043de3c902db9224e2f2250ab9b288cabd0c7e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 18:32:05 +0100
Commit message:
Commit: 97043de3c902db9224e2f2250ab9b288cabd0c7e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 18:32:05 +0100
Commit message:
n_cores + Snow --> Handling directly the whole thing with a BPPARAM object, defaulting to SerialParam to avoid odd behaviors
Package: GeDi
Commit: a7d4288dbd2710bc580b92259650f09a52dc8437
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 17:58:04 +0100
Commit message:
Commit: a7d4288dbd2710bc580b92259650f09a52dc8437
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 17:58:04 +0100
Commit message:
Switching brutally from Snow to Serial
Package: GeDi
Commit: 4d7b21bfcd2b79162f1963bbd23230179821c894
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 17:13:01 +0100
Commit message:
Commit: 4d7b21bfcd2b79162f1963bbd23230179821c894
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 17:13:01 +0100
Commit message:
* explicitly passing the BPPARAM object to handle gently parallelization * adding some checks on the method argument and using IC calculations only if needed * making example reproducible with set.seed initialization
Package: GeDi
Commit: a901779533e55808411fd9b9214b6af4bb7a940d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 17:09:18 +0100
Commit message:
Commit: a901779533e55808411fd9b9214b6af4bb7a940d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 17:09:18 +0100
Commit message:
changing tests run on similarity
Package: GeDi
Commit: c3b34bf9d6fcb02128b4121cf755b78c7af3a9f1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 17:08:27 +0100
Commit message:
Commit: c3b34bf9d6fcb02128b4121cf755b78c7af3a9f1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 17:08:27 +0100
Commit message:
avoid warning when guessing the separator
Package: edge
Commit: b69baf2e02eadfa28187baad097b22326336300c
Author: Andy Bass <ajb359@gmail.com>
Date: 2024-03-27 18:52:41 +0000
Commit message:
Commit: b69baf2e02eadfa28187baad097b22326336300c
Author: Andy Bass <ajb359@gmail.com>
Date: 2024-03-27 18:52:41 +0000
Commit message:
removed snm
Package: GeDi
Commit: 3dcdc4d1a9fa5a9cb76c7c6951f024b50410eca3
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 13:50:36 +0100
Commit message:
Commit: 3dcdc4d1a9fa5a9cb76c7c6951f024b50410eca3
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 13:50:36 +0100
Commit message:
removed the .Rproj file - not desired in the built source package for Bioc, but we can keep it locally
Package: GeDi
Commit: 8293d7d97a565825baa8f03b86e4e4d937168f60
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 13:48:11 +0100
Commit message:
Commit: 8293d7d97a565825baa8f03b86e4e4d937168f60
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 13:48:11 +0100
Commit message:
removing CITATION file as there's no DOI yet
Package: GeDi
Commit: a03036e1331fcb7ef12d47ff4875bd606e836e61
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 12:30:46 +0100
Commit message:
Commit: a03036e1331fcb7ef12d47ff4875bd606e836e61
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 12:30:46 +0100
Commit message:
cache disabled for GHA clear run
Package: GeDi
Commit: 5f0b1e0c67d0d025d2d1c29a8be9c6df8a47abd7
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 10:35:19 +0100
Commit message:
Commit: 5f0b1e0c67d0d025d2d1c29a8be9c6df8a47abd7
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 10:35:19 +0100
Commit message:
cutting down on examples runtime
Package: GeDi
Commit: 9bdd794ce9aaa90bb9d85d22264055da7c1a612f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 10:34:50 +0100
Commit message:
Commit: 9bdd794ce9aaa90bb9d85d22264055da7c1a612f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 10:34:50 +0100
Commit message:
reducing runtime of the examples - adding explicitly \dontrun{} to each *second* example in long running functions
Package: ggspavis
Commit: 380a5edba95e997983bc542a4d35e8cb5ff9382d
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-03-27 14:23:43 -0400
Commit message:
Commit: 380a5edba95e997983bc542a4d35e8cb5ff9382d
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-03-27 14:23:43 -0400
Commit message:
version
Package: ggspavis
Commit: 8ccae4f707f100ceb290fbcf8024de21cea3b022
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-03-27 14:23:26 -0400
Commit message:
Commit: 8ccae4f707f100ceb290fbcf8024de21cea3b022
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-03-27 14:23:26 -0400
Commit message:
get feature names from rownames if rowData is empty
Package: Banksy
Commit: 8d751508b44cd1b409512e5721a41d881d2ef417
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-27 17:08:18 +0000
Commit message:
Commit: 8d751508b44cd1b409512e5721a41d881d2ef417
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-27 17:08:18 +0000
Commit message:
Bump version
Package: Banksy
Commit: d5edf83fa7ba3d30257a57de157c2272ae4ba76f
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-27 17:05:39 +0000
Commit message:
Commit: d5edf83fa7ba3d30257a57de157c2272ae4ba76f
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-27 17:05:39 +0000
Commit message:
R 4.4
Package: Banksy
Commit: c59f67055cc74f3143ec12279ba869709ee7959a
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-27 16:29:37 +0000
Commit message:
Commit: c59f67055cc74f3143ec12279ba869709ee7959a
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-27 16:29:37 +0000
Commit message:
Update docs
Package: Banksy
Commit: a469e9dadb33b858986953a795839c244d7af4ff
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-27 16:29:24 +0000
Commit message:
Commit: a469e9dadb33b858986953a795839c244d7af4ff
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-27 16:29:24 +0000
Commit message:
Add scaling options for reduction methods
Package: Banksy
Commit: 86b40563d8358add19bab87b5e4a740a800e4220
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-08 22:56:17 +0000
Commit message:
Commit: 86b40563d8358add19bab87b5e4a740a800e4220
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-08 22:56:17 +0000
Commit message:
Update docs
Package: Banksy
Commit: c5ca77b518b227034df468b19415cbeca1b481e1
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-06 16:26:32 +0000
Commit message:
Commit: c5ca77b518b227034df468b19415cbeca1b481e1
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-06 16:26:32 +0000
Commit message:
Update README
Package: Banksy
Commit: 6ee046a2a714e6395af354d76a6c47a0235ff384
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:37:22 -0500
Commit message:
Commit: 6ee046a2a714e6395af354d76a6c47a0235ff384
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:37:22 -0500
Commit message:
Update README.md
Package: Banksy
Commit: 091bedcb5dd7b462e85fcae936c2f9122e86dc13
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:37:09 -0500
Commit message:
Commit: 091bedcb5dd7b462e85fcae936c2f9122e86dc13
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:37:09 -0500
Commit message:
Update README.md
Package: Banksy
Commit: 7305c41e8fad7fd221eecfc9a61d892906cd37fb
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:36:25 -0500
Commit message:
Commit: 7305c41e8fad7fd221eecfc9a61d892906cd37fb
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:36:25 -0500
Commit message:
Update README.md
Package: Banksy
Commit: be1140296b8e48eb0251df9e9645d316cd5ab54b
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:36:12 -0500
Commit message:
Commit: be1140296b8e48eb0251df9e9645d316cd5ab54b
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:36:12 -0500
Commit message:
Update README.md
Package: Banksy
Commit: ac5e3118b6e1025125549b40b55c7a2976b8760c
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:35:31 -0500
Commit message:
Commit: ac5e3118b6e1025125549b40b55c7a2976b8760c
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:35:31 -0500
Commit message:
Update README.md updated paper, reviewer file, and tweetorial
Package: Banksy
Commit: dbda6fde952e65f45409d9bca8e1f821746755cc
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-02-18 23:35:33 +0000
Commit message:
Commit: dbda6fde952e65f45409d9bca8e1f821746755cc
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-02-18 23:35:33 +0000
Commit message:
Set R version
Package: BiocFileCache
Commit: 19e9ee5be7bc44f7a187d12b4eb31a64f6a56b3f
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-03-27 12:38:59 -0400
Commit message:
Commit: 19e9ee5be7bc44f7a187d12b4eb31a64f6a56b3f
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-03-27 12:38:59 -0400
Commit message:
Version bump for file location fix
Package: BiocFileCache
Commit: cfb1bd4f6c422ed03b97b902736d55a2180031db
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-03-27 12:38:31 -0400
Commit message:
Commit: cfb1bd4f6c422ed03b97b902736d55a2180031db
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-03-27 12:38:31 -0400
Commit message:
Update test file location
Package: knowYourCG
Commit: dd12f8af59dc775c7652251ab3212c0b7a0070b8
Author: Goldberg <golddc72@pennmedicine.upenn.edu>
Date: 2024-03-27 11:36:08 -0400
Commit message:
Commit: dd12f8af59dc775c7652251ab3212c0b7a0070b8
Author: Goldberg <golddc72@pennmedicine.upenn.edu>
Date: 2024-03-27 11:36:08 -0400
Commit message:
bump to 0.99.92
Package: knowYourCG
Commit: 6234dc6fb63814b17bb14a42aef07c72807a8f54
Author: Goldberg <golddc72@pennmedicine.upenn.edu>
Date: 2024-03-27 11:34:26 -0400
Commit message:
Commit: 6234dc6fb63814b17bb14a42aef07c72807a8f54
Author: Goldberg <golddc72@pennmedicine.upenn.edu>
Date: 2024-03-27 11:34:26 -0400
Commit message:
cache data in examples
Package: limpca
Commit: 8dce21ad63bd9b5ce2ea3648de3ceed47e519afc
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-27 16:21:14 +0100
Commit message:
Commit: 8dce21ad63bd9b5ce2ea3648de3ceed47e519afc
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-27 16:21:14 +0100
Commit message:
updated code with data2LmpDataList
Package: limpca
Commit: 21f904b0a07b32fffce83d3126a7d7203718494d
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 14:38:55 +0100
Commit message:
Commit: 21f904b0a07b32fffce83d3126a7d7203718494d
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 14:38:55 +0100
Commit message:
lmpData as argument of plot functions
Package: limpca
Commit: 2f5f637b2e27a011e62868994d6161f9d50ad8c4
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 12:06:48 +0100
Commit message:
Commit: 2f5f637b2e27a011e62868994d6161f9d50ad8c4
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 12:06:48 +0100
Commit message:
debugged data checks and test
Package: limpca
Commit: 796784d7129242a18215e4a01547326a13342a14
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 11:49:30 +0100
Commit message:
Commit: 796784d7129242a18215e4a01547326a13342a14
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 11:49:30 +0100
Commit message:
data check for modelmatrix and plots
Package: limpca
Commit: 3e62e4c903c5a693f57613d6489b9953427b923e
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 10:43:19 +0100
Commit message:
Commit: 3e62e4c903c5a693f57613d6489b9953427b923e
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 10:43:19 +0100
Commit message:
warning if color, shape are numeric
Package: limpca
Commit: 997399fa6abb4d43d7e2625c5ba1f70352932d34
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 10:34:47 +0100
Commit message:
Commit: 997399fa6abb4d43d7e2625c5ba1f70352932d34
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 10:34:47 +0100
Commit message:
code style, check args pca
Package: limpca
Commit: 06bb7a8f1b0590cb1e33d9bed0a305a9da8149a6
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-22 16:54:04 +0100
Commit message:
Commit: 06bb7a8f1b0590cb1e33d9bed0a305a9da8149a6
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-22 16:54:04 +0100
Commit message:
lmpDataListCheck, lmpData input of pca fun
Package: limpca
Commit: daed6e434d5a9f6d3d6eb61e72523881ae6c7a46
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-20 16:37:31 +0100
Commit message:
Commit: daed6e434d5a9f6d3d6eb61e72523881ae6c7a46
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-20 16:37:31 +0100
Commit message:
updated doc data2lmpDataList
Package: limpca
Commit: 3a235d5e6d1588eb58e0c48802c0bb34037e9fc0
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-20 16:27:13 +0100
Commit message:
Commit: 3a235d5e6d1588eb58e0c48802c0bb34037e9fc0
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-20 16:27:13 +0100
Commit message:
updated DESCRIPTION
Package: limpca
Commit: cf6f8e82c25e346d59b979bc575ef966a98c5038
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-20 15:59:33 +0100
Commit message:
Commit: cf6f8e82c25e346d59b979bc575ef966a98c5038
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-20 15:59:33 +0100
Commit message:
updated doc
Package: scaeData
Commit: 5c742bdbb986fc50ec779c3850fdb3701d894e4e
Author: Ahmad Al Ajami <ahmad.alajami@kgu.de>
Date: 2024-03-27 15:54:55 +0100
Commit message:
Commit: 5c742bdbb986fc50ec779c3850fdb3701d894e4e
Author: Ahmad Al Ajami <ahmad.alajami@kgu.de>
Date: 2024-03-27 15:54:55 +0100
Commit message:
changed date format; version bumped
Package: autonomics
Commit: 9c061acbe9466b90b01ad4592f3b5b181da18108
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-27 15:53:58 +0100
Commit message:
Commit: 9c061acbe9466b90b01ad4592f3b5b181da18108
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-27 15:53:58 +0100
Commit message:
Undocument assertions (devel)
Package: cypress
Commit: d9a7503412fb84458bc1feb85b3a3144fc2114e4
Author: Shilin Yu <sy597@georgetown.edu>
Date: 2024-03-27 10:35:41 -0400
Commit message:
Commit: d9a7503412fb84458bc1feb85b3a3144fc2114e4
Author: Shilin Yu <sy597@georgetown.edu>
Date: 2024-03-27 10:35:41 -0400
Commit message:
edit for Namespace edit the import detail for Namespace
Package: scRNAseqApp
Commit: 9f8150a9b2392cd5c4f9445842531d542a4537d0
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-03-27 10:04:52 -0400
Commit message:
Commit: 9f8150a9b2392cd5c4f9445842531d542a4537d0
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-03-27 10:04:52 -0400
Commit message:
Update the description.
Package: scRNAseqApp
Commit: 570e9b66b092487139eb84b0de2a9b1eab9fce95
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-03-27 09:51:41 -0400
Commit message:
Commit: 570e9b66b092487139eb84b0de2a9b1eab9fce95
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-03-27 09:51:41 -0400
Commit message:
Add a hyperlink to package URL at footer.
Package: scRNAseqApp
Commit: ec228eb4500e697eb33e7c1c662edc8af6709934
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-03-21 11:16:43 -0400
Commit message:
Commit: ec228eb4500e697eb33e7c1c662edc8af6709934
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-03-21 11:16:43 -0400
Commit message:
Fix the duplicated rownames.
Package: ZygosityPredictor
Commit: 62b1b8c4545251eac79bb8f86ef244b5848b9208
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 14:53:03 +0100
Commit message:
Commit: 62b1b8c4545251eac79bb8f86ef244b5848b9208
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 14:53:03 +0100
Commit message:
fixed illegal version bump
Package: ZygosityPredictor
Commit: ee9ee77b3f1a863bf69b235cbf354e0a3a5ce4dd
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 14:50:10 +0100
Commit message:
Commit: ee9ee77b3f1a863bf69b235cbf354e0a3a5ce4dd
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 14:50:10 +0100
Commit message:
fixed final issues via R CMD check and bioccheck
Package: ZygosityPredictor
Commit: ce2c073a65c12a282ab1189b16bf1e0cd18cf6e1
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 13:55:15 +0100
Commit message:
Commit: ce2c073a65c12a282ab1189b16bf1e0cd18cf6e1
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 13:55:15 +0100
Commit message:
fixed github issue #5... bumped version
Package: ZygosityPredictor
Commit: fe2e2deea32a0ea35176848bae500584e282b9e1
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 12:07:06 +0100
Commit message:
Commit: fe2e2deea32a0ea35176848bae500584e282b9e1
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 12:07:06 +0100
Commit message:
code cleanup
Package: ZygosityPredictor
Commit: a2310b6f85cf1c99f4a969cadb7093d1375cd5d3
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 12:00:14 +0100
Commit message:
Commit: a2310b6f85cf1c99f4a969cadb7093d1375cd5d3
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 12:00:14 +0100
Commit message:
fixed github issue #6 about global variables
Package: ZygosityPredictor
Commit: 8c972269f06d6ba0f099e1334c59718b7a31f09d
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 11:30:24 +0100
Commit message:
Commit: 8c972269f06d6ba0f099e1334c59718b7a31f09d
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 11:30:24 +0100
Commit message:
replaced global varianbles with internaal environment
Package: ZygosityPredictor
Commit: 98c5436e204bdba78ba4d03f5bad0bc72dd3a10f
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-26 16:50:23 +0100
Commit message:
Commit: 98c5436e204bdba78ba4d03f5bad0bc72dd3a10f
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-26 16:50:23 +0100
Commit message:
replaced gloabl phasing matrices by ZP specific R environment
Package: ZygosityPredictor
Commit: 3a4bfda94f4e59c6e6d7dee46c700899dca08c6b
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-26 15:45:18 +0100
Commit message:
Commit: 3a4bfda94f4e59c6e6d7dee46c700899dca08c6b
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-26 15:45:18 +0100
Commit message:
moved debugging scripts into seperate directory
Package: SPLINTER
Commit: e51bf62185f2b253414196c9edc2c319e511b1cd
Author: dlow <3214561+dianalow@users.noreply.github.com>
Date: 2024-03-27 21:16:28 +0800
Commit message:
Commit: e51bf62185f2b253414196c9edc2c319e511b1cd
Author: dlow <3214561+dianalow@users.noreply.github.com>
Date: 2024-03-27 21:16:28 +0800
Commit message:
Merge remote-tracking branch 'upstream/devel' into devel
Package: SPLINTER
Commit: 28041e8bb29be96dbdb7fcb07bd18087e1b71e7b
Author: Diana Low <3214561+dianalow@users.noreply.github.com>
Date: 2024-03-27 20:40:54 +0800
Commit message:
Commit: 28041e8bb29be96dbdb7fcb07bd18087e1b71e7b
Author: Diana Low <3214561+dianalow@users.noreply.github.com>
Date: 2024-03-27 20:40:54 +0800
Commit message:
Update DESCRIPTION up version number
Package: SPLINTER
Commit: b34ff81f2264b726b5ae89dd747bf5af1c4c4389
Author: Diana Low <3214561+dianalow@users.noreply.github.com>
Date: 2024-03-27 08:17:10 +0800
Commit message:
Commit: b34ff81f2264b726b5ae89dd747bf5af1c4c4389
Author: Diana Low <3214561+dianalow@users.noreply.github.com>
Date: 2024-03-27 08:17:10 +0800
Commit message:
Merge pull request #2 from hpages/master makeTxDbFromGFF() has moved from GenomicFeatures to txdbmaker
Package: SPLINTER
Commit: 253d259c9149a18ac52a071009c625a384515e7c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-19 15:32:43 -0700
Commit message:
Commit: 253d259c9149a18ac52a071009c625a384515e7c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-19 15:32:43 -0700
Commit message:
makeTxDbFromGFF() has moved from GenomicFeatures to txdbmaker
Package: recount
Commit: c61b6727d1c722c89d451a9dac204e22b94130cc
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-27 09:07:20 -0400
Commit message:
Commit: c61b6727d1c722c89d451a9dac204e22b94130cc
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-27 09:07:20 -0400
Commit message:
txdbmaker is only available in BioC 3.19, so on GHA I'm now using that version of BioC
Package: rawDiag
Commit: 8e57d4b3fde19eeaaef3d7c3817c5b832a722d7e
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-03-27 13:49:36 +0100
Commit message:
Commit: 8e57d4b3fde19eeaaef3d7c3817c5b832a722d7e
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-03-27 13:49:36 +0100
Commit message:
doc: version bump 0.99.31
Package: rawDiag
Commit: d8fa9133b0be5596372065ad618f49f6ef95aa73
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-03-27 13:49:18 +0100
Commit message:
Commit: d8fa9133b0be5596372065ad618f49f6ef95aa73
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-03-27 13:49:18 +0100
Commit message:
feat: check if rawrr assembly is working.
Package: recount
Commit: 76937504a9766c86b70d5a25c934e868a7434c1f
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-27 08:34:46 -0400
Commit message:
Commit: 76937504a9766c86b70d5a25c934e868a7434c1f
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-27 08:34:46 -0400
Commit message:
Ran devtools::document()
Package: cTRAP
Commit: 81526c7ce27561c1867d1c7d3a06d82a9943cf1f
Author: Nuno Agostinho <nuno@ebi.ac.uk>
Date: 2024-03-27 12:11:15 +0000
Commit message:
Commit: 81526c7ce27561c1867d1c7d3a06d82a9943cf1f
Author: Nuno Agostinho <nuno@ebi.ac.uk>
Date: 2024-03-27 12:11:15 +0000
Commit message:
Bump version
Package: cTRAP
Commit: eb849fbbb9d169faf576a2d221a589e7650c856f
Author: Nuno Agostinho <nuno@ebi.ac.uk>
Date: 2024-03-27 12:10:30 +0000
Commit message:
Commit: eb849fbbb9d169faf576a2d221a589e7650c856f
Author: Nuno Agostinho <nuno@ebi.ac.uk>
Date: 2024-03-27 12:10:30 +0000
Commit message:
Squashed commit of the following: commit 5b1482190809953077523b1c5d41b94f36cc69fd Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Wed Mar 27 12:09:59 2024 +0000 Squashed commit of the following: commit 8763bdb8f4634fa30b219ef90ee3d750d44e3e6b Merge: ac97834 a177f66 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Mar 27 12:02:19 2024 +0000 Merge pull request #38 from nuno-agostinho/dev cTRAP 1.20.1 commit a177f6682dc94367ca67938029f6aa82856d23f1 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Mar 26 18:48:06 2024 +0000 Remove Windows unit tests commit bc83be6ce730e3da0280a532fac39b70dcacfafe Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Mar 26 17:41:41 2024 +0000 Remove duplicated YAML divider from vignette commit 1d91d2f9cbcdb53e44e629cf9556ec51cc50e2a1 Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Tue Mar 26 16:58:09 2024 +0000 Revert package documentation commit 31dc532a15a45b21ad329eb9586cd690d03c3bd5 Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Tue Mar 26 16:17:52 2024 +0000 Remove failing unit test commit 42dfe5270b115c9ee48d05546d2bf6d50a1def38 Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Tue Mar 26 01:57:41 2024 +0000 Fix spelling commit 6bc7321b295b121cf6cb0ca6d274faa8edea0782 Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Tue Mar 26 01:55:28 2024 +0000 Update roxygen docs commit b9e3f5fc209c6c1b4e90cf237a465cbf2c86b811 Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Tue Mar 26 01:52:01 2024 +0000 Fix ggplot2 issues commit b417cc554e9aa7b10884a90625fc8a04fcd6baba Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Mar 26 01:25:39 2024 +0000 Fix ggplot2 issues commit 807c60eab1986bba655c32cee6080703e674a1e5 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Mar 6 21:42:18 2024 +0000 Fix unit test commit 7d9c082f25947d9f5346beef25219e60315b25db Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Mar 6 21:32:43 2024 +0000 Avoid using deprecated `aes_string()` commit 1e7f5c87def7545a7f48d70489964d6622ec4662 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Mar 6 21:06:31 2024 +0000 Update r-lib/actions in GitHub Actions commit 72add994f7b5406d65d258a4cff59ad499759a61 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Mar 6 21:02:25 2024 +0000 Fix GitHub action commit 4ff0bc6f830baee1c5d533119e377e018c821d90 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Mar 6 20:58:20 2024 +0000 Bump version to 1.20.1 commit 5d7d5a7dc2bfe2b3bc5f1845289bf418795c311d Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Mar 6 20:55:41 2024 +0000 Fix unit test commit ac978340e89da80edce309259999f149e38d4c58 Merge: 491b0e9 1c3fd8a Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Jan 19 16:02:40 2024 +0000 Merge pull request #46 from nuno-agostinho/license/copyright-to-2024 Update license copyright year(s) commit 1c3fd8a6fabad6c218de2b5fa474540dea15c9c2 Author: github-actions <github-actions@github.com> Date: Mon Jan 1 03:14:52 2024 +0000 docs(license): update copyright year(s) commit 491b0e9d41ddc313c3deb95b04fe84e9d44bc985 Merge: 4ed3b2a c865b2c Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Feb 15 09:00:59 2023 +0000 Merge pull request #45 from nuno-agostinho/fix/ci-tests commit c865b2c01b2d83bd9aca45719e62ce1b00ea3801 Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Mon Feb 13 10:44:09 2023 +0000 Fix R CMD BiocCheck error commit 7a2e95ff264ca501236287678c9cd3c10aa8e40d Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Feb 12 21:48:42 2023 +0000 Avoid CI tests in Windows commit 4ed3b2a9a50740e7a7ec6cb80f8e4bb283d6be4f Merge: a24e364 e764490 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Feb 12 19:27:17 2023 +0000 Merge pull request #44 from nuno-agostinho/nuno-agostinho-patch-1 commit e76449049201d56f61e3e925081f9459bde20cff Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jan 4 09:54:08 2023 +0000 Remove redundant code commit 36cbb26dd354a0fdc07d0d1da723ca01f31351c7 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jan 4 09:04:01 2023 +0000 Include BiocCheck package commit c4a4fd8bfc27b60c44c35d7d31e944cbc34fa64b Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Jan 3 02:03:33 2023 +0000 Simplify R CMD check action commit 15c58239e87bee9be34f26e82903b6a87558ffa4 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Jan 3 01:36:36 2023 +0000 Fix R CMD check in Ubuntu commit a24e3645b1bcb741a1aecdd484d3af2fe1573a86 Merge: 06b81ba b484413 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Jan 3 00:54:16 2023 +0000 Merge pull request #43 from nuno-agostinho/nuno-agostinho-patch-1 commit b48441387542e0bb8d4ccbec711fa648db82c0cd Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Jan 3 00:54:08 2023 +0000 Install cTRAP before building pkgdown site commit 06b81ba44b54dc17436c30da558220a39d51b248 Merge: 2ac559b c42d852 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Jan 3 00:11:53 2023 +0000 Merge pull request #42 from nuno-agostinho/nuno-agostinho-patch-1 commit c42d8527a29a5bce0b261b767117ad956c4e25e1 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Jan 3 00:11:25 2023 +0000 Update pkgdown.yml commit 2ac559b91bae2552edd62ac010a1e1f6c89e60f1 Merge: 11152dc 2930a98 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Jan 3 00:00:10 2023 +0000 Merge pull request #41 from nuno-agostinho/fix/pkgdown commit 2930a98888c5f7fb2f7465f4143f33d9aca15264 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Jan 3 00:00:01 2023 +0000 Fix pkgdown site commit 11152dcf64b9e76bf3b2fe89027aaa98ca23b52c Merge: 198001e 939e0e3 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Jan 2 23:30:32 2023 +0000 Merge pull request #40 from nuno-agostinho/license/copyright-to-2023 commit 939e0e31aa726add393c49a7187d5f7bf8d5c533 Author: github-actions <github-actions@github.com> Date: Sun Jan 1 03:19:27 2023 +0000 docs(license): update copyright year(s) commit 198001e19120eccf303b8c47cd5efdf7409d5f64 Merge: 574cf69 44dcdc3 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Oct 26 00:05:00 2022 +0100 Merge pull request #39 from nuno-agostinho/fix/gh-actions commit 44dcdc3c169707e2fef552979a0046802f2c6c74 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Oct 26 00:04:46 2022 +0100 Fix r-lib/actions branch commit 2bffdb68afa835ace35f2e9f1b0e9ac13f6e5918 Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Sat Sep 10 15:29:19 2022 +0100 Fix missing bracket commit 046dfe7ea91ff0ad909ef0ecb512cd468730c4f8 Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Sat Sep 10 15:27:13 2022 +0100 Fix header in all interface functions commit ca30681dda6b8a93d41827146a148121a1c7ae3c Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Sat Sep 10 15:20:35 2022 +0100 Raise error if commonPath directory doesn't exist commit 90600da71288c4a1bf4e8224555477bf1a0f6d8a Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Sat Sep 10 15:12:29 2022 +0100 Update icon names for FontAwesome 6 commit 8bfb114b1a9e9de4557cf0294333d08cefb021c9 Merge: 8337c0c 574cf69 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sat Sep 10 15:05:16 2022 +0100 Merge pull request #37 from nuno-agostinho/master commit 574cf69ddd383d4af2afaec2b9d84d04199a0b25 Merge: 33acca5 1d06ca3 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jul 14 21:55:11 2022 +0100 Merge pull request #36 from nuno-agostinho/dev2 Dev2 commit 1d06ca3f101f331272a8c9ad600b68c9722978ba Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jul 14 12:07:41 2022 +0000 Properly import utils functions commit bc0ca85345d01eb0c765fd58f9c34cc3babe6f16 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jul 14 12:03:33 2022 +0000 Copy-editing commit 65843df5f181103308cf1ceaba3d9260776073f8 Merge: 68caee3 caadac2 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jul 14 12:02:41 2022 +0000 Merge branch 'dev' of https://github.com/nuno-agostinho/cTRAP into dev commit caadac20656b3e309d19e5ce30819ba9220c5bc4 Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Thu Jul 14 11:45:08 2022 +0100 Avoid large JSON response from DT commit a5b71ebf902c54d0b16219d36b8b4e1d67826e63 Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Mon Jul 11 17:00:16 2022 +0100 Add cTRAP version to welcome modal commit a3a8f4ba67aec85b00c3f691092d454d99574596 Merge: 33acca5 0ad8732 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Jul 11 16:39:17 2022 +0100 Merge pull request #34 from nuno-agostinho/fix/floweRy Fix Celery/Flower support commit 0ad8732a9f0a8b5022ca306d567a1fd8323cb47b Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Tue Jul 5 23:11:18 2022 +0100 Bump version to 1.14.1 commit 330e65c8c01b44872f50ac7bec07c15a6089f142 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Jul 5 22:58:10 2022 +0100 Update floweRy.R commit 33acca5db23d92f23851062f180f56cf6446efe2 Merge: b4cd38f 668eca3 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sat Jun 4 17:49:31 2022 +0100 Merge pull request #33 from nuno-agostinho/copy-edit Copy-edit benchmark instructions commit 668eca350a89ec450463d8c4b0984ea873d90e64 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sat Jun 4 17:49:17 2022 +0100 Copy-edit benchmark instructions commit 68caee308a1090457d5d70045ed0302639ac6408 Merge: f4334d6 b4cd38f Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri May 20 12:11:19 2022 +0100 Merge pull request #32 from nuno-agostinho/master Sync with master commit b4cd38f5ac63893e7696bdb839b85a7ebfc8536e Merge: 039ad81 bbcde0a Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu May 19 22:59:43 2022 +0100 Merge pull request #31 from nuno-agostinho/nuno-agostinho-patch-1 Create devcontainer.json commit bbcde0ab0e9874bab2aff64c8e453276fbba762b Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu May 19 22:59:34 2022 +0100 Create devcontainer.json commit 039ad81ca0fbf4a6b68580679efa8388597c1769 Merge: 369132a 4e06be6 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Apr 3 10:34:50 2022 +0100 Merge pull request #29 from nuno-agostinho/nuno-agostinho-patch-1 Fix URL to download zscores and checksum commit 4e06be682addddd9db0eea1bc0bd371a4f7c8b3c Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Apr 3 10:34:42 2022 +0100 Fix URL to download zscores and checksum commit 369132aea8ce5671faa4a91bc355a5557221ccce Merge: 8d1dae3 eb40fb6 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Apr 3 09:57:08 2022 +0100 Merge pull request #28 from nuno-agostinho/zscores-checksum Add CMap zscores checksum to tutorial commit eb40fb6664c70a1c0863538f50710f19f526c14b Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Apr 3 09:55:13 2022 +0100 Add CMap zscores checksum to tutorial commit 8d1dae3b999f7b846432a30a80371881569bcf6e Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Mar 13 14:57:40 2022 +0000 Fix pkgdown GitHub action (#27) * Install missing rcmdcheck package * Fix pkgdown missing topics warning commit 9a543a2957a9e897d5ad66715409ea22d902f8fe Merge: 629ca97 dd2bc24 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Mar 13 10:28:41 2022 +0000 Merge pull request #26 from nuno-agostinho/license/copyright-to-2022 Update license copyright year(s) commit dd2bc24c0df29e3724d9525b9eafcc51bf29315d Author: github-actions <github-actions@github.com> Date: Sun Mar 13 10:28:01 2022 +0000 docs(license): update copyright year(s) commit 629ca971e1269a3b9c2b80114bc7053a8bffe6d6 Merge: b112dfb 2a6574e Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Mar 13 10:27:22 2022 +0000 Merge pull request #25 from nuno-agostinho/nuno-agostinho-patch-1 Auto-update license year commit 2a6574e99c42202394aed063acc9a40050ee95b1 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Mar 13 10:27:08 2022 +0000 Auto-update license year commit b112dfb5dc7d2b5a8ffa10a97ef1e44beeaa60de Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Dec 27 16:09:54 2021 +0000 Update pkgdown.yml commit c9ffdc4752f6cb56ee17d492cb192951baccf2cd Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Dec 27 12:21:36 2021 +0000 Update pkgdown.yml commit a26f2a35af1654c751df80cf1b644fcd9d27ae0a Author: Nuno Agostinho <nuno@ebi.ac.uk> Date: Mon Dec 27 12:05:53 2021 +0000 Isolate pkgdown deployment commit 6b023df84260d6e5ed645bc9fe1bd5303c6cd26e Merge: a4d73d5 f4334d6 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 28 00:13:55 2021 +0100 Merge pull request #23 from nuno-agostinho/dev Version 1.12.0 commit f4334d6b02c87324d3c9733b8233d169c2e6fd76 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 28 00:13:27 2021 +0100 Bump version to 1.12.0 commit 8c2c1e9d2d269578ecde88186d82ed6fd440c1ef Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 28 00:07:43 2021 +0100 Bump version to 1.20.0 commit 3200dbf2217c0baed54d8ebb75b359710989f750 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 26 00:12:07 2021 +0100 Update utils.R commit 8337c0c80435611159c9d483c2ac96ddfbb1ce29 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Oct 22 10:11:20 2021 +0100 Include floweRy deps commit c70d411f6673947af23b481f6f841cd9b6755fbb Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Oct 22 10:03:57 2021 +0100 Include floweRy code to avoid problems with CRAN/Bioconductor commit 20dbe5a3c37c285505a5558fbe2c709e09a18c1e Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 21 18:05:10 2021 +0100 Update cTRAP docker commit 81ef21c8623291175d17abb74de685597783dfdd Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 21 17:52:35 2021 +0100 Fix suggest (rather than import) biomaRt commit a91a5d7f1437ab5254b35a15e74824f759b77b8c Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 21 17:46:37 2021 +0100 Include biomaRt functions and floweRy commit 5079a4d40b2c7617178eaa09db1c228a11539460 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 21 17:26:51 2021 +0100 Change task state to "Not found" if not in Celery/Flower queue commit 2a7d40d6578144a69b6abe98c5201dd90c081016 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 21 16:22:38 2021 +0100 Fix issues with R CMD check commit 7878eacc615e47f9cb2c32c007536217e8dc0a45 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 21 15:49:42 2021 +0100 Include optional packages in Suggests commit 6c5e4ffe72c113dce136229ad1f70b5c7fd82c09 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 21 15:23:29 2021 +0100 Fix error when setting app data commit efba905dd59c8e3c40221d30af059d9ba7e65cd4 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 21 15:23:10 2021 +0100 Fix issue with unit tests commit 773ddbe4b191f72d26080081585544da8ff661f8 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 21 11:48:06 2021 +0100 Remove biomaRt dependency commit e339c0be3905076449b03461a81c7a1ed426ffc6 Merge: c955b51 b1d13bd Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 21 11:37:57 2021 +0100 Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev commit c955b51dd98d2c6e75decf2fd55bdfecc0e3aecc Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 21 11:37:31 2021 +0100 Avoid using biomaRt commit b1d13bda9fe99655813aa7d69bdf917bc8a0fdd9 Merge: a28be42 951d1b1 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 19 19:15:55 2021 +0100 Merge pull request #24 from nuno-agostinho/master+dev Fix crash with shiny 1.7.0 commit 951d1b1aa8ab5776da72e12fca282aae19045048 Merge: a4d73d5 a28be42 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 19 19:15:17 2021 +0100 Merge branch 'dev' into master+dev commit a28be425f5a0894b0fdb62f0bb56bfb5c8580bf5 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 19 19:13:57 2021 +0100 Remove biomaRt from imported packages commit d79addfe2d25e7f10da17ec7b6855840f7bb11cc Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 19 19:08:47 2021 +0100 Reformat NEWS.md based on current releases of cTRAP commit 4ff1f98ee38276301c29afa06c4baf5ab073ebdd Merge: 1904325 05228eb Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 19 17:02:50 2021 +0100 Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev # Conflicts: # NEWS.md commit 190432585cfa751142f766d5079aa150b1783822 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 19 17:00:46 2021 +0100 Improve drug set enrichment interface and many other UI improvements - All drug sets are now shown and available to automatically download - Loading indicator shown while loading a new drug set - Hide "leading edge" column of drug set resulting table - Reduce internal usage of data for UI components (all data-dependent content should go through server logic) commit f70f297a09af3829603adea0433dbd8dc57b212a Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 19 16:47:29 2021 +0100 Revert (meta)data viewer design - Alert if no dataset is loaded/selected commit 757429cc13f457e70ca2e377fd9ab825157b1982 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 19 16:42:55 2021 +0100 Fix "loaded" not showing after loading CMap data commit 9a28fbea3cd124b68e62bf7b7ef73e31bb81bdbf Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 19 16:38:25 2021 +0100 Fix error when visiting tables containing expected datasets and there are no data commit 05228ebcae479822b395f3ff872b32283a1d32e2 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 19 16:38:25 2021 +0100 Fix error when visiting tables containing expected datasets and there are no data commit a82df9c41b1af142e8461468fd4e3d9ce4ad13bc Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 19 16:28:26 2021 +0100 Render dataset tags as labels to easily identify them commit 7f912c622545bf48fa4143f2058b27c41bbfc378 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 19 16:20:22 2021 +0100 Exclude expected datasets from total datasets commit eda8c173857ff9a55f0f56328b232a71de7fcc5e Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 19 16:15:11 2021 +0100 Load session via qs or RDS commit 250bf7381c2613306ad81f1d0cb16752a082b919 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 19 16:12:11 2021 +0100 Fix dataset comparison plot crash with too many zeroes to estimate density commit 0e605c4713f13fe4ff5d80ae34926b785f784680 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Oct 18 20:45:00 2021 +0100 Use qs instead of RDS for data storage - Change data URL for cTRAP's pre-processed data - Load drug sets - `cTRAP()`: save data session in qs - Use qs in remote files commit b97ee0dae11466189e41613c6cf6e311fcd1f5b8 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 12 12:06:19 2021 +0100 Fix usage of string (instead of logical) values for rankSimilarPerts variables commit 8810269ab7c71d3767d317b5a1899ca6c58ed7d4 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 12 12:05:40 2021 +0100 Fix rankSimilarPerts table showing targeting drug results commit 1606e1516e693b39a8b3d6bfb1d5894f3a6eb529 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 12 12:04:15 2021 +0100 Fix showing "Running" for tasks that were "Received" but still not running by Celery commit 3262f4711e85be075fbf861ca673c0404520404c Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 12 12:03:47 2021 +0100 Fix not being able to save variables in current environment commit 46cf2250fcfe05f3a0d2912951ac3dd35d87248e Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 12 12:02:24 2021 +0100 Add link for datasets in table to their plots commit 8eff3db34c3651da5ddb251785baa188bc0fc2eb Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 12 11:56:01 2021 +0100 Avoid updating task if not found in Celery task list commit 5d793bc71acd408b1a971f66aa1a09b5011068a1 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Oct 11 16:31:09 2021 +0100 ENCODE data table: hide unneded columns by default and revert interface changes commit 344af914d843bd05f919a6e76727d55f02348422 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Oct 11 16:30:08 2021 +0100 Predict targeting drugs in global UI commit 2e778382e51e8d3afb6339927c766c1fa9c95978 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Oct 11 12:16:29 2021 +0100 Improve appearance of Celery task status - Minor code copy-editing commit d354cabf36e765b75a747905f6d9d8bc59483458 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 7 18:35:00 2021 +0100 Check if output files from Celery tasks are ready to be loaded - Update state of tasks commit e0070053ec9e1772fe0518a34feb7d0f5c7f7711 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 7 16:00:31 2021 +0100 Create dummy "expected" dataset in data to be replaced with final results from Celery commit 01c5e16189c765bd05c8eb07fcc07eaae81298b9 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 7 15:59:08 2021 +0100 Allow to create new session after initial screen - Clean existing data when creating new session commit 054ab44740d6b4740a7d40a60de7a41ef55d138b Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Oct 6 17:20:54 2021 +0100 Minor code copy-editing commit b5978d0e8768c8212ae130c113004cf486b5bf77 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Oct 6 16:13:51 2021 +0100 Fix issues with R CMD check and other minor issues - Improve Celery task - Allow to set custom path for ENCODE data - Properly pass port/host options to runApp - Fix expiration help text not showing commit a4d73d5d323558f549e71996bd018d0c42ed442b Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Oct 4 17:37:32 2021 +0100 Fix issues with R CMD check commit 6021a2108fe80f9779aabb4f3db10e30734bcac8 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Oct 4 16:51:23 2021 +0100 Fix crash with shiny 1.7.0 commit e3770847ce1103615a36e0971e5f3f4fbb157ddd Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Oct 1 19:51:40 2021 +0100 Add support for Celery/Flower - Copy-edit code commit 2575b40195ecf07b23afbad796de039413c0a669 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Oct 1 18:07:19 2021 +0100 Fix issues with shiny 1.7.0 - Avoid using generic positions when modifying Shiny objects commit 126693015d385fc8ff87de13503a85c17342c2a9 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Sep 27 15:55:05 2021 +0100 Minor improvements commit 0f71a81edc453ca3f5749919b6b99ddbcc13ac68 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Sep 23 16:52:32 2021 +0100 Automatically save session and load datasets in directory - Automatically load RDS data from session directory every 5 seconds - Automatically save RDS file with elements in session when: - Adding new datasets from UI - Loading a session from a RDS file - Loading data from session directory - Notify when loading new datasets - Show some progress bars for slower operations - Add loading status in navigation menu - Copy-edit UI text commit 962b39625f91ada7e37f2467981380c4172f6e39 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Sep 20 16:34:24 2021 +0100 Improve usage of Shiny modules commit 9997935764cb9f47ae07ee2915ed897cc6fd0c7f Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Sep 9 01:13:15 2021 +0100 Add UI for similar pertubations ranking commit a8d93436ed6dc79c8321316299e3c1d5c0ef15a7 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Sep 8 12:21:50 2021 +0100 `cTRAP()`: new global interface - Support sessions - Increase file size upload limit commit d92e061c61d53cf3ef4e19a378a1f3bf133ba31f Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jul 21 13:59:02 2021 +0100 Add benchmark instructions commit 9a9c269452d86cb57547247d398fadbea9a7a527 Merge: 914320a 64ce211 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jul 21 13:48:22 2021 +0100 Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev commit 914320a1a0d504b763330f27bb6cb048279136f8 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jul 21 13:48:15 2021 +0100 cTRAP benchmark commit 64ce211a8881cadaa68021c9d39c48707206a380 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Jun 11 18:20:26 2021 +0100 Update Dockerfile commit fd376e9af77d6ad0225b1656eff2aa5d50984f11 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jun 9 13:43:48 2021 +0100 Fix biomaRt usage warning commit 3a10760b2a5252e939564a5bc807feda16b4cf91 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jun 9 12:41:30 2021 +0100 Remove biomaRt dependency commit 415cce93af74aff20edd42d2423ab0e68c683dee Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jun 9 12:21:57 2021 +0100 Bump version to 1.10.1 commit e3ad90412bbfcb69aff984061b12aa388050b461 Merge: ec324aa e031783 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jun 9 12:21:13 2021 +0100 Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev commit ec324aad00d1438a8b4dac224eb86405032fab6a Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jun 9 12:20:56 2021 +0100 Use AnnotationHub instead of biomaRt to convert gene identifiers commit e0317832519a4073df6c3dc6a8a59e5d8758f9bc Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jun 9 11:03:04 2021 +0100 Push Docker images to DockerHub also commit 5e05ac9333072fc8d0fe913814be9bde1333cdad Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jun 2 21:30:03 2021 +0100 Update docker.yaml commit 829e9cca6ff32903272ef78d287f1671eda065e3 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon May 24 22:04:21 2021 +0100 Fix Docker install instructions commit cad6f8ac82bce4fab45f7b6207be33b0340656e5 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon May 24 21:08:33 2021 +0100 Add Docker install instructions commit 22332e7b785b916cabff5afba66c5adac6823224 Merge: 6848808 9a37355 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sat May 22 18:01:12 2021 +0100 Merge pull request #22 from nuno-agostinho/master Update docker.yaml commit 9a373551c46965464a85764475ab0247130bdb5b Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sat May 22 18:00:38 2021 +0100 Update docker.yaml commit 6848808f7edb3afa161d62e6e51e262167980b64 Merge: c46c25c 7cc03d7 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu May 20 19:22:58 2021 +0100 Merge pull request #21 from nuno-agostinho/master Update dev from master commit 7cc03d7c0bdd84fb9874d871000dc51d42640f99 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu May 20 18:19:41 2021 +0100 Update R-CMD-check.yaml commit faa40bbaf0b2b32f1a395d875cb52857e479a665 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu May 20 17:54:49 2021 +0100 Update R-CMD-check.yaml commit e8fe1b639ee3cb002b27bbd588fb719efbabbb1d Merge: 9f8a667 c46c25c Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu May 20 14:56:13 2021 +0100 Merge pull request #20 from nuno-agostinho/dev Dev commit c46c25c4d7de299d95209b68283b584d012e6a42 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu May 13 20:12:33 2021 +0100 Fix issues with R CMD build/check commit 37b8db7c46f85fc8d854168b2126d2ef72b97153 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu May 13 19:35:40 2021 +0100 Fix issues with R CMD build/check commit 262b0338b3a1ee940f7c99926b930dfddb862d87 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu May 13 18:34:00 2021 +0100 Bump version to 1.10.0 commit df87aa5fa829e3e7c0cbdcdb8830a156a0a4c653 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu May 13 18:31:03 2021 +0100 Ignore .DS_Store commit 29fd6a70ae3383955dd9f3004b9df0733259f666 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu May 13 17:10:55 2021 +0100 Minor improvements commit d96b0c24d63dc9e8f0fb338f7b09d12ca50bb9ff Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu May 13 17:09:56 2021 +0100 Improvement to graphical interface - Allow to compare different datasets - Allow to click-and-drag points to filter the table commit 0107097a7258b6484219e537a08de05b7bfc42fc Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Mar 23 15:39:36 2021 +0000 Update available columns and plot using user-selected one - Minor copy-editing commit 123ad6b23c9869623f2b8b03268d6cf20d927b39 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Mar 23 15:34:07 2021 +0000 Fix wrong element used in vignette commit 672c95bae3d280f53921f9e90244fbf54c341780 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Mar 23 15:33:31 2021 +0000 Improve data plotting in `launchResultPlotter()` - Show tables below specific plots - Allow to drag-and-select points in plot to filter table results - Minor code improvements commit 696fc29ae4bd16e9d785fbef4250072b2fea5f94 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Mar 23 15:23:25 2021 +0000 Improve `launchDiffExplorer()` - Add proxy table - Copy-edit code commit 75e74597b3e32cf8add1a1cee0bdb92a9005eee0 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Mar 23 15:18:18 2021 +0000 `launchCMapDataLoader()`: fix issues with CMap control perturbations commit c200c2c4fbbbc6f4e7e6567ff0904669897e73ea Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Mar 18 18:28:04 2021 +0000 `plotTargetingDrug()`: Fix warning regarding missing values commit 4f40b17fcdf9e56a8d5ae08c3400d14e3d281c08 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Mar 18 18:26:52 2021 +0000 `launchDrugSetEnrichmentAnalysis()` major fixes - Correctly match compounds like in CLI - Correctly use sorting column when plotting commit 7caf66c0a8d542a8ef4c47abd9f013c4fa6573de Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Mar 18 18:20:38 2021 +0000 `launchCMapDataLoader()`: add bubble plot of CMap perturbations commit 82ab28bab7c76eb152adb8a965dfb3e1cdf2e884 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Mar 17 11:06:29 2021 +0000 Improve `plotTargetingDrugsVSsimilarPerturbations()` - Fix highlighting of plot points depending whether drug activity is directly proportional to drug sensitivity - Add rug plot - Copy-editing of code commit 8252cb92e4fb685146cb130ef61ebab2442b27ca Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Mar 17 10:46:47 2021 +0000 Rename first column's name of the resulting table to `descriptor` commit be66eb8b118705a839199e62c9cb2f589160405c Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Mar 17 10:37:38 2021 +0000 Improve handling of HDF5 data for expression/drug sensitivity association - If argument rows/cols is NULL, load rows/cols according to rownames/colnames of the first argument - In verbose mode, print number of columns and rows to load - Close all open HDF5 connections (avoiding warnings of open connections) - `plotTargetingDrug()` now supports loading HDF5 data to plot - `plotTargetingDrug()` labels now avoid showing missing values commit 6085cc136ad7b9687141092c612b17857f04750f Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Mar 15 15:40:24 2021 +0000 Fix wrong labels when plotting `targetingDrugs` objects commit d82f293c59e124d56f1bb363290434b8ec08db8a Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Mar 11 20:41:39 2021 +0000 Subset custom objects by column when only passing one argument - Slightly improve performance of cmapR functions commit 4d759cbf2204e517c64b7287f99cb70ea4a6197e Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Mar 11 15:21:44 2021 +0000 Avoid explicitly showing NA in plot labels commit fda582a6a8ffb95f5a9b4918e4f6af5f4120e074 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Mar 9 11:40:37 2021 +0000 Persist selection of other elements when selecting another perturbation type commit 06e8ddd96ddc5a082e1b7002ab669f3c3f4b0338 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Mar 8 18:03:58 2021 +0000 GUI: Load multiple CMap perturbation types at once commit 38040682df3c47845d0579c157dc607d3de9f917 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Feb 26 19:51:33 2021 +0000 Improve graphical interface for drug set enrichment analysis - New launchDrugSetEnrichmentAnalysis() function - In DSEA, change "pathway" to "descriptor" - Word break long strings as needed commit c8f6aa94f514c7ba006c7d0d2e8b5bbe7d54c34d Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Feb 9 18:15:03 2021 +0000 Allow to change chunk size and copy-edit documentation commit 7a993f3781fb0db386e48d1f7ea8bd2352e9d684 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Jan 25 18:41:22 2021 +0000 Increase optional message verbosity commit d6ff29bb96cca3f94c3d7b48b2a0595d5672fe0e Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Jan 25 15:36:42 2021 +0000 Small changes commit 296f9b21a6ab7e6c145681a6b3e688cfeb7ef5a6 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Jan 22 15:21:07 2021 +0000 Chunk data columns based on chunk size of 1 GiB or less commit b1aa07819210ea261d29453478196326310a66a6 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jan 21 14:44:44 2021 +0000 Fix GSEA scores affected by lower number of loaded genes commit f932ea5d44deffca2121056c56662c287c6d90ed Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jan 21 09:41:04 2021 +0000 Add tibble to Imports commit 2e08d24aeaf36326610a037d7f593f87f1d2792f Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jan 21 01:06:12 2021 +0000 Reduce `predictTargetingDrugs()` memory footprint - Load and process NCI60 gene expression and drug sensitivity correlation matrix in chunks (by giving specific rows and cols to load) - Save NCI60 correlation matrix in HDF5 format to allow fast data subset loading - Read attributes from HDF5 file without loading data values themselves into memory - Load data for intersecting genes only (instead of all as previously done for CMap z-scores data) commit 1c8ecaccb56b6c4e0430c28a0668c3b022463e44 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Dec 7 14:51:57 2020 +0000 Improve drug set enrichment analysis - Allow to set key columns to match compounds between datasets - Use same internal algorithm used to match compounds in `plotTargetingDrugsVSsimilarPerturbations()` and refactor code - Fix bug where trying to convert non-numeric values to numeric for key columns - Reorganise code commit 3c51a4f3589ecef46eed25cf40071b45a508f403 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Dec 2 14:54:07 2020 +0000 Fix issues with missing values - Fix setting names when there are missing values - Fix error when there is a low number of non-missing values commit 741776aece429d4112a977841899fd2c742ec406 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Dec 2 11:14:29 2020 +0000 Directly set metadata conditions on preparing CMap perturbations commit dc5fa2ce2580020b0f9cd9333bf19212da1400a9 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Nov 24 15:46:13 2020 +0000 Include example of differential expression for dev scripts commit d1359242c97ff231649711baa4a98cfc83378660 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Nov 24 15:45:21 2020 +0000 Test differential expression for cystic fibrosis dataset commit 52179075912d5da67012e2ca5dea3ed68b315193 Merge: 5539163 e8ce386 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Nov 24 15:43:07 2020 +0000 Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev commit 5539163151801106be162eee7cfc42bf01bbca57 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Nov 24 15:42:52 2020 +0000 Include parallel package commit e8ce38686b6fba8f52414c5b60ef046bb71e7833 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Nov 24 14:31:55 2020 +0000 Update R-CMD-check.yaml commit 00f1d40522afb63633568117755ae1e0f6cc6de2 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Nov 24 13:48:46 2020 +0000 Include fastmatch in packages and ignore TXT files commit 562bf2ef9e152ec61a6df001d32b4485f679e245 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Nov 24 13:25:01 2020 +0000 Set drug set size and max set number from numeric columns commit e16e3826ebe39baf7d1bdb42a764075e2bda6808 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Nov 24 13:20:14 2020 +0000 Import fgsea commit 73236f2258ba7ed922618cf69e2aeeb300a13d49 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Nov 24 13:19:10 2020 +0000 Allow geneset sizes of 0 commit 1d2f2e35713ce91043fdfae751ca3206c9adfd75 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Nov 24 12:12:30 2020 +0000 Support multi-threading commit 9f8a667e364e8779ebdbffe8ecae292274afd2bb Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Nov 23 12:33:55 2020 +0000 Fix setting environment variable commit 0d8d3e536657e56ec2b40df2f3e789e35f0d4955 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Nov 23 12:05:22 2020 +0000 Avoid bioc-devel while R-devel is not available commit 35b93f85e99b888d30df27e4b7fb7871a847d338 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Nov 20 10:03:07 2020 +0000 Fix non-proper function usage commit cec61881dc51bde97a736519c86c2534384824d0 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Nov 20 00:39:43 2020 +0000 Fix usage of non-imported external function commit 001788fce6e94e3f3db01e503b779277fa4aa223 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Nov 20 00:18:15 2020 +0000 Fix original column order when comparing data by chunks commit 1f35b4689fb80bb79dc5362557afe3ca4cb4d7f1 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Nov 19 17:45:33 2020 +0000 Fix original column order when comparing data by chunks commit c34566c79909b64a0f0735c91e62e32d28a604f7 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Nov 19 15:19:57 2020 +0000 Fix error when using pre-loaded z-scores commit d106ee19eee70028d6f55f6ab2441f7daf8a179e Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Nov 19 14:39:41 2020 +0000 Reduce redundant loading of CMap z-scores commit 093c1b9fd73d7a5bc83fc02d1af4548ac3fa1560 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Nov 18 12:51:55 2020 +0000 Fix drug sensitivity script commit b13ee45bff3d41fa2684376d191658fb7905567c Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Nov 18 12:50:38 2020 +0000 Speed up GSEA-based score calculation commit 15229dd8dd812057c551446ed776ce348074e427 Merge: c29a84b dd8aedf Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Oct 30 11:10:21 2020 +0000 Merge pull request #15 from nuno-agostinho/dev cTRAP 1.8 commit 7311d8f6320810184ad6edcbd5287cc765af127e Author: Unknown <unknown@example.com> Date: Tue Oct 27 18:41:26 2020 +0000 Improve compound descriptors - Fix compound names and information in NCI60 3D descriptors - Replace 99999 with missing values in all compound descriptors commit 79caf31461b919e5bfa38c35e8573fe354e1438b Author: Unknown <unknown@example.com> Date: Tue Oct 27 18:37:16 2020 +0000 Test multimodality of drug descriptors commit dd8aedf59ed85b0f21fd9cffc76a4d0c38cdf004 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Oct 23 17:57:16 2020 +0100 Fix issues in R CMD build/check/BiocCheck commit 27deee0e974cb02f4adcf1159470eb02006c2918 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 22 19:24:59 2020 +0100 Include more useful dev scripts commit 91a27d6a05acfc81fe86cd9475e169dd74ec7287 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Oct 22 19:19:49 2020 +0100 Create evenely-distributed sets for numerical drug descriptors commit a237e3ceab189650b2c75bbab639389ee669f057 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Oct 9 12:18:47 2020 +0100 Add graphical interface functions - `plotTargetingDrugsVSsimilarPerturbations()`: automatically look for matching compounds in multiple columns of both datasets - `plotTargetingDrugsVSsimilarPerturbations()`: allow to manually select columns on which to merge datasets - `downloadENCODEknockdownMetadata()`: Save ENCODE metadata to a RDS file - Include dev folder commit 354b26559df96eacd7e68004486cbfd9dbd3791f Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Oct 9 12:18:29 2020 +0100 Simplify tutorial commit c29a84b546e5ac163179103683fdd3505fb7c246 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Aug 17 19:50:47 2020 +0100 Fix pkgdown install commit 979d873bb0fdf0b7354a0997ac52a10f741881da Merge: af82d42 d21bb4e Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Aug 17 18:01:33 2020 +0100 Merge pull request #14 from nuno-agostinho/dev Bump version to 1.6.1 commit d21bb4eff0ff60e05406a418420fd6372f2efbc1 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Aug 17 17:58:57 2020 +0100 Bump version to 1.6.1 commit af82d42bc129829053e13729e53c494d2a5b2292 Merge: d6be0a1 15d0584 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Aug 17 17:41:20 2020 +0100 Merge pull request #12 from nuno-agostinho/dev 1.4.1 commit 15d058469022db03170b5a51b6db7ea388ae6255 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Aug 17 17:39:45 2020 +0100 Remove TODO list from NEWS commit f2e860079ef46ec66133c82f20d2807132ecaebb Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Aug 17 15:24:42 2020 +0100 Fix issues with R CMD check - Suppress ggplot2 warning on using vectorised argument in `element_text()` - Document `title` argument in `plotComparison()` - Correctly import other package's functions in the needed functions commit 02e4600768009ed437ee006949cb0db61f4caa25 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Aug 17 12:45:23 2020 +0100 Fix ranked genes in compact GSEA plots taking too much space commit 558fa3fdf53e3607dccf42916280ae8750d3bcc1 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Aug 17 12:44:56 2020 +0100 Show first/last values of ranked genes in GSEA plots commit 6bf5556bbf7e0150fec2a6420acc815673d0d597 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Aug 17 12:12:52 2020 +0100 Fix legacy code in GSEA plots for targeting drugs commit 4855a2440ff2d37470fea98e3c24ae952f753ea1 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Aug 17 12:02:30 2020 +0100 Set plot title when using `plot()` commit c17360b9f12a5039f871b7f85460c6d8199b0b87 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Aug 16 21:04:24 2020 +0100 Fix GitHub Actions badge commit 771d5f80711a98aa487f259284e582e2e993072d Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Aug 16 00:42:36 2020 +0100 Fix Docker name commit 98adb199687028c130eadb4e08045eae43f75f87 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Aug 16 00:38:07 2020 +0100 Fix Docker name commit 8176d8520e08ca6cf807a3fdc8c351fb4b65dfa9 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sat Aug 15 10:56:36 2020 +0100 Use latest Bioconductor docker commit 5373a8f410a3dc7ad7633b75b64c4f8207994945 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Aug 14 13:16:04 2020 +0100 Fix R CMD issues and copy-edit documentation commit c413a30097af999ac085b7b4fec5e012318f382d Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Aug 14 12:26:29 2020 +0100 Use GitHub Actions commit 95a2082c07f2260f0065ec4949a25e8017af6aa8 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Aug 14 00:36:03 2020 +0100 Copy-edit documentation commit 0a502918ff6a81765409eab7bca69e7a538bd2b4 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Aug 14 00:34:57 2020 +0100 Preserve original order when converting results to table commit cf9672fe0b928c13ec7f01ca868175cc4d761b32 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Aug 13 23:33:03 2020 +0100 Fix changes related with ENCODE metadata commit 5b651b89b28dd9e46d3c163e66bb19eee5b1eb12 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Aug 13 18:21:21 2020 +0100 Plot GSEA of multiple perturbations commit 9f1a17d3a26680ecf313183cbbd0dacf1a534f6e Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Mar 4 14:38:22 2020 +0000 Generalise as.table for referenceComparison objects commit d9e041576608c50169ac06a6f20bb00355a402b5 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Mar 2 15:52:09 2020 +0000 Fix warning when trying to read average cell line perturbations in z-scores file commit 636d48b0f3a3ebd1b6caddde4c76db5b52eca0f2 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Feb 27 10:24:42 2020 +0000 Replace WCTS for WTCS as appropriate commit bd4d1283ca180fc09f72ac84aeb47c5f38cbdbaa Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Feb 27 10:24:10 2020 +0000 Improve `as.table()` commit c7db4e3aabadcb647d63e8ebe2f47eb1a8545fc8 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Feb 25 10:57:20 2020 +0000 Fix truncated warning commit 6b1fcb5ab0192e3c63b60497f5a2ca9c5b74a56a Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Feb 25 10:39:19 2020 +0000 Include genesize for custom geneset commit cdc7084b96397885700865c9d58600de99398f58 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Feb 25 10:32:27 2020 +0000 Copy-edit function documentation commit bed21e5b6d99640e67dffee67ed2a489f4b6f339 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Feb 24 18:04:00 2020 +0000 Allow to set different gene set size for top up- and down-regulated genes commit 9f9d106bfad5ff484451e6374e4bd509ec4852dd Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Feb 24 18:00:14 2020 +0000 Fix plot of CMap perturbations not showing enrichment score (ES) parts - Same behaviour as performed in 1.4 release commit 068a47115c258e87040bcdf167d13d1e7a8cd633 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Feb 24 12:01:11 2020 +0000 Copy-edit NEWS, tutorial and function arguments and documentation commit f18993e7f36cec3b83929b0f059d1de6a8e077ec Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Feb 24 11:57:31 2020 +0000 Allow to directly input zscores data when plotting commit ac12716ad641682ce802027c77379812ffc1a58e Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Feb 18 20:36:59 2020 +0000 Test enrichment of custom gene set and plot targeting drug results - `plotDrugSetEnrichment()` now returns a list whose names are drug set names - `plotMetricDistribution()` now supports only two or less gene hits - Copy-edit messages and function documentation - Copy-edit tutorial (e.g. resize figures) commit 24113a82d8c745c33dddef4859dd633d9dd98e64 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Feb 4 11:40:33 2020 +0000 Use Linux and bioc-release for later build stages commit b50e74d5974eb67596912175c899268ef36b14f7 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Feb 4 10:03:42 2020 +0000 Use Linux and bioc-release for later build stages commit df4e68061c2edccf853fecf04fda7aa5bdbe9520 Merge: 8de1337 8f8d794 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Feb 3 19:02:07 2020 +0000 Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev # Conflicts: # .travis.yml commit 8de133703ac1825ebcdab314fc006734a9b2d812 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Feb 3 18:59:32 2020 +0000 Fix warning from config file commit 8f8d794c7b0db2e8ff601a438f0d9cf0e80bc6f0 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Feb 3 18:59:32 2020 +0000 Improve Travis CI automation - Include macOS support - Include pkgdown site deployment - Remove warnings from configuration file commit b2a95c4cab07fbaf823fe8ffc9b20d4ca4ff6e9e Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Feb 3 18:35:06 2020 +0000 Spell checker support - Fix documentation misspells commit d22ff7beae561d379670dd20fe0f0b94f97f0964 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Feb 3 16:18:08 2020 +0000 Create pkgdown site in GitHub pages, improve Travis CI and include spellcheck - Copy-edit function documentation - Improve Travis CI stage builds - Add spellcheck commit ef1067736d0ee89555b5eb51dc19ad53f7ebb4dc Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Jan 31 17:54:47 2020 +0000 Update NEWS.md commit 38b1f974d82d699aacfff0295ef229f54cc3487a Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Jan 31 17:54:25 2020 +0000 Improve function documentation commit de89b2d261b69000f0af28c3d7bdd42d64c948ec Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Jan 31 17:54:01 2020 +0000 Copy-edit tutorial commit 32bee1170040822ec99e8f5f629a031e7bc7df98 Merge: 48e97d0 d6be0a1 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Nov 18 11:44:31 2019 +0000 Merge branch 'master' into dev commit 48e97d03ffa40e5d5e3177eb7ea75c0df2ffc6fa Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Nov 18 11:35:51 2019 +0000 Bump version to 1.4.1 commit d19c22d3d34e5a91a2d0820fbeb2ad7467fe1b5e Merge: ac9661f cae2411 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Nov 18 11:34:25 2019 +0000 Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev commit ac9661f915d3836fd3e90129cd25099b1e6fa39c Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Nov 18 11:34:07 2019 +0000 Improve tutorial commit 07d5ee48b3d4037ba0467eaeb9301d73f0816261 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Nov 18 11:32:41 2019 +0000 Copy-edit CMap-related console messages commit 310a2808e9a112531fc3420a6d8c2613947f9e2f Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Nov 18 11:29:10 2019 +0000 List available gene expression and drug sensitivity associations commit d6be0a17fdb10c53295059bd02101585a4f5bd95 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Nov 11 23:12:14 2019 +0000 Fix Dockerfile commit 86a58282c2ee7120f0cd8d572b2b9ac7777e37fd Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Nov 11 22:44:16 2019 +0000 Bump version to 1.4 commit 2d9a9f466e4642372c96d814f576c1209eca8777 Merge: 08457c7 cae2411 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Nov 11 18:43:09 2019 +0000 Merge pull request #8 from nuno-agostinho/dev cTRAP 1.4 commit cae2411c020a59c1259fc5834b23fc56e58ab207 Merge: 28a6eec 5ee5dd4 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Oct 28 16:15:35 2019 +0000 Support Linux+Mac CI in Bioconductor release+devel commit 28a6eecc51d8ae0aa5fd27deb0346bfd08426e18 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Oct 28 16:14:48 2019 +0000 Fix downloading binary data in Windows commit 5ee5dd4700e111e642438d3f5c9885833ddf4629 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Oct 28 11:42:23 2019 +0000 Support Linux+Mac CI in Bioconductor release+devel commit 84e2e1433d7a7cd30aeb35078cf5dd550f909899 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Oct 25 18:52:53 2019 +0100 Fix issues with downloading CMap data in Travis CI commit b90ae9dd86751972aca421ccb08d04e80938d8bf Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Oct 25 18:33:48 2019 +0100 Update NEWS date commit 7525748033c6f1c7be98cef1c0ba8410d6cd80c6 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Oct 25 18:33:39 2019 +0100 Include rmarkdown for CI builds (specially Travis CI) commit 65c85f6d1c858222ff9c614fcab418d24b0b161a Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Oct 25 18:24:12 2019 +0100 Fix R CMD build/check issues - Fix 80% of non-runnable examples - Fix ASCII characters on cmapPerturbationsCompounds commit 2e2b53c0231b6a91c271e6519aa8c5c0bb4a7cb8 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Oct 21 16:38:44 2019 +0100 Minor changes commit 757381cf607f160b405e2e2c11ee087aa2a7d16f Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Oct 9 14:45:26 2019 +0100 Remove two depencies commit 7c66c201823f67f3af56c2088ccf886e40b84d65 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 8 18:57:15 2019 +0100 Load missing library for unit tests commit 5bed9e16fecaa4eb694f21a73eba1dc53f87c9ce Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 8 18:56:42 2019 +0100 Improve vignette commit 72c2067fe07bd2a882255db35585fc2b1596e94b Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 8 18:55:59 2019 +0100 Improve function documentation commit d57c21c079c815b4bb7a402a8658da3d899fc46a Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 8 18:55:00 2019 +0100 Update links to download CMap data from GEO commit 87722655caab4617fc48f1920a89ee78bc94ea6d Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Oct 8 18:10:39 2019 +0100 Add recommended biocView commit e554ddfbdce8a1b9b85c0d25a4a9dcdf678ef7c6 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Oct 7 18:24:26 2019 +0100 Fix downloadENCODEknockdownMetadata not returning metadata commit 5759fe66f37a42e24b81e1bc5d5c65ce1bc811ca Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Sep 30 17:11:18 2019 +0100 Improve gene expression and drug sensitivity correlation - Add dataset versions (GDSC 7 and CTRP 2.1) - Use -AUC values instead of AUC values for NCI-60 drug activity metric (so it is directly proportional to drug sensitivity) - Allow to state whether drug activity metric is directly proportional to drug sensitivity or not commit cf0959616b89e8a4114dead4fa9b555c8806af78 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Aug 16 15:14:10 2019 +0100 Improve drug set enrichment analysis - Add support for 2D and 3D CMap descriptors - Improve name of drug sets - Improve compound matching between drug sets and data of interest by using respective metadata and compound information (when available) - Improve unit tests - Scale number of breaks in metric distribution according to number of ranked elements - Add title of drug set in use for GSEA plotting - Minor code copy-editing commit 3e715b3722af09f03f2815cad800e8244d41e6ae Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Aug 16 15:04:29 2019 +0100 Add Dockerfile for Docker images commit 58568ef4e0bcbe36b0d68b6c42691ca6cba45bc3 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Aug 7 18:49:49 2019 +0100 Set dataset version for expression-drug sensitivity associations commit c27a88121a3207a903248aaab7c717fd08743069 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Aug 6 18:09:38 2019 +0100 Fix R CMD check issues and export loadDrugDescriptors commit 982ea9eb5fb2cb49f3a0b3264b7cebb5ae73c8e5 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Aug 6 14:52:32 2019 +0100 Fix unit tests for CMap perturbation ranking commit 4501e94f3145eb24fd28dd1a0126d8902d74101c Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Aug 5 17:06:59 2019 +0100 Cross-reference functions in function documentation - Fix issues related with R CMD check - Copy-edit function documentation - Organise code - Export function convertENSEMBLtoGeneSymbols - Import missing packages - Add alias to rankSimilarPerturbations() commit 7757ace30681980d06f1a978f2b517cb44fb477c Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Aug 5 16:12:21 2019 +0100 Analyse drug set enrichment - Prepare drug sets based on a table with compound identifiers and respective descriptors - Test drug set enrichment - Copy-edit plotting code - Copye-edit NEWS - Add in tutorial commit 4c046303daeb691003c0068d665868d787c1c911 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jul 18 19:05:31 2019 +0100 Predict targeting drugs based on drug sensitivity data - Export function ot convert ENSEMBL to gene symbols - Stop if no intersecting genes are found - Improve vignette, including demo of new features - Copy-edit documentation - Include compound information in cmapPerturbationsCompounds - Sort results based on rank product's (or other method's) rank commit ba77e3d317930f5d68c04ace6038c26512690009 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jul 11 16:41:33 2019 +0100 Fix literal NAs in compound metadata commit ba1d86c7247971e1e428a58d17fb27846b7a831a Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jul 11 15:42:27 2019 +0100 Include information on mean perturbation scores in metadata commit 26e3fac3c3c415b4d00bb78e2d3da93af90b1115 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jul 11 15:40:39 2019 +0100 Fix missing imported functions in use commit d069d66202b934f9c165ef2175c3fa8ecbd4f764 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jul 11 15:30:13 2019 +0100 Fix classes of demo datasets commit 4628cf9d089e9cdaa03156140c607ae4e5705e60 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jul 10 18:28:42 2019 +0100 Improve chunk loading of CMap perturbations commit cf749415989dee9b638a4e54eea0797131321850 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Jul 9 10:50:41 2019 +0100 Improve function names related to perturbation comparison - Rename "compareAgainstCMap" with "rankSimilarPerturbations" - Rename class "cmapPerturbations" to "perturbationChanges" - Rename class "cmapComparison" to "similarPerturbations" commit 0b0f6ad901c23edb84a7c84c2e7a4c0dc49ab0e6 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Jul 8 17:32:47 2019 +0100 Fix error when trying to calculate the mean for cell lines with no intersecting conditions available commit ab423c3de86d8ed88947fefe8e24c97ec2751721 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Jul 8 17:31:58 2019 +0100 Include rank product's rank in tutorial commit 0b6da8578f1c4b4d41e5dacf093c318fb69a1ea9 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Jul 1 13:02:30 2019 +0100 Clean up CMap perturbation comparison code commit 6d25ad9a1a24f2dcc1343b9537aa3580bcb42753 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jun 26 16:41:20 2019 +0100 Calculate rank product's rank commit 23b9fb4f5a0740e8fcf36a13cf15ff6a2334d1c4 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Jun 21 14:20:08 2019 +0100 Display summary of laoded perturbations after running `prepareCMapPerturbations()` - Copy-edit NEWS file commit 59d9a8a2f8fde407802edb91dc6998b3d2c42516 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Jun 21 14:18:52 2019 +0100 Assign missing values to identifiers of summarised perturbation scores commit f94100f38f13a107611278bf844202436efa6a8b Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Jun 10 20:22:28 2019 +0100 Fix R CMD BiocCheck issues commit dff63d9cdf524b874ee52caaa9b2d6659aee29f2 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Jun 10 20:10:43 2019 +0100 Update R dependency commit f303096f18b5d0f7de0d136aa94960ad97993f5c Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sat Jun 8 15:35:31 2019 +0100 Allow cmapPerturbations to load z-scores directly if preferred commit c704ba04f1b87ee70955b23e65765ffcb77c2715 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sat Jun 8 15:06:28 2019 +0100 Unfix assembly filtering (ENCODE API issues) commit 8a61a6dac408133574ea32f48bdb73c0adebe67f Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sat Jun 8 14:38:14 2019 +0100 Ask to download CMap perturbation z-score file if not found commit 2b02ea9d41a7e506552d91783cf4ffcacc24f084 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jun 6 14:18:30 2019 +0100 Fix ENCODE metadata downloading a table of missing values commit 4fcdbc6ac4af450a68189b49c2e5bfa8eb0d3e43 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jun 6 14:18:03 2019 +0100 Improve plot unit tests commit 48a780e5656e7bcf6652b70579101c8f1c5aa503 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jun 6 13:06:47 2019 +0100 Perform correlations on all filtered perturbations Faster than by cell line, as previously done commit fd761a6c3dfdbd947aadd77b0dbb1f83a383d385 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Jun 6 13:05:25 2019 +0100 Fix getCMapPerturbationTypes not correctly showing control perturbations commit 3769bd9d96e7f13cb9c8353e7146781bbe446734 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Jun 3 15:49:43 2019 +0100 Fix bug when comparing differential expression profile against a single CMap cell line perturbation commit 29482d92b4ac9b15d7d8533e1646dc3a1fe5e20d Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu May 30 17:21:53 2019 +0100 Decrease RAM requirements by loading chunks of CMap z-scores on-demand - Instead of loading CMap perturbations, prepare its attributes and save its filename for loading chunks of data on-demand - Modify compareAgainstCMap() and plot() functions to load chunks of CMap perturbation data on-demand based on its filename - Copy-edit code and comments commit 76de2f694e81034583cac38b624f19c61a1b77b5 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon May 27 17:07:38 2019 +0100 Improve loading of compound information - Significantly improve time taken to aggregate compound information from both drug and sample files - Allow to use real filename of either the drug or sample file - Show filepath of file to load commit 6dae1ab66bcf6fac3936f11ccb1d5b3fda8087a4 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed May 22 23:39:55 2019 +0100 Rename vignette filename commit 80bb53ed9d971f595596622a1081e95160a5bb75 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed May 22 23:18:57 2019 +0100 Fix NEWS commit 17f45db3513a62f79268503c6e654686fe0628fd Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed May 22 23:08:16 2019 +0100 Update version number commit 44daf6e0a677b48b9ae4c92b90f1aba811b1cb7b Merge: b965ee5 a1f9059 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed May 22 23:01:12 2019 +0100 Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev commit a1f9059dc26b518b8df58c1ccdee867446e0cf2e Merge: b94b605 08457c7 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed May 22 18:49:18 2019 +0100 Merge branch 'master' into dev commit b965ee509e7f7d496cbf601445fe3b854d50324c Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed May 22 18:34:21 2019 +0100 Fix R CMD check issues commit b94b605dd8a8da7fce168589cb5fcc1b15cfa37c Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed May 22 18:19:45 2019 +0100 Colour scatter plot based on cell lines for cmapPerturbations objects commit 23b06b7ea10184fd5c98d0a1f5af45a3ec7fc573 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue May 21 17:24:29 2019 +0100 Update tutorial commit 3a38efd31d8f25b8402fea8ceed6f4d60213a399 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue May 21 17:01:47 2019 +0100 Fix issues with R CMD check - Add unregistered dependencies to NAMESPACE - Update data to avoid non-ASCII characters - Update, copy-edit and simplify code to get example data - Copy-edit code, documentation and unit tests commit 2ed1521104ef25d7b5eb7a223ed697bc1ea76d9a Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon May 20 18:16:18 2019 +0100 Include missing packages and sort them commit e5303e6f5653b664e22d9ddc7eed0aab87888db0 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon May 20 18:09:45 2019 +0100 Parse CMap identifiers commit 869b31018d31f88865a8512ad1c0dd16d34f01e0 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon May 20 17:50:07 2019 +0100 Test plotting non-ranked perturbations commit 2c53a62fdd40ad9e72b64a71bd63b881a6d991f8 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon May 20 17:24:29 2019 +0100 Increase verbosity when (down)loading data commit 31dd24dd0f384d8b8b2bbee7c0d42e2c6475f99e Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon May 20 17:23:40 2019 +0100 Plot non-ranked perturbations when plotting a cmapComparison object commit a88f650421fc2e87a58c936c11a673372cee8242 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon May 20 17:20:49 2019 +0100 Improve compareAgainstCMap function and copy-edit commit ffd96f0f8aec576e771ad309d4d653e90b410d1e Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue May 7 18:48:27 2019 +0100 Improve plotting and add unit tests - Warn if cmapComparison object was not run with a given method - Automatically select 'spearman' as the default method commit 14481989b5d90a5c7df50810c319a768c2310133 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue May 7 16:49:17 2019 +0100 Fix bug when comparing against CMAP using only one method and fix test units for compareAgainstCMap commit b1a696a6baa3309e71a41c8fb4d26dd7af5bb3f2 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue May 7 15:25:25 2019 +0100 Minor changes commit cb43cf05a2cc8c067ae792cece3bcd06dbb695b2 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue May 7 15:24:13 2019 +0100 Rank similar perturbations based on individual cell line commit af2df9a36d2ba2d87ce84ff1f515bcff4428d0ea Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon May 6 16:00:18 2019 +0100 Fix non-exported function commit 32e11baed4197cc32c0dfb91c3b4f424bee3bbb1 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri May 3 00:08:12 2019 +0100 Fix issues with plot testing and copy-edit NEWS commit 98ef9aaafaa244e7fa24373bd37f6591296c7aec Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri May 3 00:07:16 2019 +0100 Update tutorial vignette commit a7a601e4468d162f959e789e46cf3a8279d6d890 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri May 3 00:04:37 2019 +0100 Improve plotting functions commit 164d88c4bc28b69f43cbe29eb18148853fc88d6d Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri May 3 00:02:23 2019 +0100 Update demo datasets commit 9022435dfcbe49f289212136c52598c140ea4adb Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Apr 29 11:17:11 2019 +0100 Improve compareAgainstCMap commit 76ccfefb02a67d4ef05c57a7181a6a280225f362 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Apr 25 13:52:49 2019 +0100 Improve metadata retrieval and helper functions commit 54a413f5446d03e6d2cf257f5b1b4a75a48622c7 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Apr 23 12:53:49 2019 +0100 Improve metadata integration from CMap commit 189be68657ce74be29eacbb561e96993cc470a1d Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Apr 23 12:43:41 2019 +0100 Download and load multiple genes and cell lines from ENCODE metadata commit 78fb7cc6111da544f4b1a8d72cf86a278cae70a2 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Apr 23 11:52:37 2019 +0100 Improve performance of handling cmapPerturbations objects commit 36c533c0c34684372a4616ca5a88dec8a828a62c Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Apr 23 11:49:49 2019 +0100 Update .gitignore commit 355cda028c6cb1f6ad7c8571e09ccaf0cc879fc9 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Apr 18 14:37:28 2019 +0100 Replace instances refering to L1000 with CMap commit db34dcb0e9acb4185cd344e1b6c2bb2710de5bdf Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Apr 18 13:43:54 2019 +0100 Minor changes commit 5e8cda2ea1d5023a9d73ff1ef7644740c2a421b8 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Apr 18 13:43:13 2019 +0100 Rename function names containing download to load commit 907b20f7722d0eee74a3e1c6047fbff64be5a8e5 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Thu Apr 18 13:23:43 2019 +0100 Update .gitignore commit 69c59c2e07286dab54f54ff0bb2d309edbcb24ca Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Jan 30 17:30:12 2019 +0000 Major changes - Improve plotting with new plot types - Update function documentation - Update vignette commit e127a0badad7195a01b9170e36dafc537e4b286d Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Dec 5 15:59:42 2018 +0000 Update and copy-edit the tutorial commit 8746c644e85b278500c2ec8d92c826b78752c52d Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Dec 5 15:57:00 2018 +0000 Update function documentation commit b97b1020fd32bbb70e25b08333b855182e9c37e2 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Dec 5 15:55:00 2018 +0000 Improve comparison performance when testing for correlation commit 65e0cce55becbd4f62f604c811c458f8bde98d60 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Dec 3 17:53:13 2018 +0000 Create l1000perturbations object with associated metadata and functions to edit said object - Correctly set name of perturbagen types when comparing against CMap perturbations - Avoid calculating the mean across cell lines if only one cell line is provided when comparing against CMap perturbations - Automatically order results when comparing against CMap perturbations - Update internal datasets - Update .gitignore commit 08457c7b836670c6080c04fd92755d4dd15ac376 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Dec 3 15:56:15 2018 +0000 Add tag ImmunoOncology to BiocViews commit ec346fc5fbd6d68305f6b0431f9cee2d2ab04dce Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Tue Nov 27 15:52:27 2018 +0000 Replace instances of -666 in CMap data to show up as missing values commit 45be6754e1e9648bafbcb0867de428444f234ffb Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Nov 21 15:45:26 2018 +0000 Update NEWS and bump version number commit 309bde4c6c90f9429c358961b6e7ac18fadf5451 Merge: 1d0814a fc66327 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Mon Nov 12 15:47:59 2018 +0000 Merge branch 'master' into dev commit fc663279c4dc280cd44c193787b2056aa2c7a2e0 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Nov 11 18:23:17 2018 +0000 Fix comparison against CMap perturbations using GSEA commit 1d0814a3081d779545246c3376812f2114fde713 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Wed Nov 7 17:43:27 2018 +0000 Include BSD3 license for cmapR commit ecb24ebeb47ea27b5fb71e7b911f4de0bf59b923 Merge: 2611ec8 74e338b Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Nov 4 17:43:40 2018 +0000 1.0.1 commit 74e338b39bb0a4bcbe872f2a0f19e46b181cfa43 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Sun Nov 4 01:37:17 2018 +0000 Suggest biomaRt to build vignette commit daf0ce22ee2e2978cd82f4ce6a925c530ed1e401 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Nov 2 15:15:27 2018 +0000 Fix issues with duplicated gene symbols commit 6b880aa0864a5bcca9e54b1fb17eeb4199e0f7c7 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Nov 2 14:57:07 2018 +0000 Select p-value adjustment method when performing correlation analyses commit 72da59d442564046f8923a4fd953169ec3c26be9 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Nov 2 14:40:35 2018 +0000 By default, show CMap perturbation types except for controls commit f8387e863ef814685c8ad07d71c59eb469968bf0 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Nov 2 14:39:23 2018 +0000 Update NEWS commit d1e7a94c57ef85978231bad2aa4fa0eee9f77411 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Nov 2 14:32:27 2018 +0000 Fix obsolete function calls in function documentation commit 9697b622f232a35d1f4f8bf3a3f05d5e803ff9b5 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Nov 2 14:32:07 2018 +0000 Remove "_t" from column names from the results The t-statistic may or may not be used by the user commit 7d301bfb02af285f1947535c2776745a23c8e4a4 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Nov 2 13:40:24 2018 +0000 Remove biomaRt dependency commit bcf9769b0c64d89ffd090abe5cececd653ea5c16 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Nov 2 13:07:22 2018 +0000 Update title, author names, version and README commit 9b56c207c74cc02ee0c0441d734fde98f16e9328 Author: Nuno Agostinho <nunodanielagostinho@gmail.com> Date: Fri Nov 2 13:05:28 2018 +0000 Hide non-exported functions from reference manual
Package: CATALYST
Commit: 462b12173c6fde7a88b13887ba8c181e1360577a
Author: HelenaLC <helena@crowells.eu>
Date: 2024-03-27 10:53:43 +0100
Commit message:
Commit: 462b12173c6fde7a88b13887ba8c181e1360577a
Author: HelenaLC <helena@crowells.eu>
Date: 2024-03-27 10:53:43 +0100
Commit message:
unit test & docs fixes
Package: multicrispr
Commit: 5aadbd37f2c2eebc4762c7a40923164738e5a3d1
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-27 10:52:56 +0100
Commit message:
Commit: 5aadbd37f2c2eebc4762c7a40923164738e5a3d1
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-27 10:52:56 +0100
Commit message:
Eliminate assertive.sets (in devel)
Package: multicrispr
Commit: 549f0f55a8ac0417aae261dd6859e43b2c2f6257
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-27 10:20:35 +0100
Commit message:
Commit: 549f0f55a8ac0417aae261dd6859e43b2c2f6257
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-27 10:20:35 +0100
Commit message:
Eliminate assertive.numbers
Package: iSEEindex
Commit: 853cbfbf11f5d70fa0d13a9e67e63bc862796425
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-27 10:24:05 +0100
Commit message:
Commit: 853cbfbf11f5d70fa0d13a9e67e63bc862796425
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-27 10:24:05 +0100
Commit message:
Fix docs (#58) * Rerender documentation * Update to recommended format for package documentation * Version bump
Package: iSEEu
Commit: 7961e3f45aac1e7d2d8d20eaf2dcd3a8ddb8711f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 15:11:47 +0100
Commit message:
Commit: 7961e3f45aac1e7d2d8d20eaf2dcd3a8ddb8711f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 15:11:47 +0100
Commit message:
Extra docs vignette markdownboard (#116) * adding documentation for two additional panels - already in the codebase, just not highlighted yet in the vignette * adding screenshots, created via appshot on the app objects * newer roxygen version * manpage re-created * udpated news * version bump, 1.15.1 * updating GHA to use latest Bioc devel version
Package: multicrispr
Commit: 85551536efca2bea7bb24f7100eb0a9003a900dc
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-27 10:04:42 +0100
Commit message:
Commit: 85551536efca2bea7bb24f7100eb0a9003a900dc
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-27 10:04:42 +0100
Commit message:
Eliminate assertive.files (in devel)
Package: SingleCellAlleleExperiment
Commit: bf86234a4900285d0856d77017f355812f71f9df
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-27 09:18:38 +0100
Commit message:
Commit: bf86234a4900285d0856d77017f355812f71f9df
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-27 09:18:38 +0100
Commit message:
version bump, incorporating changes made related to the review process in scaeData
Package: SingleCellAlleleExperiment
Commit: ab4eb864823e2e25b8ce2bb9911f38fea1625c5f
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-27 09:12:23 +0100
Commit message:
Commit: ab4eb864823e2e25b8ce2bb9911f38fea1625c5f
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-27 09:12:23 +0100
Commit message:
deleted pkg-level man page; ready to version bump
Package: SingleCellAlleleExperiment
Commit: f372be377c8812d5a083e7a9f2c7388a3bdb1b27
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-26 13:23:27 +0100
Commit message:
Commit: f372be377c8812d5a083e7a9f2c7388a3bdb1b27
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-26 13:23:27 +0100
Commit message:
added R 4.4 in Description/depends; made a note in NEWS for changes made related to the scaeData review; ready to bump version
Package: SingleCellAlleleExperiment
Commit: 8f306448be842ea1ba8dbdc97e0b69f114eb948b
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-26 12:16:23 +0100
Commit message:
Commit: 8f306448be842ea1ba8dbdc97e0b69f114eb948b
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-26 12:16:23 +0100
Commit message:
changed read in for the lookup table; updated all examples/tests/vignette according to new read in; deleted example_test parameter in read_allele_counts() function; added package level man page (currently colliding with SCAE-Constructor)
Package: SingleCellAlleleExperiment
Commit: f4bfddc169d2da0f29c0600d1e122ebce17b6dd1
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-22 12:01:56 +0100
Commit message:
Commit: f4bfddc169d2da0f29c0600d1e122ebce17b6dd1
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-22 12:01:56 +0100
Commit message:
added installation section to vignette; removed .Rproj file; made some codestyle changes across all files containing code
Package: FLAMES
Commit: 94fa129d3ba7b2e4a3580bb53a134d667383d0c0
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-27 16:29:08 +1100
Commit message:
Commit: 94fa129d3ba7b2e4a3580bb53a134d667383d0c0
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-27 16:29:08 +1100
Commit message:
update ssw
Package: Rsubread
Commit: e5b232195e2f4507bc592386f601f71d8435b293
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2024-03-27 13:20:56 +1100
Commit message:
Commit: e5b232195e2f4507bc592386f601f71d8435b293
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2024-03-27 13:20:56 +1100
Commit message:
removed a big that having very few reads written reversed in BAM output from cellCounts.
Package: SingleCellExperiment
Commit: 69aa3c7203819385ecdf640eaa84302bf739373d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-03-26 17:43:09 -0700
Commit message:
Commit: 69aa3c7203819385ecdf640eaa84302bf739373d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-03-26 17:43:09 -0700
Commit message:
Minor docfix.
Package: SingleCellExperiment
Commit: 8407934af979927c31c073bac1ad4ea07bbd16db
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-27 01:32:09 +0100
Commit message:
Commit: 8407934af979927c31c073bac1ad4ea07bbd16db
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-27 01:32:09 +0100
Commit message:
Check for NULL metadata when returning a matrix from *Pair() functions (#74) This auto-fills the sparse matrix with TRUE values, just to avoid outright failure.
Package: IgGeneUsage
Commit: 309f5468c974d4fd795ef5ec43213fe14cc6ea41
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-26 23:50:43 +0100
Commit message:
Commit: 309f5468c974d4fd795ef5ec43213fe14cc6ea41
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-26 23:50:43 +0100
Commit message:
update of case study 5
Package: EpiTxDb
Commit: d628bc86814af06628ae7cdf409cf8576254749f
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:25:19 +0100
Commit message:
Commit: d628bc86814af06628ae7cdf409cf8576254749f
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:25:19 +0100
Commit message:
Changed config after default branch rename
Package: Structstrings
Commit: 351ac7c49a97db0f0dbceda03367b4ce13c33a85
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:23:32 +0100
Commit message:
Commit: 351ac7c49a97db0f0dbceda03367b4ce13c33a85
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:23:32 +0100
Commit message:
Changed config after default branch rename
Package: Structstrings
Commit: 46abcd101da164a1c3e83284ca2fa89dff89d53a
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 22:59:25 +0100
Commit message:
Commit: 46abcd101da164a1c3e83284ca2fa89dff89d53a
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 22:59:25 +0100
Commit message:
Update README.md
Package: tRNAscanImport
Commit: 1ac7921d0e6cf00c27a1dd2af3d94f24549246b5
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:18:42 +0100
Commit message:
Commit: 1ac7921d0e6cf00c27a1dd2af3d94f24549246b5
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:18:42 +0100
Commit message:
Changed config after default branch rename
Package: tRNAscanImport
Commit: 716afc5f429adaa1b75fa78b1c3f2966e954053f
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:14:04 +0100
Commit message:
Commit: 716afc5f429adaa1b75fa78b1c3f2966e954053f
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:14:04 +0100
Commit message:
Update README.md
Package: tRNAdbImport
Commit: da09c4c9f8a434a76d0afa1e78680edc3c579ca3
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:17:19 +0100
Commit message:
Commit: da09c4c9f8a434a76d0afa1e78680edc3c579ca3
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:17:19 +0100
Commit message:
Changed config after default branch rename
Package: tRNAdbImport
Commit: 3c637daf5b24da4ebf04626f1086f1941bfba5e2
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:13:43 +0100
Commit message:
Commit: 3c637daf5b24da4ebf04626f1086f1941bfba5e2
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:13:43 +0100
Commit message:
Update README.md
Package: tRNA
Commit: eaf74ae73343fc4d18297340de507373886e2052
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:13:49 +0100
Commit message:
Commit: eaf74ae73343fc4d18297340de507373886e2052
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:13:49 +0100
Commit message:
Changed config after default branch rename
Package: Modstrings
Commit: d020ab16a6d18a6eaab09756a2a4e1b4c6e0a0cb
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:10:57 +0100
Commit message:
Commit: d020ab16a6d18a6eaab09756a2a4e1b4c6e0a0cb
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:10:57 +0100
Commit message:
Changed config after default branch rename
Package: Modstrings
Commit: 25dd0b47c603b404e530b90e9f6588a4c09fe553
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:01:12 +0100
Commit message:
Commit: 25dd0b47c603b404e530b90e9f6588a4c09fe553
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:01:12 +0100
Commit message:
Update README.md
Package: RNAmodR
Commit: edc8dbf321f830eedb956866fb03eb4b8ad59cc9
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:03:09 +0100
Commit message:
Commit: edc8dbf321f830eedb956866fb03eb4b8ad59cc9
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:03:09 +0100
Commit message:
Changed config after default branch rename
Package: RNAmodR
Commit: 184805de98b17de5e47f1128288e09e8094385cb
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 21:55:25 +0100
Commit message:
Commit: 184805de98b17de5e47f1128288e09e8094385cb
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 21:55:25 +0100
Commit message:
Merge pull request #28 from hpages/master Replace GenomicFeatures::makeTxDbFromGFF with txdbmaker::makeTxDbFromGFF
Package: RNAmodR
Commit: 51dcdb43dd5de26b21fadfb71082a098fdb60d35
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-26 10:15:39 -0700
Commit message:
Commit: 51dcdb43dd5de26b21fadfb71082a098fdb60d35
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-26 10:15:39 -0700
Commit message:
Replace GenomicFeatures::makeTxDbFromGFF with txdbmaker::makeTxDbFromGFF
Package: RNAmodR
Commit: 7423101b1bc54a90a81f9af074308e78e1f99a79
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-18 22:21:43 +0100
Commit message:
Commit: 7423101b1bc54a90a81f9af074308e78e1f99a79
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-18 22:21:43 +0100
Commit message:
Update README.md
Package: scaeData
Commit: b6a053d22fcdd73ffa2f5b5d89aeff9ae86c3215
Author: AGImkeller <89422241+AGImkeller@users.noreply.github.com>
Date: 2024-03-26 21:39:18 +0100
Commit message:
Commit: b6a053d22fcdd73ffa2f5b5d89aeff9ae86c3215
Author: AGImkeller <89422241+AGImkeller@users.noreply.github.com>
Date: 2024-03-26 21:39:18 +0100
Commit message:
Merge pull request #4 from AGImkeller/bioc_review Revision per Bioconductor's feedback
Package: scaeData
Commit: 1dd32f26cf9eb175fc5e8fc7d05616007b2961b8
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:11:09 +0100
Commit message:
Commit: 1dd32f26cf9eb175fc5e8fc7d05616007b2961b8
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:11:09 +0100
Commit message:
updating the GHA to reflect the newly added dependency, to be picked (for now) from github
Package: scaeData
Commit: 4dc73463a83f68c732bf5d2654a1a3430c567865
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:04:38 +0100
Commit message:
Commit: 4dc73463a83f68c732bf5d2654a1a3430c567865
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:04:38 +0100
Commit message:
version bump, 0.99.3
Package: scaeData
Commit: cf4073a556517ba1e6ad495c5b1844299a115925
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:04:27 +0100
Commit message:
Commit: cf4073a556517ba1e6ad495c5b1844299a115925
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:04:27 +0100
Commit message:
edited News with latest changes
Package: scaeData
Commit: 99a11f497f14a9a801d581a17dde330f8d69d00a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:02:22 +0100
Commit message:
Commit: 99a11f497f14a9a801d581a17dde330f8d69d00a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:02:22 +0100
Commit message:
adding SCAE as suggested dependency, and indenting a bit the lines of the DESCRIPTION file
Package: scaeData
Commit: c68cde6845cc59ebe84e5d3f6b57daca2903aa26
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:01:08 +0100
Commit message:
Commit: c68cde6845cc59ebe84e5d3f6b57daca2903aa26
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:01:08 +0100
Commit message:
evaluating the last chunk now, to allow a full end-to-end run
Package: scaeData
Commit: f59bb236a4774881418cd7d8a53936175f74f2ba
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 23:20:52 +0100
Commit message:
Commit: f59bb236a4774881418cd7d8a53936175f74f2ba
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 23:20:52 +0100
Commit message:
explicitly reporting LICENSE.md in .Rbuildignore
Package: scaeData
Commit: 5e0fd32efd174032c979d6c390bafd405cc107a0
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 23:15:33 +0100
Commit message:
Commit: 5e0fd32efd174032c979d6c390bafd405cc107a0
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 23:15:33 +0100
Commit message:
Adding also Matrix as suggested dependency, as it is also used in the vignette
Package: scaeData
Commit: 330a97d84d9e63d0da6915198009c69a3a468885
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 22:45:07 +0100
Commit message:
Commit: 330a97d84d9e63d0da6915198009c69a3a468885
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 22:45:07 +0100
Commit message:
few adjustments in the vignette last chunk - still need some fixes if we want that to be fully eval'd
Package: scaeData
Commit: b901e3c298b9cd9ed1ab23e8cd215ca7c8c65345
Author: Ahmad Al Ajami <ahmad.alajami@kgu.de>
Date: 2024-03-25 22:05:44 +0100
Commit message:
Commit: b901e3c298b9cd9ed1ab23e8cd215ca7c8c65345
Author: Ahmad Al Ajami <ahmad.alajami@kgu.de>
Date: 2024-03-25 22:05:44 +0100
Commit message:
updated the vignette per bioc reviewer's feedback
Package: scaeData
Commit: 5bd68f1a6bc0c79eacd6b6767b19f6e0f9efae7c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 22:02:31 +0100
Commit message:
Commit: 5bd68f1a6bc0c79eacd6b6767b19f6e0f9efae7c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 22:02:31 +0100
Commit message:
adding rendered manpage, with correct aliases (scaeData/scaeData-package/scaeData-pkg)
Package: scaeData
Commit: 22467c6f8622983e003cdae797ce2748eeea0565
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 22:02:00 +0100
Commit message:
Commit: 22467c6f8622983e003cdae797ce2748eeea0565
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 22:02:00 +0100
Commit message:
adding pkg-level documentation, as suggested in the review
Package: splatter
Commit: ea842a225ba46ed365deddd590eea56c88e61543
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 21:18:58 +0100
Commit message:
Commit: ea842a225ba46ed365deddd590eea56c88e61543
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 21:18:58 +0100
Commit message:
Update NEWS and bump version
Package: splatter
Commit: ed1afeaee603f10d92272194c170110500731ff3
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 21:09:59 +0100
Commit message:
Commit: ed1afeaee603f10d92272194c170110500731ff3
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 21:09:59 +0100
Commit message:
Minor fixes from BiocCheck
Package: splatter
Commit: 8614ad6c181b3b0034ae181ce9075a9c5cd2dee5
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 20:53:25 +0100
Commit message:
Commit: 8614ad6c181b3b0034ae181ce9075a9c5cd2dee5
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 20:53:25 +0100
Commit message:
Only ask to install dependencies when interactive
Package: splatter
Commit: 9472e2fcaa29253ce5d0d19ca370372182dc6b32
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 20:50:23 +0100
Commit message:
Commit: 9472e2fcaa29253ce5d0d19ca370372182dc6b32
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 20:50:23 +0100
Commit message:
Add @keywords internal/@noRd to function docs
Package: splatter
Commit: 81cf3e7b0da6235e474527427a498e98f8113882
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 17:58:31 +0100
Commit message:
Commit: 81cf3e7b0da6235e474527427a498e98f8113882
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 17:58:31 +0100
Commit message:
Restyle code Use something more modern/sane with styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4)) (and some adjusting)
Package: splatter
Commit: 31a986716ad397df127d563eb0443c3e01807e92
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:44:01 +0100
Commit message:
Commit: 31a986716ad397df127d563eb0443c3e01807e92
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:44:01 +0100
Commit message:
Update DESCRIPTION Add GitHub usernames and Bioconductor URL
Package: splatter
Commit: 411b3faebc22848da564d6b228545841e175b366
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:38:13 +0100
Commit message:
Commit: 411b3faebc22848da564d6b228545841e175b366
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:38:13 +0100
Commit message:
Replace package man page with usethis auto page
Package: splatter
Commit: ceac288173349048f831ed3e11a55a45eb156d76
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:36:39 +0100
Commit message:
Commit: ceac288173349048f831ed3e11a55a45eb156d76
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:36:39 +0100
Commit message:
Bump roxygen version to 7.3.1
Package: splatter
Commit: bd62c5906a72681b95861152f7c1401b45106e92
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:35:05 +0100
Commit message:
Commit: bd62c5906a72681b95861152f7c1401b45106e92
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:35:05 +0100
Commit message:
Specify expected warnings in tests Removes unhelpful output
Package: splatter
Commit: 7b8b13c3613cfd992519392896a7df7399c2c8ea
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:22:31 +0100
Commit message:
Commit: 7b8b13c3613cfd992519392896a7df7399c2c8ea
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:22:31 +0100
Commit message:
Properly sink output in scDDSimulate() when verbose=FALSE
Package: splatter
Commit: 0454898d63cc7f1a2ed5c45e5726029f063b8ba0
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:17:54 +0100
Commit message:
Commit: 0454898d63cc7f1a2ed5c45e5726029f063b8ba0
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:17:54 +0100
Commit message:
Set verbose=FALSE in tests for scDDSimulate()
Package: splatter
Commit: 1fb0eff93f4bb8099cd572b18c02501e03377aad
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:17:27 +0100
Commit message:
Commit: 1fb0eff93f4bb8099cd572b18c02501e03377aad
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:17:27 +0100
Commit message:
Properly sink output in BASiCSEstimate when verbose=FALSE
Package: rRDP
Commit: 80028da1529d2a76862bd81f41cdd570f0f7ded2
Author: Michael Hahsler <mhahsler@smu.edu>
Date: 2024-03-26 15:17:20 -0500
Commit message:
Commit: 80028da1529d2a76862bd81f41cdd570f0f7ded2
Author: Michael Hahsler <mhahsler@smu.edu>
Date: 2024-03-26 15:17:20 -0500
Commit message:
Upgrade to RDP 2.14.
Package: rRDPData
Commit: 973e13232d3f5b7448fd86fef5bb6e43ae816510
Author: Michael Hahsler <mhahsler@smu.edu>
Date: 2024-03-26 15:02:00 -0500
Commit message:
Commit: 973e13232d3f5b7448fd86fef5bb6e43ae816510
Author: Michael Hahsler <mhahsler@smu.edu>
Date: 2024-03-26 15:02:00 -0500
Commit message:
updated man page.
Package: MGnifyR
Commit: 60c01d2b09cfa9ffe86228e528b1389a7cf27104
Author: TuomasBorman <tvborm@utu.fi>
Date: 2024-03-26 20:51:26 +0200
Commit message:
Commit: 60c01d2b09cfa9ffe86228e528b1389a7cf27104
Author: TuomasBorman <tvborm@utu.fi>
Date: 2024-03-26 20:51:26 +0200
Commit message:
Update vignette
Package: MGnifyR
Commit: f52572187eca6430a614da13ee64dca62c76acc2
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-26 20:31:56 +0200
Commit message:
Commit: f52572187eca6430a614da13ee64dca62c76acc2
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-26 20:31:56 +0200
Commit message:
Final changes for Bioc submission (#40) * up * up * Fix links in ?MGnifyR * up * up
Package: VariantAnnotation
Commit: 038a3fc1a8da381a39bd542b2340578b264b4525
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-26 11:53:04 -0700
Commit message:
Commit: 038a3fc1a8da381a39bd542b2340578b264b4525
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-26 11:53:04 -0700
Commit message:
The makeTxDb*() functions have moved from GenomicFeatures to txdbmaker
Package: BSgenome
Commit: 96ff87f2d9963d2fb41bedd6a030294a3696fa4f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-26 11:46:31 -0700
Commit message:
Commit: 96ff87f2d9963d2fb41bedd6a030294a3696fa4f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-26 11:46:31 -0700
Commit message:
The makeTxDb*() functions have moved from GenomicFeatures to txdbmaker
Package: MGnifyR
Commit: d6bb555d18119eeb093bf67ad0d292355fe6fd95
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-21 13:47:30 +0200
Commit message:
Commit: d6bb555d18119eeb093bf67ad0d292355fe6fd95
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-21 13:47:30 +0200
Commit message:
Add findingpheno acknowledgement (#39)
Package: MGnifyR
Commit: 8e2080f5bbeffbb9550778f9ecdab8ce44949bf0
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-20 16:03:18 +0200
Commit message:
Commit: 8e2080f5bbeffbb9550778f9ecdab8ce44949bf0
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-20 16:03:18 +0200
Commit message:
Enable GHA for mac and win (#38) * Enable GHA for MAC and WIN * up
Package: rRDPData
Commit: 5d7bf939382a928846d13c985492ee5944b80e35
Author: Michael Hahsler <mhahsler@smu.edu>
Date: 2024-03-26 13:18:18 -0500
Commit message:
Commit: 5d7bf939382a928846d13c985492ee5944b80e35
Author: Michael Hahsler <mhahsler@smu.edu>
Date: 2024-03-26 13:18:18 -0500
Commit message:
Update data to the RDP Classifier 2.14 released in August 2023. Added fungalits_unite, fungalits_warcup, and fungallsu.
Package: DegNorm
Commit: 2e3e9c950849869289b8651f8c735aba4774cff5
Author: Dr. Ji-Ping Wang <jzwang@northwestern.edu>
Date: 2024-03-26 13:17:24 -0500
Commit message:
Commit: 2e3e9c950849869289b8651f8c735aba4774cff5
Author: Dr. Ji-Ping Wang <jzwang@northwestern.edu>
Date: 2024-03-26 13:17:24 -0500
Commit message:
txdbmaker correction
Package: recount
Commit: fea8aa399f4cdb39051720e83e8b0022e6605203
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-26 13:48:49 -0400
Commit message:
Commit: fea8aa399f4cdb39051720e83e8b0022e6605203
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-26 13:48:49 -0400
Commit message:
Use GHA with BioC 3.18
Package: recount
Commit: 08104fbaf45183caced5c3f957d59a424eee2627
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-26 13:44:57 -0400
Commit message:
Commit: 08104fbaf45183caced5c3f957d59a424eee2627
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-26 13:44:57 -0400
Commit message:
v1.29.1 -- bump version after merging https://github.com/leekgroup/recount/pull/24 by @hpages. Thank you!
Package: recount
Commit: 60d0e5e2e1b74cadde290b714eb0ba212ea3eddc
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-26 13:42:05 -0400
Commit message:
Commit: 60d0e5e2e1b74cadde290b714eb0ba212ea3eddc
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-26 13:42:05 -0400
Commit message:
Merge branch 'devel' of github.com:leekgroup/recount into devel
Package: recount
Commit: 4d918700995a73fc30de187e2a88660733925450
Author: Leonardo Collado-Torres <lcolladotor@gmail.com>
Date: 2024-03-26 13:41:51 -0400
Commit message:
Commit: 4d918700995a73fc30de187e2a88660733925450
Author: Leonardo Collado-Torres <lcolladotor@gmail.com>
Date: 2024-03-26 13:41:51 -0400
Commit message:
Merge pull request #24 from hpages/devel The makeTxDb*() functions have moved from GenomicFeatures to txdbmaker
Package: recount
Commit: e95d6fb01d8f9509cf36a136ccfa141ea34d8bc5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-26 10:31:05 -0700
Commit message:
Commit: e95d6fb01d8f9509cf36a136ccfa141ea34d8bc5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-26 10:31:05 -0700
Commit message:
The makeTxDb*() functions have moved from GenomicFeatures to txdbmaker
Package: rRDP
Commit: 924e72780c20d105602f55c83139f4096cb04926
Author: Michael Hahsler <mhahsler@smu.edu>
Date: 2024-03-26 12:31:50 -0500
Commit message:
Commit: 924e72780c20d105602f55c83139f4096cb04926
Author: Michael Hahsler <mhahsler@smu.edu>
Date: 2024-03-26 12:31:50 -0500
Commit message:
We use now Roxygen and markdown.
Package: smartid
Commit: b958720e44be896b1973d826243de7bb47565b2b
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 04:07:22 +1100
Commit message:
Commit: b958720e44be896b1973d826243de7bb47565b2b
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 04:07:22 +1100
Commit message:
Add package:: before colData to avoid no visible function.
Package: smartid
Commit: 03dc19f19f2b09eb884f4ac2eee86d05a08fb40d
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 03:52:01 +1100
Commit message:
Commit: 03dc19f19f2b09eb884f4ac2eee86d05a08fb40d
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 03:52:01 +1100
Commit message:
Include package.R file to avoid undefined function.
Package: smartid
Commit: e6ba0364123a2682ece357ca279565b63476fdc4
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 03:32:08 +1100
Commit message:
Commit: e6ba0364123a2682ece357ca279565b63476fdc4
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 03:32:08 +1100
Commit message:
Removed un-used commented codes and update vignette.
Package: smartid
Commit: 892a8f38a6add7898d5f53b386326b5c011e4457
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 03:02:00 +1100
Commit message:
Commit: 892a8f38a6add7898d5f53b386326b5c011e4457
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 03:02:00 +1100
Commit message:
Remove un-used codes and use && instead of & in condition.
Package: smartid
Commit: 34bf266e44ce38b9db19152538357871b75e4243
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 02:55:33 +1100
Commit message:
Commit: 34bf266e44ce38b9db19152538357871b75e4243
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 02:55:33 +1100
Commit message:
Fix metadata slot problem.
Package: smartid
Commit: 470b22fbe50c3fc465e97ded002b920c54184f85
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 02:25:19 +1100
Commit message:
Commit: 470b22fbe50c3fc465e97ded002b920c54184f85
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 02:25:19 +1100
Commit message:
Use 4 spaces as indents, replace accessors @ with functions.
Package: smartid
Commit: 3002a02250d6be1f2645f843b1beea950624c610
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 02:00:55 +1100
Commit message:
Commit: 3002a02250d6be1f2645f843b1beea950624c610
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 02:00:55 +1100
Commit message:
Replace sapply with vapply and add drop=F in [].
Package: smartid
Commit: baa33a1774b46b4d13c8eda8c0599f630c24c0a8
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 00:59:38 +1100
Commit message:
Commit: baa33a1774b46b4d13c8eda8c0599f630c24c0a8
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 00:59:38 +1100
Commit message:
Replace print with show.
Package: smartid
Commit: 751531f514cb6c67098aa9e484e377e28123711d
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 00:43:16 +1100
Commit message:
Commit: 751531f514cb6c67098aa9e484e377e28123711d
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 00:43:16 +1100
Commit message:
Styler and spell check.
Package: smartid
Commit: 02d615d785e5be88f6087b156263b225f2e69eaa
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 00:17:13 +1100
Commit message:
Commit: 02d615d785e5be88f6087b156263b225f2e69eaa
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 00:17:13 +1100
Commit message:
Update bioc-check yml file.
Package: smartid
Commit: cdd877d3575baabdd447ed8044a169bccf99d7f3
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 00:13:41 +1100
Commit message:
Commit: cdd877d3575baabdd447ed8044a169bccf99d7f3
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 00:13:41 +1100
Commit message:
Update vignette and bioc-check yml file.
Package: smartid
Commit: ec25f84216708d507d315f3906b638f65d79340b
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-26 23:37:46 +1100
Commit message:
Commit: ec25f84216708d507d315f3906b638f65d79340b
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-26 23:37:46 +1100
Commit message:
Bump R version to >= 4.4 and update vignette and function details.
Package: CytoMethIC
Commit: f2d0383bb99f7f41757ee06fcc6eaad86e5cc7f4
Author: Jacob Fanale <jakefanale@gmail.com>
Date: 2024-03-26 12:56:23 -0400
Commit message:
Commit: f2d0383bb99f7f41757ee06fcc6eaad86e5cc7f4
Author: Jacob Fanale <jakefanale@gmail.com>
Date: 2024-03-26 12:56:23 -0400
Commit message:
update NEWS
Package: CytoMethIC
Commit: 91f81855fbda9a57f0b73ae28db898afd1d419b2
Author: Jacob Fanale <jakefanale@gmail.com>
Date: 2024-03-26 12:16:02 -0400
Commit message:
Commit: 91f81855fbda9a57f0b73ae28db898afd1d419b2
Author: Jacob Fanale <jakefanale@gmail.com>
Date: 2024-03-26 12:16:02 -0400
Commit message:
bump to 0.99.26
Package: CytoMethIC
Commit: 2fe98f309e7641eb5f8e625c811d907074beb28a
Author: Jacob Fanale <jakefanale@gmail.com>
Date: 2024-03-26 12:15:06 -0400
Commit message:
Commit: 2fe98f309e7641eb5f8e625c811d907074beb28a
Author: Jacob Fanale <jakefanale@gmail.com>
Date: 2024-03-26 12:15:06 -0400
Commit message:
Review 1 Changes
Package: CytoMethIC
Commit: 7c292c9fcd4048cc617f5dd25aef79f735a9cd10
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2024-03-25 13:11:37 -0400
Commit message:
Commit: 7c292c9fcd4048cc617f5dd25aef79f735a9cd10
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2024-03-25 13:11:37 -0400
Commit message:
minor, message omitted
Package: TCGAbiolinks
Commit: 2cfe182595da1bcff32446caf525f096dbe54863
Author: Tiago Silva <tiagosilva@Tiagos-MacBook-Pro-2.local>
Date: 2024-03-26 11:40:05 -0400
Commit message:
Commit: 2cfe182595da1bcff32446caf525f096dbe54863
Author: Tiago Silva <tiagosilva@Tiagos-MacBook-Pro-2.local>
Date: 2024-03-26 11:40:05 -0400
Commit message:
Minor code style changes
Package: TCGAbiolinks
Commit: 3f5efb99525e6fc0925331db989081f178ab97e8
Author: Tiago Silva <tiagosilva@Tiagos-MacBook-Pro-2.local>
Date: 2024-03-26 11:36:07 -0400
Commit message:
Commit: 3f5efb99525e6fc0925331db989081f178ab97e8
Author: Tiago Silva <tiagosilva@Tiagos-MacBook-Pro-2.local>
Date: 2024-03-26 11:36:07 -0400
Commit message:
Removing dnet from package as it is not available in CRAN.
Package: QFeatures
Commit: f1e56d1dc830586388113327b62a383154978a00
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 16:14:32 +0100
Commit message:
Commit: f1e56d1dc830586388113327b62a383154978a00
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 16:14:32 +0100
Commit message:
load more data (not lazyLoading anymore)
Package: QFeatures
Commit: 415ba77b8748c1ce7a23495527a172cd23208177
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 16:10:01 +0100
Commit message:
Commit: 415ba77b8748c1ce7a23495527a172cd23208177
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 16:10:01 +0100
Commit message:
load necessary data (not lazyLoading anymore)
Package: QFeatures
Commit: af5f841ace1e24916b72a80c394b11e40ece7c82
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 15:58:59 +0100
Commit message:
Commit: af5f841ace1e24916b72a80c394b11e40ece7c82
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 15:58:59 +0100
Commit message:
minor fix based on BiocCheck
Package: QFeatures
Commit: cc42c7ab4493b63c2e9306604aa368b5cd566677
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 15:53:25 +0100
Commit message:
Commit: cc42c7ab4493b63c2e9306604aa368b5cd566677
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 15:53:25 +0100
Commit message:
udpate unit test
Package: QFeatures
Commit: c703655e67ead820b04aa0111dc007b7a579ac02
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 15:38:19 +0100
Commit message:
Commit: c703655e67ead820b04aa0111dc007b7a579ac02
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 15:38:19 +0100
Commit message:
fix as.vector() - closes issue #203
Package: QFeatures
Commit: 21f74a8ba049fa53fc5fda549fdb9f4ae64dbc75
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-07 21:02:03 +0100
Commit message:
Commit: 21f74a8ba049fa53fc5fda549fdb9f4ae64dbc75
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-07 21:02:03 +0100
Commit message:
update notes #1199
Package: QFeatures
Commit: b0b8c9a2a5c728ee4dacb6a4c1810824cf8dd7b7
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-07 06:57:55 +0100
Commit message:
Commit: b0b8c9a2a5c728ee4dacb6a4c1810824cf8dd7b7
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-07 06:57:55 +0100
Commit message:
add notes from issue 199
Package: cypress
Commit: 3c8ef7de9f097bcda0cd5925cee0a864f802a4ba
Author: Shilin Yu <sy597@georgetown.edu>
Date: 2024-03-26 10:24:49 -0400
Commit message:
Commit: 3c8ef7de9f097bcda0cd5925cee0a864f802a4ba
Author: Shilin Yu <sy597@georgetown.edu>
Date: 2024-03-26 10:24:49 -0400
Commit message:
edit for vigenette edit for csDE
Package: multicrispr
Commit: 125c9082bbd264e8a98c9698319f451cdf1ba344
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-26 14:27:39 +0100
Commit message:
Commit: 125c9082bbd264e8a98c9698319f451cdf1ba344
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-26 14:27:39 +0100
Commit message:
R CMD check Fixes
Package: multicrispr
Commit: 08b95964bcd8d659aec85d9c28cb4ba1633d7afd
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-26 13:59:45 +0100
Commit message:
Commit: 08b95964bcd8d659aec85d9c28cb4ba1633d7afd
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-26 13:59:45 +0100
Commit message:
R CMD check Fixes
Package: multicrispr
Commit: 63f75879aff31a9d0fc18e0b121935a006209dcc
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-26 13:39:30 +0100
Commit message:
Commit: 63f75879aff31a9d0fc18e0b121935a006209dcc
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-26 13:39:30 +0100
Commit message:
Eliminate `assertive.base`
Package: mia
Commit: ecd661f43b39cc2e087534d21d475e69e6f8a944
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-14 10:26:38 +0200
Commit message:
Commit: ecd661f43b39cc2e087534d21d475e69e6f8a944
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-14 10:26:38 +0200
Commit message:
getExperimentCrossCorrelation and SampleMap (#504)
Package: mia
Commit: aa1d488af9981075d52f4a5805d86e0419447690
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-05 15:25:59 +0200
Commit message:
Commit: aa1d488af9981075d52f4a5805d86e0419447690
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-05 15:25:59 +0200
Commit message:
getPrevalence, NA values (#486)
Package: mia
Commit: 6a356cd826d45aa5dc9a3b9cf0cbcff795a9de41
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-05 12:25:10 +0200
Commit message:
Commit: 6a356cd826d45aa5dc9a3b9cf0cbcff795a9de41
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-05 12:25:10 +0200
Commit message:
cluster: fixes (#477)
Package: mia
Commit: 5f18f82539aa191e226033637c9008cf2b05aabe
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-04 16:42:03 +0200
Commit message:
Commit: 5f18f82539aa191e226033637c9008cf2b05aabe
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-04 16:42:03 +0200
Commit message:
Add pages to pkgdown (#500)
Package: mia
Commit: 45544f3a4823f8b4af32dcf6dafc3dedeb98fe58
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-03-04 15:51:12 +0200
Commit message:
Commit: 45544f3a4823f8b4af32dcf6dafc3dedeb98fe58
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-03-04 15:51:12 +0200
Commit message:
Deprecate taxonomyTree and addTaxonomyTree (#496) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Co-authored-by: TuomasBorman <tvborm@utu.fi> Co-authored-by: Leo Lahti <leo.lahti@iki.fi>
Package: mia
Commit: 1269d9c6a3b70c1e8323748c6a4bc0a780510f77
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-01 21:48:03 +0200
Commit message:
Commit: 1269d9c6a3b70c1e8323748c6a4bc0a780510f77
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-01 21:48:03 +0200
Commit message:
loadFromMetaphlan: support taxonomy-named column (#499)
Package: mia
Commit: d159f74430cdf193ec3dca25f1c56a3ee2b4b672
Author: Himmi Lindgren <137785061+himmil@users.noreply.github.com>
Date: 2024-02-28 11:14:27 +0200
Commit message:
Commit: d159f74430cdf193ec3dca25f1c56a3ee2b4b672
Author: Himmi Lindgren <137785061+himmil@users.noreply.github.com>
Date: 2024-02-28 11:14:27 +0200
Commit message:
New arguments for perSampleDominantFeatures (#479) Co-authored-by: Leo Lahti <leo.lahti@iki.fi>
Package: mia
Commit: be6bcbd1711d31bb9ae731edc2e6abb625823310
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-02-26 14:16:12 +0200
Commit message:
Commit: be6bcbd1711d31bb9ae731edc2e6abb625823310
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-02-26 14:16:12 +0200
Commit message:
Fix splitOn bug (#495)
Package: mia
Commit: 97b01b62cf9ad820bc7d2ec659783f6b8bb56c3a
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-02-21 18:17:15 +0200
Commit message:
Commit: 97b01b62cf9ad820bc7d2ec659783f6b8bb56c3a
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-02-21 18:17:15 +0200
Commit message:
agglomerateByRank fix: empty ranks (#493)
Package: mia
Commit: 61f2d16cbf6dabf90a8c2435d057937b35220eed
Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com>
Date: 2024-02-19 11:55:52 +0000
Commit message:
Commit: 61f2d16cbf6dabf90a8c2435d057937b35220eed
Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com>
Date: 2024-02-19 11:55:52 +0000
Commit message:
Clarify pseudocount argument (#490) Co-authored-by: artur_sannikov <artur.sannikov96@gmail.com>
Package: mia
Commit: 4d1a093aa937a9c66d60d56445328ff05c47e580
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-02-13 12:32:43 +0200
Commit message:
Commit: 4d1a093aa937a9c66d60d56445328ff05c47e580
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-02-13 12:32:43 +0200
Commit message:
agglomerateByRank: agglomerate tree fix (#487)
Package: mia
Commit: 2d0c38d47c2ad5b7cfc4bf9f890d07cd6c3488b6
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-01-30 16:09:58 +0200
Commit message:
Commit: 2d0c38d47c2ad5b7cfc4bf9f890d07cd6c3488b6
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-01-30 16:09:58 +0200
Commit message:
loadFromMetaphlan: support for strain level (#485)
Package: rGREAT
Commit: 70a34fb23aed6f5534930ab59f1383e01e4057b9
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 10:28:29 +0100
Commit message:
Commit: 70a34fb23aed6f5534930ab59f1383e01e4057b9
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 10:28:29 +0100
Commit message:
positions are enforced to be integers
Package: rGREAT
Commit: 18de7beca19a01008272679e7b57fbe5d6f25a92
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 10:20:19 +0100
Commit message:
Commit: 18de7beca19a01008272679e7b57fbe5d6f25a92
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 10:20:19 +0100
Commit message:
remove o/so files
Package: rGREAT
Commit: de671d63755bf7dadd39b7fa5799fe7567b48d79
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 10:19:21 +0100
Commit message:
Commit: de671d63755bf7dadd39b7fa5799fe7567b48d79
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 10:19:21 +0100
Commit message:
use try() to wrap seqlevelsStyle() to get rid of the error
Package: gDRstyle
Commit: ebeb99a552c9ba4d02c4dc659827d3e45707bd34
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2024-03-26 09:21:39 +0100
Commit message:
Commit: ebeb99a552c9ba4d02c4dc659827d3e45707bd34
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2024-03-26 09:21:39 +0100
Commit message:
Merge pull request #79 from gdrplatform/add_as_cran_flag feat: add support for running `R CMD CHECK` with `--as-cran`
Package: gDRstyle
Commit: c7d5c6b2c003eeaadc31c8ac9d7c54c367327017
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-03-26 06:56:51 +0100
Commit message:
Commit: c7d5c6b2c003eeaadc31c8ac9d7c54c367327017
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-03-26 06:56:51 +0100
Commit message:
chore: update gititnore rules
Package: gDRstyle
Commit: cb983a9530f0e485abf61bdc64158a8fda35f200
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-03-26 06:53:00 +0100
Commit message:
Commit: cb983a9530f0e485abf61bdc64158a8fda35f200
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-03-26 06:53:00 +0100
Commit message:
chore: udpate deps
Package: gDRstyle
Commit: 80b265ad54caa764ab1fd07371a8124c35de5fb1
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-03-25 18:30:49 +0100
Commit message:
Commit: 80b265ad54caa764ab1fd07371a8124c35de5fb1
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-03-25 18:30:49 +0100
Commit message:
feat: add support for running `R CMD CHECK` with `--as-cran`
Package: simona
Commit: fe29f94c0ed1a4f47205a259346fa6f882a495fa
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 08:58:43 +0100
Commit message:
Commit: fe29f94c0ed1a4f47205a259346fa6f882a495fa
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 08:58:43 +0100
Commit message:
Merge branch 'master' into devel
Package: simona
Commit: b250510d53dde1f934e0209b08bbcd752b281c08
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 08:58:28 +0100
Commit message:
Commit: b250510d53dde1f934e0209b08bbcd752b281c08
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 08:58:28 +0100
Commit message:
update docs
Package: simona
Commit: 764a58bad0a119b93f565d37dcdfc934f185b5ab
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-02-29 11:07:54 +0100
Commit message:
Commit: 764a58bad0a119b93f565d37dcdfc934f185b5ab
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-02-29 11:07:54 +0100
Commit message:
add 'alternative_terms' argument in create_ontology_DAG()
Package: simona
Commit: 6a1aeef188fe5fff9b8a88db2a48c44a63526081
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-02-27 20:30:55 +0100
Commit message:
Commit: 6a1aeef188fe5fff9b8a88db2a48c44a63526081
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-02-27 20:30:55 +0100
Commit message:
update website
Package: DAPAR
Commit: 642f0cdd44111903d4ad219f0fe274ec43026d12
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-03-26 08:14:40 +0100
Commit message:
Commit: 642f0cdd44111903d4ad219f0fe274ec43026d12
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-03-26 08:14:40 +0100
Commit message:
Delete limmaAnalysis2.R
Package: DAPAR
Commit: 11fd87c516f99835b354e358084aed18969a09c8
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-03-26 04:25:07 +0100
Commit message:
Commit: 11fd87c516f99835b354e358084aed18969a09c8
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-03-26 04:25:07 +0100
Commit message:
Delete R/limmaAnalysis2.R
Package: DAPAR
Commit: 76f854364bd7b4e644e562b1674b867b7691a31f
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-03-26 04:21:53 +0100
Commit message:
Commit: 76f854364bd7b4e644e562b1674b867b7691a31f
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-03-26 04:21:53 +0100
Commit message:
Update limmaAnalysis.R
Package: SpatialFeatureExperiment
Commit: 9e6586feba5b93638c8ca6dcb7d9660c1ac6f2ae
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2024-03-25 22:10:26 -0700
Commit message:
Commit: 9e6586feba5b93638c8ca6dcb7d9660c1ac6f2ae
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2024-03-25 22:10:26 -0700
Commit message:
Temporary fix
Package: smartid
Commit: fe762f19636d6ada24f4faf01a45b4815d404203
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-26 15:49:47 +1100
Commit message:
Commit: fe762f19636d6ada24f4faf01a45b4815d404203
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-26 15:49:47 +1100
Commit message:
Fix note for no visible binding variable.
Package: smartid
Commit: a72ecd64066d968857f8fcf68689636fb51ef85f
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-26 15:33:43 +1100
Commit message:
Commit: a72ecd64066d968857f8fcf68689636fb51ef85f
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-26 15:33:43 +1100
Commit message:
Added test for gs_score function and bump version.
Package: tidytof
Commit: 4fce362df3f0193b14f263a4788dc2ab0f711bf9
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 21:26:06 -0700
Commit message:
Commit: 4fce362df3f0193b14f263a4788dc2ab0f711bf9
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 21:26:06 -0700
Commit message:
increment version
Package: tidytof
Commit: 6a6be801a470b222158e868b6f947d5cb53bc6aa
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 21:05:10 -0700
Commit message:
Commit: 6a6be801a470b222158e868b6f947d5cb53bc6aa
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 21:05:10 -0700
Commit message:
update tests
Package: motifTestR
Commit: d7f3201b529d06381089a0ea91619054426877dc
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-03-26 13:34:15 +1030
Commit message:
Commit: d7f3201b529d06381089a0ea91619054426877dc
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-03-26 13:34:15 +1030
Commit message:
Added script references in man pages
Package: IgGeneUsage
Commit: d43cb097c073d428546aeed99c946a38e7084bb1
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-26 04:22:39 +0100
Commit message:
Commit: d43cb097c073d428546aeed99c946a38e7084bb1
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-26 04:22:39 +0100
Commit message:
update bugfix in paired analysis
Package: cypress
Commit: 65260e797f6afbbacd58a5d61808ed2f49e9868d
Author: Shilin Yu <sy597@georgetown.edu>
Date: 2024-03-25 22:20:53 -0400
Commit message:
Commit: 65260e797f6afbbacd58a5d61808ed2f49e9868d
Author: Shilin Yu <sy597@georgetown.edu>
Date: 2024-03-25 22:20:53 -0400
Commit message:
update for bpparam update for new item bpparam
Package: matter
Commit: b32a112d9d5a4780c80541b53eb130f28f0b1b67
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-25 22:11:06 -0400
Commit message:
Commit: b32a112d9d5a4780c80541b53eb130f28f0b1b67
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-25 22:11:06 -0400
Commit message:
v2.5.10 bump
Package: matter
Commit: 1b7c35a9402e1fe8a05312eae720a044e84a9fb9
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-25 22:10:10 -0400
Commit message:
Commit: 1b7c35a9402e1fe8a05312eae720a044e84a9fb9
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-25 22:10:10 -0400
Commit message:
mi_learn()
Package: matter
Commit: f6626a51694bb7a9fa9a1f380c2e9d5a7bedf0d1
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-25 19:26:47 -0400
Commit message:
Commit: f6626a51694bb7a9fa9a1f380c2e9d5a7bedf0d1
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-25 19:26:47 -0400
Commit message:
mscore()
Package: matter
Commit: 29df2313a810ad231e910efc6cc0a2e8a6e692dc
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-25 17:20:39 -0400
Commit message:
Commit: 29df2313a810ad231e910efc6cc0a2e8a6e692dc
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-25 17:20:39 -0400
Commit message:
sgmix()
Package: matter
Commit: a365b2bf958ace0386526377447e1596b9bf3508
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-24 21:27:11 -0400
Commit message:
Commit: a365b2bf958ace0386526377447e1596b9bf3508
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-24 21:27:11 -0400
Commit message:
nscentroids()
Package: matter
Commit: fe7e7886bb08b7ebf43fce01825be84caf7e263a
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-22 21:43:13 -0400
Commit message:
Commit: fe7e7886bb08b7ebf43fce01825be84caf7e263a
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-22 21:43:13 -0400
Commit message:
pass verbose to distfun in fastmap()
Package: matter
Commit: 65eb8a972841fe5fd71e1c1dc3933938330914da
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-22 14:40:38 -0400
Commit message:
Commit: 65eb8a972841fe5fd71e1c1dc3933938330914da
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-22 14:40:38 -0400
Commit message:
rowscale()/colscale() set corresponding attr to NULL when center/scale=FALSE
Package: matter
Commit: 8e021e370f838f07b606ba809bde075ccfaecd81
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-22 12:16:40 -0400
Commit message:
Commit: 8e021e370f838f07b606ba809bde075ccfaecd81
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-22 12:16:40 -0400
Commit message:
vectorize predict.pls() over k
Package: matter
Commit: 0fb32e66534a57ff74a60f196c557eaee77d7f1c
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-21 21:59:12 -0400
Commit message:
Commit: 0fb32e66534a57ff74a60f196c557eaee77d7f1c
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-21 21:59:12 -0400
Commit message:
rm nchunks arg from predict.pls
Package: matter
Commit: 707c317ff9cfd96204dfeeb7c41900f376a41a4f
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-21 21:05:45 -0400
Commit message:
Commit: 707c317ff9cfd96204dfeeb7c41900f376a41a4f
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-21 21:05:45 -0400
Commit message:
add nchunks arg to prcomp() and pls()
Package: matter
Commit: 4e3b25d97f548d1c7ee3fc30872134839e8442ae
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-19 15:04:42 -0400
Commit message:
Commit: 4e3b25d97f548d1c7ee3fc30872134839e8442ae
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-19 15:04:42 -0400
Commit message:
fix issue in simspec()
Package: matter
Commit: b7d76ceec98555fd3d7b2837c73a7ac8805f62bc
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-18 13:04:44 -0400
Commit message:
Commit: b7d76ceec98555fd3d7b2837c73a7ac8805f62bc
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-18 13:04:44 -0400
Commit message:
export linear_ind() and array_ind()
Package: matter
Commit: c961d7008aef888f41c84388f6ce150032e7d283
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-17 23:04:39 -0400
Commit message:
Commit: c961d7008aef888f41c84388f6ce150032e7d283
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-17 23:04:39 -0400
Commit message:
v2.5.10 fix potential infinite loop in binpeaks()
Package: matter
Commit: 9e24dc625a9c4bf65bda52da129682f945adbc89
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-17 20:57:38 -0400
Commit message:
Commit: 9e24dc625a9c4bf65bda52da129682f945adbc89
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-17 20:57:38 -0400
Commit message:
v2.5.10 remove duplicate peaks in findpeaks_cwt()
Package: matter
Commit: a0d2c5fc3f83cc1a79a04bbc9f862a9720416784
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-16 20:45:40 -0400
Commit message:
Commit: a0d2c5fc3f83cc1a79a04bbc9f862a9720416784
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-16 20:45:40 -0400
Commit message:
v2.5.10 update estres() arg tol.ref => ref
Package: matter
Commit: ef637de8d4f14348c99a077e4d211bd39dc9e4d2
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-16 16:55:01 -0400
Commit message:
Commit: ef637de8d4f14348c99a077e4d211bd39dc9e4d2
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-16 16:55:01 -0400
Commit message:
v2.5.10 peakheights() + bug fixes
Package: matter
Commit: eeea9a5b1c7ea8c97a1c02c8164a28a3e480e739
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-16 12:39:35 -0400
Commit message:
Commit: eeea9a5b1c7ea8c97a1c02c8164a28a3e480e739
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-16 12:39:35 -0400
Commit message:
add peakheights()
Package: matter
Commit: 0d86ffda4a01a84e343dc51181bfdebf9a40aa4c
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-15 22:22:17 -0400
Commit message:
Commit: 0d86ffda4a01a84e343dc51181bfdebf9a40aa4c
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-15 22:22:17 -0400
Commit message:
reorder approx interp codes
Package: matter
Commit: d538c891325071f77537b532c2ec4096424f7bc8
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-15 22:07:51 -0400
Commit message:
Commit: d538c891325071f77537b532c2ec4096424f7bc8
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-15 22:07:51 -0400
Commit message:
fix as_tol() again
Package: matter
Commit: a7a716a9bc1343c90333946486c9a02c97517746
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-15 22:04:53 -0400
Commit message:
Commit: a7a716a9bc1343c90333946486c9a02c97517746
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-15 22:04:53 -0400
Commit message:
update as_tol()
Package: matter
Commit: 98e01e21b4a0a8958a550d4eddbb08fb2e38967e
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-15 16:15:26 -0400
Commit message:
Commit: 98e01e21b4a0a8958a550d4eddbb08fb2e38967e
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-15 16:15:26 -0400
Commit message:
rename some variables
Package: matter
Commit: 273666ff07ad20bf2aa7def7a948ed84c58dd2c0
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-13 16:00:35 -0400
Commit message:
Commit: 273666ff07ad20bf2aa7def7a948ed84c58dd2c0
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-13 16:00:35 -0400
Commit message:
v2.5.9 fix outfile write order in chunk apply functions
Package: standR
Commit: 23da1fae3c6a97c1b07301a793568239418443c5
Author: ningbioinfo <ning.liu@adelaide.edu.au>
Date: 2024-03-26 10:04:03 +1030
Commit message:
Commit: 23da1fae3c6a97c1b07301a793568239418443c5
Author: ningbioinfo <ning.liu@adelaide.edu.au>
Date: 2024-03-26 10:04:03 +1030
Commit message:
i Please enter the commit message for your changes. Lines starting
Package: standR
Commit: 5b386298917e7b2d6b325903a07b4209075ea2aa
Author: ningbioinfo <ning.liu@adelaide.edu.au>
Date: 2024-03-26 10:03:21 +1030
Commit message:
Commit: 5b386298917e7b2d6b325903a07b4209075ea2aa
Author: ningbioinfo <ning.liu@adelaide.edu.au>
Date: 2024-03-26 10:03:21 +1030
Commit message:
fix bug in citation page
Package: M3Drop
Commit: cced8b74275e96bcef3f5c7680840a353f7b44c8
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-25 18:22:33 -0400
Commit message:
Commit: cced8b74275e96bcef3f5c7680840a353f7b44c8
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-25 18:22:33 -0400
Commit message:
fixed scater version compatibility
Package: M3Drop
Commit: 928dc1662cf8c54c44f8b63500524356a7ebccdc
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-25 18:10:41 -0400
Commit message:
Commit: 928dc1662cf8c54c44f8b63500524356a7ebccdc
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-25 18:10:41 -0400
Commit message:
Remove old scater support
Package: hdxmsqc
Commit: cfddc4754bdb6d90bb597d78ee267451bd8222ab
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2024-03-25 21:51:08 +0000
Commit message:
Commit: cfddc4754bdb6d90bb597d78ee267451bd8222ab
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2024-03-25 21:51:08 +0000
Commit message:
updated NEWSs vignette describes how to pefrom quality control for mass-spectrometry based hydrogen deuterium exchange experiment.
Package: txdbmaker
Commit: 971331726b80d8d7109b7e9f9436935fc0651c60
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-25 15:04:20 -0700
Commit message:
Commit: 971331726b80d8d7109b7e9f9436935fc0651c60
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-25 15:04:20 -0700
Commit message:
update TODO
Package: IgGeneUsage
Commit: 936fed9832a4a25b117df2508993877322c2279f
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 22:48:49 +0100
Commit message:
Commit: 936fed9832a4a25b117df2508993877322c2279f
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 22:48:49 +0100
Commit message:
update before more serious tests
Package: txdbmaker
Commit: 09fe795bb3c622b2139a9044e634a6bd71682f59
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-25 14:48:03 -0700
Commit message:
Commit: 09fe795bb3c622b2139a9044e634a6bd71682f59
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-25 14:48:03 -0700
Commit message:
remove markdown from Suggests (not needed)
Package: AnVIL
Commit: 40451868ee43d9fbe1baaa28f9f88277d321e6c5
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-03-25 17:43:28 -0400
Commit message:
Commit: 40451868ee43d9fbe1baaa28f9f88277d321e6c5
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-03-25 17:43:28 -0400
Commit message:
version bump 1.15.9
Package: AnVIL
Commit: a24698b30e2bc6f8c32c5d212459666321a88597
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-03-25 17:43:14 -0400
Commit message:
Commit: a24698b30e2bc6f8c32c5d212459666321a88597
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-03-25 17:43:14 -0400
Commit message:
use assertions from BiocBaseUtils
Package: tidytof
Commit: 2f40d01f461bd9c25eeb3d5520672e1430f104c5
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 14:30:51 -0700
Commit message:
Commit: 2f40d01f461bd9c25eeb3d5520672e1430f104c5
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 14:30:51 -0700
Commit message:
update tests/dependencies
Package: pathview
Commit: 24250b848480afb1935540479d7ff56b6b4c6427
Author: Weijun Luo <luo_weijun@yahoo.com>
Date: 2024-03-25 17:38:52 -0400
Commit message:
Commit: 24250b848480afb1935540479d7ff56b6b4c6427
Author: Weijun Luo <luo_weijun@yahoo.com>
Date: 2024-03-25 17:38:52 -0400
Commit message:
version 1.43.1
Package: M3Drop
Commit: 0c58f40baa90f678af2c9444ec2711fb01833fb9
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-25 17:26:09 -0400
Commit message:
Commit: 0c58f40baa90f678af2c9444ec2711fb01833fb9
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-25 17:26:09 -0400
Commit message:
Update Version & Date
Package: BloodCancerMultiOmics2017
Commit: d6eaa9ce29a3eda24ff9d25de7b0c7b492b84365
Author: MalgorzataOles <dr.malgorzata.oles@gmail.com>
Date: 2024-03-25 21:43:18 +0100
Commit message:
Commit: d6eaa9ce29a3eda24ff9d25de7b0c7b492b84365
Author: MalgorzataOles <dr.malgorzata.oles@gmail.com>
Date: 2024-03-25 21:43:18 +0100
Commit message:
version bump in devel
Package: BloodCancerMultiOmics2017
Commit: 9d4a88533c0be5e00e5e3b53d8542dbddeaa538c
Author: MalgorzataOles <dr.malgorzata.oles@gmail.com>
Date: 2024-03-25 21:40:48 +0100
Commit message:
Commit: 9d4a88533c0be5e00e5e3b53d8542dbddeaa538c
Author: MalgorzataOles <dr.malgorzata.oles@gmail.com>
Date: 2024-03-25 21:40:48 +0100
Commit message:
bug fix: change guide-box to guide-box-right
Package: GenomicAlignments
Commit: 3479ba78b0b99ec5a496adf1044f7e1cc72bf18e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-25 12:52:40 -0700
Commit message:
Commit: 3479ba78b0b99ec5a496adf1044f7e1cc72bf18e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-25 12:52:40 -0700
Commit message:
minor edits + version bump
Package: GenomicAlignments
Commit: 5410f9c597a250b73d2490bad316ff1eaba924b5
Author: Halimat Chisom Atanda <66901562+Chisomgold@users.noreply.github.com>
Date: 2024-03-26 05:47:57 +1000
Commit message:
Commit: 5410f9c597a250b73d2490bad316ff1eaba924b5
Author: Halimat Chisom Atanda <66901562+Chisomgold@users.noreply.github.com>
Date: 2024-03-26 05:47:57 +1000
Commit message:
Convert WorkingWithAlignedNucleotides from Rnw to Rmd (#22) Co-authored-by: jwokaty <jwokaty@users.noreply.github.com>
Package: ASpli
Commit: 6ffebd3c49c75f240d416cc8942ef4a5b8d4bba4
Author: achernom <algo107@gmail.com>
Date: 2024-03-25 16:16:15 -0300
Commit message:
Commit: 6ffebd3c49c75f240d416cc8942ef4a5b8d4bba4
Author: achernom <algo107@gmail.com>
Date: 2024-03-25 16:16:15 -0300
Commit message:
update version numbering
Package: ASpli
Commit: 06d26e863ea59ef1c3a071c9640f989fed599afc
Author: achernom <algo107@gmail.com>
Date: 2024-03-22 16:47:26 -0300
Commit message:
Commit: 06d26e863ea59ef1c3a071c9640f989fed599afc
Author: achernom <algo107@gmail.com>
Date: 2024-03-22 16:47:26 -0300
Commit message:
Correct some glitches on man/*Rd docs
Package: ASpli
Commit: 87346eab659f0e957629ccf367fb85b4c6eb72f1
Author: achernom <algo107@gmail.com>
Date: 2024-03-22 16:15:33 -0300
Commit message:
Commit: 87346eab659f0e957629ccf367fb85b4c6eb72f1
Author: achernom <algo107@gmail.com>
Date: 2024-03-22 16:15:33 -0300
Commit message:
update package version and date
Package: ASpli
Commit: 6f08d3d62184d69acafc1e1ed9c53ecfbd72ea8c
Author: achernom <algo107@gmail.com>
Date: 2024-03-22 16:12:43 -0300
Commit message:
Commit: 6f08d3d62184d69acafc1e1ed9c53ecfbd72ea8c
Author: achernom <algo107@gmail.com>
Date: 2024-03-22 16:12:43 -0300
Commit message:
correct package version comparison to correctly build vignettes
Package: ASpli
Commit: a1395d7ec01452da5d16a659afe8d2e840a7f43f
Author: achernom <algo107@gmail.com>
Date: 2024-03-20 15:43:55 -0300
Commit message:
Commit: a1395d7ec01452da5d16a659afe8d2e840a7f43f
Author: achernom <algo107@gmail.com>
Date: 2024-03-20 15:43:55 -0300
Commit message:
makeTxDbFromGFF() has moved to the txdbmaker package, so now call txdbmaker::makeTxDbFromGFF()
Package: tidytof
Commit: 61551d4000427c17aa32241bab71277b0a3f9c57
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 11:37:10 -0700
Commit message:
Commit: 61551d4000427c17aa32241bab71277b0a3f9c57
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 11:37:10 -0700
Commit message:
increment version
Package: tidytof
Commit: e7d05e4a31a8f9f89585731aaa79f5364aeb9530
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 10:44:40 -0700
Commit message:
Commit: e7d05e4a31a8f9f89585731aaa79f5364aeb9530
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 10:44:40 -0700
Commit message:
update testthat.R
Package: hdxmsqc
Commit: 2d035bfea50d9d4c6bd55b81bb6cf044601ecc3e
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2024-03-25 18:32:40 +0000
Commit message:
Commit: 2d035bfea50d9d4c6bd55b81bb6cf044601ecc3e
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2024-03-25 18:32:40 +0000
Commit message:
more documentation
Package: hdxmsqc
Commit: 48f2e9562fec18801ec9c979f673e260dd96486a
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2024-03-25 18:30:32 +0000
Commit message:
Commit: 48f2e9562fec18801ec9c979f673e260dd96486a
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2024-03-25 18:30:32 +0000
Commit message:
package updates according to review
Package: saseR
Commit: a4790cd45151b53fb5dfe72da7b6847e4d4a47e0
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2024-03-25 19:19:34 +0100
Commit message:
Commit: a4790cd45151b53fb5dfe72da7b6847e4d4a47e0
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2024-03-25 19:19:34 +0100
Commit message:
add binGenome functions from ASpli
Package: cypress
Commit: b58203237a3f73063eacd4cc3f24033c163e1470
Author: Shilin Yu <sy597@georgetown.edu>
Date: 2024-03-25 13:59:59 -0400
Commit message:
Commit: b58203237a3f73063eacd4cc3f24033c163e1470
Author: Shilin Yu <sy597@georgetown.edu>
Date: 2024-03-25 13:59:59 -0400
Commit message:
edit for comment oding modified in compliance with BioC requirement.
Package: IgGeneUsage
Commit: 451f61add5d6e7be308fb27edf72d7fae04eff3e
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 18:49:41 +0100
Commit message:
Commit: 451f61add5d6e7be308fb27edf72d7fae04eff3e
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 18:49:41 +0100
Commit message:
new models commited
Package: IgGeneUsage
Commit: 898ffacbcda76ca4e9642170f3dfda8d86092fb7
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 18:49:10 +0100
Commit message:
Commit: 898ffacbcda76ca4e9642170f3dfda8d86092fb7
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 18:49:10 +0100
Commit message:
paired analysis integrated
Package: BASiCS
Commit: cc133767c2f35ee840b875545e2121a84e2341fe
Author: Catalina Vallejos <catalina.vallejos@ed.ac.uk>
Date: 2024-03-25 17:34:38 +0000
Commit message:
Commit: cc133767c2f35ee840b875545e2121a84e2341fe
Author: Catalina Vallejos <catalina.vallejos@ed.ac.uk>
Date: 2024-03-25 17:34:38 +0000
Commit message:
bug fix in subset method
Package: BSgenomeForge
Commit: a8380e769627939467c6f25bae7d0c0ef0d28ea7
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-25 10:20:08 -0700
Commit message:
Commit: a8380e769627939467c6f25bae7d0c0ef0d28ea7
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-25 10:20:08 -0700
Commit message:
make vignette compatible with rmarkdown 2.26
Package: tidytof
Commit: b2ea3cfa2377dd71fa59a30398817b2128349e5e
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 09:57:01 -0700
Commit message:
Commit: b2ea3cfa2377dd71fa59a30398817b2128349e5e
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 09:57:01 -0700
Commit message:
increment version
Package: tidytof
Commit: 01685cc50d8ea79f917fe7bb069ca3658e548680
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 09:56:20 -0700
Commit message:
Commit: 01685cc50d8ea79f917fe7bb069ca3658e548680
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 09:56:20 -0700
Commit message:
update docs
Package: BiocCheck
Commit: 77fa12d556ced823f4312934e1a8ee95f2be2c2e
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-03-25 12:48:05 -0400
Commit message:
Commit: 77fa12d556ced823f4312934e1a8ee95f2be2c2e
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-03-25 12:48:05 -0400
Commit message:
version bump 1.39.27
Package: BiocCheck
Commit: 1b5a10fabe9ac54aa0c4fec4b468acd75fb1fb27
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-03-25 12:48:00 -0400
Commit message:
Commit: 1b5a10fabe9ac54aa0c4fec4b468acd75fb1fb27
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-03-25 12:48:00 -0400
Commit message:
avoid system call and use devtools::build
Package: ZygosityPredictor
Commit: 4fced5261740705d7c43a6c04564e2a0a9d6eeb2
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-25 17:38:58 +0100
Commit message:
Commit: 4fced5261740705d7c43a6c04564e2a0a9d6eeb2
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-25 17:38:58 +0100
Commit message:
fixed build errors
Package: tidytof
Commit: b16165c8783c681995cd08f362e428df3aab9fe8
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 08:08:42 -0700
Commit message:
Commit: b16165c8783c681995cd08f362e428df3aab9fe8
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 08:08:42 -0700
Commit message:
increment version
Package: tidytof
Commit: e6f17a10c56ba3ffd7789ef98b265433436d4847
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 08:07:55 -0700
Commit message:
Commit: e6f17a10c56ba3ffd7789ef98b265433436d4847
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 08:07:55 -0700
Commit message:
update docs
Package: GrafGen
Commit: e7c0db1939f26daa375fbb27145a631c4b2234a4
Author: wheelerb <wheelerb@imsweb.com>
Date: 2024-03-25 11:49:50 -0400
Commit message:
Commit: e7c0db1939f26daa375fbb27145a631c4b2234a4
Author: wheelerb <wheelerb@imsweb.com>
Date: 2024-03-25 11:49:50 -0400
Commit message:
changes for review
Package: funOmics
Commit: 3bf724321d1f467149f43fa1a86cc2d710a14ae9
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 15:53:36 +0100
Commit message:
Commit: 3bf724321d1f467149f43fa1a86cc2d710a14ae9
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 15:53:36 +0100
Commit message:
UPDATE: vignette, DESCRIPTION v.5
Package: IgGeneUsage
Commit: 15ebf37ee22bdbca00967bb4365d1c39a02f46cb
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 15:52:22 +0100
Commit message:
Commit: 15ebf37ee22bdbca00967bb4365d1c39a02f46cb
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 15:52:22 +0100
Commit message:
update data generation
Package: IgGeneUsage
Commit: 9c56201ee92df58d7b1ec02585e7f313ad9ae713
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 15:33:53 +0100
Commit message:
Commit: 9c56201ee92df58d7b1ec02585e7f313ad9ae713
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 15:33:53 +0100
Commit message:
updated vignette to include data on analysis with replicates
Package: funOmics
Commit: 2020c21f798a4995983d697a99338a92039142ec
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 15:52:21 +0100
Commit message:
Commit: 2020c21f798a4995983d697a99338a92039142ec
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 15:52:21 +0100
Commit message:
UPDATE: add processing comment to vignette
Package: funOmics
Commit: 362f742cde6aa746070c25e45c494893e032a85e
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 15:43:01 +0100
Commit message:
Commit: 362f742cde6aa746070c25e45c494893e032a85e
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 15:43:01 +0100
Commit message:
UPDATE: vignette from branch master to devel
Package: M3Drop
Commit: 5f314bfbade4e60d5b33940b10933ae5f18f0aff
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-22 14:48:46 -0400
Commit message:
Commit: 5f314bfbade4e60d5b33940b10933ae5f18f0aff
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-22 14:48:46 -0400
Commit message:
Properly fix PearsonResiduals Example
Package: M3Drop
Commit: 40da566dd2b192e5bef16867af39ac7b0f235ff7
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-22 14:41:27 -0400
Commit message:
Commit: 40da566dd2b192e5bef16867af39ac7b0f235ff7
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-22 14:41:27 -0400
Commit message:
Fix Pearson Residual Example
Package: funOmics
Commit: d35bb2b7084b6343eedd5040c4d9c25503c0505c
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 14:54:18 +0100
Commit message:
Commit: d35bb2b7084b6343eedd5040c4d9c25503c0505c
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 14:54:18 +0100
Commit message:
UPDATE: DESCRIPTION & README from branch master to devel
Package: funOmics
Commit: e900a3df88713b6df8aeb772a8e486cd40f1e1f7
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 14:22:37 +0100
Commit message:
Commit: e900a3df88713b6df8aeb772a8e486cd40f1e1f7
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 14:22:37 +0100
Commit message:
FIX: Updated NAMESPACE
Package: zellkonverter
Commit: a64ff2d45173575ccdd83625df9b4077448a7dee
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 13:50:20 +0100
Commit message:
Commit: a64ff2d45173575ccdd83625df9b4077448a7dee
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 13:50:20 +0100
Commit message:
Bump roxygen version
Package: zellkonverter
Commit: 52f0583cf919880b2f80a74112980917a7d03810
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 13:50:00 +0100
Commit message:
Commit: 52f0583cf919880b2f80a74112980917a7d03810
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 13:50:00 +0100
Commit message:
Update WORDLIST
Package: zellkonverter
Commit: 24efa6a832fc75a89767ce2f75ce8b0a72a874b7
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 13:47:33 +0100
Commit message:
Commit: 24efa6a832fc75a89767ce2f75ce8b0a72a874b7
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 13:47:33 +0100
Commit message:
Add environment for anndata v0.10.6
Package: zellkonverter
Commit: e8202deefea4d4452ba7fe01ca7c55026065b26c
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 13:05:08 +0100
Commit message:
Commit: e8202deefea4d4452ba7fe01ca7c55026065b26c
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 13:05:08 +0100
Commit message:
Improve warnings when converting matrices fails
Package: zellkonverter
Commit: 5834f30f072529d95add4d8ddefa7608ee84e577
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 12:56:14 +0100
Commit message:
Commit: 5834f30f072529d95add4d8ddefa7608ee84e577
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 12:56:14 +0100
Commit message:
Correctly handle use_hdf5=TRUE with newer anndata Class of the matrix read by Python is different Fixes #114
Package: BioNERO
Commit: 5de1a416daf0f8ddae3b161cbe64f4681e9322e1
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2024-03-25 13:39:54 +0100
Commit message:
Commit: 5de1a416daf0f8ddae3b161cbe64f4681e9322e1
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2024-03-25 13:39:54 +0100
Commit message:
Version bump in devel
Package: BioNERO
Commit: bea1a817518d345c3b325910dd33a17907c17975
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2024-03-25 13:39:24 +0100
Commit message:
Commit: bea1a817518d345c3b325910dd33a17907c17975
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2024-03-25 13:39:24 +0100
Commit message:
Added exp2gcn_blockwise() + increased unit test coverage
Package: escape
Commit: 99fed6482d39477cbff92171849cf68c067da5c9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-03-25 06:24:52 -0500
Commit message:
Commit: 99fed6482d39477cbff92171849cf68c067da5c9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-03-25 06:24:52 -0500
Commit message:
silencing some tests
Package: multicrispr
Commit: a2e2370e1f0ec179529b23b41841e31754818959
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-25 12:05:37 +0100
Commit message:
Commit: a2e2370e1f0ec179529b23b41841e31754818959
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-25 12:05:37 +0100
Commit message:
removed obsolete file `00_properties_has-dims.R`
Package: funOmics
Commit: 4bf583b2abc61369e685f08eafe48b994e269e5c
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 11:14:29 +0100
Commit message:
Commit: 4bf583b2abc61369e685f08eafe48b994e269e5c
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 11:14:29 +0100
Commit message:
UPDATE: update functions.R in branch with get_kegg_sets()
Package: funOmics
Commit: dd0ae6f72f27a115bca712ee33ea86279a545711
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 11:13:55 +0100
Commit message:
Commit: dd0ae6f72f27a115bca712ee33ea86279a545711
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 11:13:55 +0100
Commit message:
UPDATE: update functions.R in branch with get_kegg_sets()
Package: PIUMA
Commit: 0b48fe985e1c92ce255cb8bfc21e68aaca0869c9
Author: BioinfoMonzino <mattia.chiesa@cardiologicomonzino.it>
Date: 2024-03-25 10:48:56 +0100
Commit message:
Commit: 0b48fe985e1c92ce255cb8bfc21e68aaca0869c9
Author: BioinfoMonzino <mattia.chiesa@cardiologicomonzino.it>
Date: 2024-03-25 10:48:56 +0100
Commit message:
0.99.6 BioC review
Package: funOmics
Commit: 3e963097488647c3c067f9bd34814de5650858bb
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 10:46:01 +0100
Commit message:
Commit: 3e963097488647c3c067f9bd34814de5650858bb
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 10:46:01 +0100
Commit message:
FIX: un-ignore man/ documentation
Package: funOmics
Commit: 323db5fdd9ea82a9b336d943008b628ab159299b
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 10:43:42 +0100
Commit message:
Commit: 323db5fdd9ea82a9b336d943008b628ab159299b
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 10:43:42 +0100
Commit message:
FIX: un-ignore man/ documentation
Package: funOmics
Commit: e7b15bd312400e3ec980cb4be6c815e086a82ebf
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 10:20:37 +0100
Commit message:
Commit: e7b15bd312400e3ec980cb4be6c815e086a82ebf
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 10:20:37 +0100
Commit message:
UPDATE: DESCRIPTION version
Package: PIUMA
Commit: eeb78895a59ddf16b898caf11b2176b73ecaef07
Author: BioinfoMonzino <mattia.chiesa@cardiologicomonzino.it>
Date: 2024-03-25 10:19:03 +0100
Commit message:
Commit: eeb78895a59ddf16b898caf11b2176b73ecaef07
Author: BioinfoMonzino <mattia.chiesa@cardiologicomonzino.it>
Date: 2024-03-25 10:19:03 +0100
Commit message:
0.99.5 BioC review
Package: Repitools
Commit: cf61279df20d622a2e736c9b190040a40d7cdea9
Author: Mark Robinson <mark@imlssherborne.uzh.ch>
Date: 2024-03-17 22:03:03 +0100
Commit message:
Commit: cf61279df20d622a2e736c9b190040a40d7cdea9
Author: Mark Robinson <mark@imlssherborne.uzh.ch>
Date: 2024-03-17 22:03:03 +0100
Commit message:
ported a few things from Ringo
Package: decoupleR
Commit: 68bf5f61dbc5bcb6aa87d27896205e97a9ffb5be
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 13:38:34 +0100
Commit message:
Commit: 68bf5f61dbc5bcb6aa87d27896205e97a9ffb5be
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 13:38:34 +0100
Commit message:
Bump version: 2.9.5 → 2.9.6
Package: decoupleR
Commit: 3fe7322e85d41d7c11e41957555f8b88cd27b55a
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 13:38:28 +0100
Commit message:
Commit: 3fe7322e85d41d7c11e41957555f8b88cd27b55a
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 13:38:28 +0100
Commit message:
`test get_progeny mouse`: removed bypass on build servers, since the slow_doctest issue has been addressed in c1485180
Package: decoupleR
Commit: ea4ecbb11bc36ce407806dbb645f95063a997f26
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 12:22:31 +0100
Commit message:
Commit: ea4ecbb11bc36ce407806dbb645f95063a997f26
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 12:22:31 +0100
Commit message:
Bump version: 2.9.4 → 2.9.5
Package: decoupleR
Commit: c1485180d09a486a6125a93fdb2b7be19e1608f4
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 12:22:13 +0100
Commit message:
Commit: c1485180d09a486a6125a93fdb2b7be19e1608f4
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 12:22:13 +0100
Commit message:
disable OmnipathR slow doctest bypass
Package: decoupleR
Commit: 41d18b6c394b4cbb4e693a096413a0b2c3f68993
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:28:52 +0100
Commit message:
Commit: 41d18b6c394b4cbb4e693a096413a0b2c3f68993
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:28:52 +0100
Commit message:
Bump version: 2.9.3 → 2.9.4
Package: decoupleR
Commit: 41706b28a86fa12d5bb638190b85ee979198da8a
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:28:47 +0100
Commit message:
Commit: 41706b28a86fa12d5bb638190b85ee979198da8a
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:28:47 +0100
Commit message:
docs rebuild
Package: decoupleR
Commit: cf951afe98188ee4833fd07548c3ef901972d59d
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:28:41 +0100
Commit message:
Commit: cf951afe98188ee4833fd07548c3ef901972d59d
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:28:41 +0100
Commit message:
namespace updates by roxygen
Package: decoupleR
Commit: f085045fbe71d8f7264566deea326435c71cb842
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:28:25 +0100
Commit message:
Commit: f085045fbe71d8f7264566deea326435c71cb842
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:28:25 +0100
Commit message:
`test-gsva`: `minsize = 1` instead of 0
Package: decoupleR
Commit: 73df90bfe86f6bd6dd86654db4cd7ac68f233684
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:27:27 +0100
Commit message:
Commit: 73df90bfe86f6bd6dd86654db4cd7ac68f233684
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:27:27 +0100
Commit message:
`ulm`: use `tidyr::pivot_longer` instead of `reshape2::melt`; fixes R CMD check warning; + coding style
Package: decoupleR
Commit: 712e1863c5b1f344d2e21971cd8419a739e3a1ec
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:26:21 +0100
Commit message:
Commit: 712e1863c5b1f344d2e21971cd8419a739e3a1ec
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:26:21 +0100
Commit message:
`mdt`: updated to new `dplyr` API (`reframe`); fixes deprecation warning; + coding style
Package: decoupleR
Commit: 589a7650b05aac7754c85e40ff955b3ad2fbc8dd
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:24:19 +0100
Commit message:
Commit: 589a7650b05aac7754c85e40ff955b3ad2fbc8dd
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:24:19 +0100
Commit message:
`aucell`: updated to new `AUCell`/`BiocParallel` API, fixes deprecation warning
Package: decoupleR
Commit: 7dbd1156d1db084b9f2840884a6b1f06f1d31adc
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:22:51 +0100
Commit message:
Commit: 7dbd1156d1db084b9f2840884a6b1f06f1d31adc
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:22:51 +0100
Commit message:
`gsva`: restored column order
Package: decoupleR
Commit: fdc1c22de6ecfc817bc8c3c7a9e5a6d874dda06f
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:22:32 +0100
Commit message:
Commit: fdc1c22de6ecfc817bc8c3c7a9e5a6d874dda06f
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:22:32 +0100
Commit message:
`gsva`: warn if `minsize == 0`
Package: decoupleR
Commit: 4ee8ac65da319dc968f006be7373dd12c766d7e2
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 13:45:41 +0100
Commit message:
Commit: 4ee8ac65da319dc968f006be7373dd12c766d7e2
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 13:45:41 +0100
Commit message:
`run_gsva`: typo
Package: decoupleR
Commit: d623008d9d5a5f1677717d30c8cbff153296def8
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 00:09:40 +0100
Commit message:
Commit: d623008d9d5a5f1677717d30c8cbff153296def8
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 00:09:40 +0100
Commit message:
Bump version: 2.9.2 → 2.9.3
Package: decoupleR
Commit: f1eae69259c21949295c8e8144fb59b7bc18656a
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 00:09:30 +0100
Commit message:
Commit: f1eae69259c21949295c8e8144fb59b7bc18656a
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 00:09:30 +0100
Commit message:
do not import `GSVA` functions, it is suggested dependency
Package: decoupleR
Commit: cb3cdea89621e23784ce902a6583e07006d6fde9
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 17:47:30 +0100
Commit message:
Commit: cb3cdea89621e23784ce902a6583e07006d6fde9
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 17:47:30 +0100
Commit message:
Bump version: 2.9.1 → 2.9.2
Package: decoupleR
Commit: 9498daae02ed4b0ea153f8b614aca24330cafe08
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 17:47:23 +0100
Commit message:
Commit: 9498daae02ed4b0ea153f8b614aca24330cafe08
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 17:47:23 +0100
Commit message:
`run_gsva`: updated to new `GSVA::gsva` API; fixed: `minsize` arg had no effect
Package: decoupleR
Commit: 26d6fed9fa19298e7977857b3e41d99b82896b50
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 16:56:25 +0100
Commit message:
Commit: 26d6fed9fa19298e7977857b3e41d99b82896b50
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 16:56:25 +0100
Commit message:
import `cor` and `pt` from `stats` in `.ulm_analysis`
Package: decoupleR
Commit: 50fe673f90cf42e2df5ffb22de36e194705747d8
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 16:52:48 +0100
Commit message:
Commit: 50fe673f90cf42e2df5ffb22de36e194705747d8
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 16:52:48 +0100
Commit message:
`tests/progeny-mouse`: disable on BioC build servers
Package: decoupleR
Commit: 11cde41c61bb0ad12a8217e2e6042d25bc2bd597
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 16:44:24 +0100
Commit message:
Commit: 11cde41c61bb0ad12a8217e2e6042d25bc2bd597
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 16:44:24 +0100
Commit message:
`rbuildignore` removed `inst/doc`
Package: decoupleR
Commit: 79f24fe83703c0b9e7537fd88b76c027a9bbc3c2
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 14:13:57 +0100
Commit message:
Commit: 79f24fe83703c0b9e7537fd88b76c027a9bbc3c2
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 14:13:57 +0100
Commit message:
Merge branch 'master' of github.com:saezlab/decoupleR
Package: decoupleR
Commit: c0ea29d354c868b7383485c2cbc2682097a77a84
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 14:13:48 +0100
Commit message:
Commit: c0ea29d354c868b7383485c2cbc2682097a77a84
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 14:13:48 +0100
Commit message:
added bump2version config to rbuildignore
Package: decoupleR
Commit: ea34746e834996a1171d65a3b610fd722f4e08e4
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2024-02-20 14:43:45 +0100
Commit message:
Commit: ea34746e834996a1171d65a3b610fd722f4e08e4
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2024-02-20 14:43:45 +0100
Commit message:
Updated readme
Package: DMRcate
Commit: 86df50bb8de4abe3aa040b75b94d7eb76eacc0d5
Author: timpet <t.peters@garvan.org.au>
Date: 2024-03-25 15:43:16 +1100
Commit message:
Commit: 86df50bb8de4abe3aa040b75b94d7eb76eacc0d5
Author: timpet <t.peters@garvan.org.au>
Date: 2024-03-25 15:43:16 +1100
Commit message:
DMRcate_2.99.4
Package: standR
Commit: b20520e18e4dfa80cb7a554b493f88fd2f9b2429
Author: ningbioinfo <ning.liu@adelaide.edu.au>
Date: 2024-03-25 15:01:41 +1030
Commit message:
Commit: b20520e18e4dfa80cb7a554b493f88fd2f9b2429
Author: ningbioinfo <ning.liu@adelaide.edu.au>
Date: 2024-03-25 15:01:41 +1030
Commit message:
version bump
Package: standR
Commit: 0755f5ae72bd18f3d1aedc84a663db63d1651545
Author: ningbioinfo <ning.liu@adelaide.edu.au>
Date: 2024-03-25 15:01:04 +1030
Commit message:
Commit: 0755f5ae72bd18f3d1aedc84a663db63d1651545
Author: ningbioinfo <ning.liu@adelaide.edu.au>
Date: 2024-03-25 15:01:04 +1030
Commit message:
add citation document
Package: tidytof
Commit: 59311df58335792ec13076a2a913db09d6ebc5c9
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 21:11:35 -0700
Commit message:
Commit: 59311df58335792ec13076a2a913db09d6ebc5c9
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 21:11:35 -0700
Commit message:
increment version
Package: tidytof
Commit: fadf8982b18829fa4818ddba60a9efbc67c7e05d
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 20:39:01 -0700
Commit message:
Commit: fadf8982b18829fa4818ddba60a9efbc67c7e05d
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 20:39:01 -0700
Commit message:
update docs
Package: tidyFlowCore
Commit: 0ede10bcc13c669fa02bbdedc851e49add9ed342
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 20:28:32 -0700
Commit message:
Commit: 0ede10bcc13c669fa02bbdedc851e49add9ed342
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 20:28:32 -0700
Commit message:
increment version
Package: tidyFlowCore
Commit: 035f0343a4175c0e7e81e37c7a0570e8a26e5279
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 20:06:13 -0700
Commit message:
Commit: 035f0343a4175c0e7e81e37c7a0570e8a26e5279
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 20:06:13 -0700
Commit message:
Update docs
Package: tidyFlowCore
Commit: 238c4c4fd34f0b775c7d463b7924e9f1f2e159ea
Author: Timothy Keyes <keyes.timothy@gmail.com>
Date: 2024-03-24 19:46:20 -0700
Commit message:
Commit: 238c4c4fd34f0b775c7d463b7924e9f1f2e159ea
Author: Timothy Keyes <keyes.timothy@gmail.com>
Date: 2024-03-24 19:46:20 -0700
Commit message:
Delete tidyflowCore.Rproj
Package: tidyFlowCore
Commit: 6305790efc339ca002e74b361e2f63098c026bcf
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 19:43:34 -0700
Commit message:
Commit: 6305790efc339ca002e74b361e2f63098c026bcf
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 19:43:34 -0700
Commit message:
remove unneeded files
Package: beachmat
Commit: a8fcb49857cd2a3745357b0dc51862e10962c712
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-03-24 18:22:27 -0700
Commit message:
Commit: a8fcb49857cd2a3745357b0dc51862e10962c712
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-03-24 18:22:27 -0700
Commit message:
Initialization no-ops when supplied with an external ptr. Downstream functions can call initializeCpp without worrying about whether initialization has already been performed on the input.
Package: FLAMES
Commit: 16383263f35824d46c3502cbf4cbfa8756de30d5
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-21 10:23:30 +1100
Commit message:
Commit: 16383263f35824d46c3502cbf4cbfa8756de30d5
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-21 10:23:30 +1100
Commit message:
fix find_variants docs
Package: FLAMES
Commit: 29de37b374499cfed9e3de2425e5153e8388f801
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-21 10:18:33 +1100
Commit message:
Commit: 29de37b374499cfed9e3de2425e5153e8388f801
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-21 10:18:33 +1100
Commit message:
Merge branch 'devel' of https://github.com/OliverVoogd/FLAMES into youyupei/devel
Package: FLAMES
Commit: 1847f1575f76124c026757428b37e28aa3f28fbb
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-20 23:14:54 +1100
Commit message:
Commit: 1847f1575f76124c026757428b37e28aa3f28fbb
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-20 23:14:54 +1100
Commit message:
fix gff not found error in quantification-only mode
Package: FLAMES
Commit: 4f9249190e886d5f49d6114047ef6e16f37b9c81
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-20 16:20:43 +1100
Commit message:
Commit: 4f9249190e886d5f49d6114047ef6e16f37b9c81
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-20 16:20:43 +1100
Commit message:
update sc_mutations
Package: FLAMES
Commit: 40f1ae2b73e94ad22d6daaff6e63626acb6c5fbd
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-20 11:35:11 +1100
Commit message:
Commit: 40f1ae2b73e94ad22d6daaff6e63626acb6c5fbd
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-20 11:35:11 +1100
Commit message:
move txdbmaker to suggests
Package: FLAMES
Commit: efbc6842b94bef22e3dfaeef2c36d555521eadd8
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-20 10:41:55 +1100
Commit message:
Commit: efbc6842b94bef22e3dfaeef2c36d555521eadd8
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-20 10:41:55 +1100
Commit message:
use annotated transcript for quantification if there is no isoform discovery result
Package: FLAMES
Commit: c2b1ff091b21dd2753a7ad951491138ebc3846ba
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-19 11:34:21 +1100
Commit message:
Commit: c2b1ff091b21dd2753a7ad951491138ebc3846ba
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-19 11:34:21 +1100
Commit message:
Merge branch 'devel' of https://github.com/OliverVoogd/FLAMES into youyupei/devel
Package: FLAMES
Commit: c4017e4a73086e0f7cc3eb6d8baaf6d67704c3e2
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-19 11:28:39 +1100
Commit message:
Commit: c4017e4a73086e0f7cc3eb6d8baaf6d67704c3e2
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-19 11:28:39 +1100
Commit message:
update BLAZE to v2.2.*
Package: FLAMES
Commit: 2c531603e6f4b7e3451591e4e569fc975335a987
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-19 10:53:55 +1100
Commit message:
Commit: 2c531603e6f4b7e3451591e4e569fc975335a987
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-19 10:53:55 +1100
Commit message:
misc: docs
Package: FLAMES
Commit: 4e02489cc7b5a92f2e5ca8ccfea0188ea9204823
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-19 10:25:13 +1100
Commit message:
Commit: 4e02489cc7b5a92f2e5ca8ccfea0188ea9204823
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-19 10:25:13 +1100
Commit message:
misc: docs, imports
Package: FLAMES
Commit: 9b36c0437484f1156c552ed96169505d92827aa9
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-18 20:01:35 +1100
Commit message:
Commit: 9b36c0437484f1156c552ed96169505d92827aa9
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-18 20:01:35 +1100
Commit message:
add find_variant
Package: FLAMES
Commit: e2cc3aca586284239fd4ef47fff640041bec47fe
Author: youyupei <youyupei@gmail.com>
Date: 2024-02-20 16:46:31 +1100
Commit message:
Commit: e2cc3aca586284239fd4ef47fff640041bec47fe
Author: youyupei <youyupei@gmail.com>
Date: 2024-02-20 16:46:31 +1100
Commit message:
add option to disable novel isoform discovery in bambu
Package: ZygosityPredictor
Commit: 8ecce1bbb2b6c10ee33f57556c8649e0f3dbfe07
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-24 22:12:51 +0100
Commit message:
Commit: 8ecce1bbb2b6c10ee33f57556c8649e0f3dbfe07
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-24 22:12:51 +0100
Commit message:
improved debugging
Package: ZygosityPredictor
Commit: a8f475cabc9782ef8795c0a292f29e75531fc40b
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-24 17:22:38 +0100
Commit message:
Commit: a8f475cabc9782ef8795c0a292f29e75531fc40b
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-24 17:22:38 +0100
Commit message:
fixed github issue #1... deviating chromosome annotations chr1 - 1
Package: ZygosityPredictor
Commit: 4424799b584504b0e34c4d6bbf539ac94b732eba
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-24 17:03:04 +0100
Commit message:
Commit: 4424799b584504b0e34c4d6bbf539ac94b732eba
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-24 17:03:04 +0100
Commit message:
fixed github issue #2... character tcn column
Package: ZygosityPredictor
Commit: 54b3e27b850aeb573bccf0de16e1b1594b71da67
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-07 18:27:42 +0100
Commit message:
Commit: 54b3e27b850aeb573bccf0de16e1b1594b71da67
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-07 18:27:42 +0100
Commit message:
moved external debugging script into repo
Package: ZygosityPredictor
Commit: ed0dc64170c0e6640f47851e0cd8e5f7b05e0b58
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-07 18:17:22 +0100
Commit message:
Commit: ed0dc64170c0e6640f47851e0cd8e5f7b05e0b58
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-07 18:17:22 +0100
Commit message:
included debug functionality
Package: bettr
Commit: c4fe4cd19105ba2d7c7022a64e16637dcaefa76e
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 17:31:19 +0100
Commit message:
Commit: c4fe4cd19105ba2d7c7022a64e16637dcaefa76e
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 17:31:19 +0100
Commit message:
Merge pull request #23 from federicomarini/add-stop-button Add stop button
Package: bettr
Commit: 75aae77de7508e05814b788fc502883cf72be43f
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 17:10:49 +0100
Commit message:
Commit: 75aae77de7508e05814b788fc502883cf72be43f
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 17:10:49 +0100
Commit message:
Add button to close app and return data
Package: bettr
Commit: a4452006de66be5c8ab9ccfc61c6ca7428777026
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 16:35:51 +0100
Commit message:
Commit: a4452006de66be5c8ab9ccfc61c6ca7428777026
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 16:35:51 +0100
Commit message:
Bump version
Package: iCOBRA
Commit: 4c15d3ba9ba019ded7986852307c76cc6ce9e2aa
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 16:06:43 +0100
Commit message:
Commit: 4c15d3ba9ba019ded7986852307c76cc6ce9e2aa
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 16:06:43 +0100
Commit message:
Add 'Close app' button to close the shiny app
Package: iCOBRA
Commit: 4c7234dbd1d9eb8b5bac2ac710199219144999d5
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 16:00:26 +0100
Commit message:
Commit: 4c7234dbd1d9eb8b5bac2ac710199219144999d5
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 16:00:26 +0100
Commit message:
Bump version
Package: alevinQC
Commit: db44b143a1a87c959a1e96dcf74a04f212388dac
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 15:56:46 +0100
Commit message:
Commit: db44b143a1a87c959a1e96dcf74a04f212388dac
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 15:56:46 +0100
Commit message:
Add 'Close app' button to stop app and export data
Package: alevinQC
Commit: 40ac72e2333aaef603ed2dc062ef160ed4b74349
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 15:54:44 +0100
Commit message:
Commit: 40ac72e2333aaef603ed2dc062ef160ed4b74349
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 15:54:44 +0100
Commit message:
Update package documentation format
Package: alevinQC
Commit: 5b3842ca3b8c46782381183362bb21ce208cedd5
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 15:53:51 +0100
Commit message:
Commit: 5b3842ca3b8c46782381183362bb21ce208cedd5
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 15:53:51 +0100
Commit message:
Bump version
Package: GeneTonic
Commit: 6e695297b8a4f39c0bc3dd61d66e27211f5446ce
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 14:43:09 +0100
Commit message:
Commit: 6e695297b8a4f39c0bc3dd61d66e27211f5446ce
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 14:43:09 +0100
Commit message:
forcing installation from source (?) for ComplexUpset to make it work
Package: GeneTonic
Commit: b4e8db05bd5a099c4408505302633b3b41aa8c17
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 14:14:42 +0100
Commit message:
Commit: b4e8db05bd5a099c4408505302633b3b41aa8c17
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 14:14:42 +0100
Commit message:
manually forcing the required version of ggplot2
Package: GeneTonic
Commit: 3cf6deb48ea1e96e03f76b67b52837ade2730d44
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 13:54:26 +0100
Commit message:
Commit: 3cf6deb48ea1e96e03f76b67b52837ade2730d44
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 13:54:26 +0100
Commit message:
version bump, 2.7.3
Package: GeneTonic
Commit: f836789aef94b28e2efb592ef9b65cf8e2e2f965
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 13:53:41 +0100
Commit message:
Commit: f836789aef94b28e2efb592ef9b65cf8e2e2f965
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 13:53:41 +0100
Commit message:
back to deplyoing from macOS instance
Package: GeneTonic
Commit: 2fde72c320d29d14a86982f2a3587766d64b7353
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-21 15:45:53 +0100
Commit message:
Commit: 2fde72c320d29d14a86982f2a3587766d64b7353
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-21 15:45:53 +0100
Commit message:
disabling the tooltip-based help
Package: GeneTonic
Commit: fa536afd472131cbcf79157b8d071c3c91240f61
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-18 16:46:25 +0100
Commit message:
Commit: fa536afd472131cbcf79157b8d071c3c91240f61
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-18 16:46:25 +0100
Commit message:
deploying (temporarily?) from the ubuntu-latest config
Package: GeneTonic
Commit: 481b29c35ed6294e3c76d8da7fb6a11850705d3a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-18 16:41:14 +0100
Commit message:
Commit: 481b29c35ed6294e3c76d8da7fb6a11850705d3a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-18 16:41:14 +0100
Commit message:
updating GHAs to match with new branch names, should enable auto-deployment
Package: ClustIRR
Commit: c3e5e40ba2775aea3030bb80f4435430bf5ac508
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-24 15:14:49 +0100
Commit message:
Commit: c3e5e40ba2775aea3030bb80f4435430bf5ac508
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-24 15:14:49 +0100
Commit message:
commit vignette and man fixes, version bump -> to devel
Package: ClustIRR
Commit: 7bca6efa2828bbf3d3aab66f16e86ecd1f36fae5
Author: Kai Wollek <kai.wollek@stud.uni-duisburg-essen.de>
Date: 2024-03-22 16:06:45 +0100
Commit message:
Commit: 7bca6efa2828bbf3d3aab66f16e86ecd1f36fae5
Author: Kai Wollek <kai.wollek@stud.uni-duisburg-essen.de>
Date: 2024-03-22 16:06:45 +0100
Commit message:
fixed some tests
Package: ClustIRR
Commit: 42277e35ba8e4c5384e506566c854148b032eb2f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-15 16:20:52 +0100
Commit message:
Commit: 42277e35ba8e4c5384e506566c854148b032eb2f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-15 16:20:52 +0100
Commit message:
simplification
Package: ClustIRR
Commit: 5dc115580f399f7a555749018419721a7c7e1af1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-15 15:42:25 +0100
Commit message:
Commit: 5dc115580f399f7a555749018419721a7c7e1af1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-15 15:42:25 +0100
Commit message:
bugfix, clones with duplicated CDR3 excldued from graphing, now added
Package: ClustIRR
Commit: 4d3806654453b3accfbe110472ce905aecc30729
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-15 15:41:43 +0100
Commit message:
Commit: 4d3806654453b3accfbe110472ce905aecc30729
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-15 15:41:43 +0100
Commit message:
vbump
Package: ClustIRR
Commit: c8956bc39d1efe6e111b4eaf245fb112a2b894ec
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-04 21:53:23 +0100
Commit message:
Commit: c8956bc39d1efe6e111b4eaf245fb112a2b894ec
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-04 21:53:23 +0100
Commit message:
Merge branch 'main' of github.com:snaketron/ClustIRR
Package: ClustIRR
Commit: fcbe614ab48a668118232d2a50e4b9461bf8dc3a
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-04 21:52:51 +0100
Commit message:
Commit: fcbe614ab48a668118232d2a50e4b9461bf8dc3a
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-04 21:52:51 +0100
Commit message:
bugfix in global_clust -> double normalization when computing ncweight
Package: ClustIRR
Commit: ccdec582ddf561d36902c6509362f12eb569b294
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-04 21:52:10 +0100
Commit message:
Commit: ccdec582ddf561d36902c6509362f12eb569b294
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-04 21:52:10 +0100
Commit message:
version bump
Package: ClustIRR
Commit: 75eac9fa130d135afe0c9c6436ea56c07db26498
Author: kaozkai <freibeuter69@freenet.de>
Date: 2024-03-04 16:30:04 +0100
Commit message:
Commit: 75eac9fa130d135afe0c9c6436ea56c07db26498
Author: kaozkai <freibeuter69@freenet.de>
Date: 2024-03-04 16:30:04 +0100
Commit message:
- added sentence about ClustIRR not clonotyping / clone_size column to vignette - fixed small typo in README
Package: ClustIRR
Commit: 99f2991a83a7da011bdadae4b2a19e2f9b11b499
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-26 11:47:42 +0100
Commit message:
Commit: 99f2991a83a7da011bdadae4b2a19e2f9b11b499
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-26 11:47:42 +0100
Commit message:
merge
Package: ClustIRR
Commit: d823f57cdc048d5fc0f6b2bc87997adbfa1c8c01
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-26 11:44:52 +0100
Commit message:
Commit: d823f57cdc048d5fc0f6b2bc87997adbfa1c8c01
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-26 11:44:52 +0100
Commit message:
before merge
Package: ClustIRR
Commit: 71fa206b4584d4056c83347290ca0ad90437a29c
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-02-26 11:32:04 +0100
Commit message:
Commit: 71fa206b4584d4056c83347290ca0ad90437a29c
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-02-26 11:32:04 +0100
Commit message:
naming bugfix 0.85 -> 0.8
Package: ClustIRR
Commit: c9db5f096402f95a2494b2bdc4439d7fb8636e54
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-01 11:23:00 +0100
Commit message:
Commit: c9db5f096402f95a2494b2bdc4439d7fb8636e54
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-01 11:23:00 +0100
Commit message:
change: input are clones, not clonotyping within ClustIRR, this is the job of the user and here are plenty of algorithms for this (e.g. consider the clonotyping caveats of BCRs -> we should not compete here)
Package: ClustIRR
Commit: 3b05a075a1be0aa4b220d82c3a6107307d0b5fef
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-26 14:29:09 +0100
Commit message:
Commit: 3b05a075a1be0aa4b220d82c3a6107307d0b5fef
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-26 14:29:09 +0100
Commit message:
minor bugfixes
Package: ClustIRR
Commit: dd36c3b624de9534eee9101f96ff6d7e5051e247
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-26 14:17:58 +0100
Commit message:
Commit: dd36c3b624de9534eee9101f96ff6d7e5051e247
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-26 14:17:58 +0100
Commit message:
init
Package: ClustIRR
Commit: e030823b5413cef29234d5aeb9b6e23201912025
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-26 13:54:31 +0100
Commit message:
Commit: e030823b5413cef29234d5aeb9b6e23201912025
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-26 13:54:31 +0100
Commit message:
version parameter removed
Package: ClustIRR
Commit: 1d31dd1b761f4efce5510ffba19e7556fe35d838
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-21 18:24:15 +0100
Commit message:
Commit: 1d31dd1b761f4efce5510ffba19e7556fe35d838
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-21 18:24:15 +0100
Commit message:
version bump
Package: ClustIRR
Commit: 6542d463cc096c19892934f11ebcb408a7e40c59
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-21 18:23:52 +0100
Commit message:
Commit: 6542d463cc096c19892934f11ebcb408a7e40c59
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-21 18:23:52 +0100
Commit message:
minor doc fixes
Package: ClustIRR
Commit: ef39c060dcf389823d218e7ac8b457e984fec25f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-18 16:04:42 +0100
Commit message:
Commit: ef39c060dcf389823d218e7ac8b457e984fec25f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-18 16:04:42 +0100
Commit message:
0.85 -> 0.80
Package: ClustIRR
Commit: 9460abc84503044d62fa9bb5b5b2c2a35c392a56
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-17 22:38:58 +0100
Commit message:
Commit: 9460abc84503044d62fa9bb5b5b2c2a35c392a56
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-17 22:38:58 +0100
Commit message:
0.9->0.85 simplification thr.
Package: ClustIRR
Commit: 355f199573414d4521b050034e361a3438aa75a2
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-17 17:46:32 +0100
Commit message:
Commit: 355f199573414d4521b050034e361a3438aa75a2
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-17 17:46:32 +0100
Commit message:
bugfix
Package: ClustIRR
Commit: b35d2c303ab6047b1a6d6203bb5f5d37778ce593
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-17 17:34:41 +0100
Commit message:
Commit: b35d2c303ab6047b1a6d6203bb5f5d37778ce593
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-17 17:34:41 +0100
Commit message:
distance normalized by max len
Package: ClustIRR
Commit: a995e553e0c3f843dff8e6b93d615997aa947567
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:46:12 +0100
Commit message:
Commit: a995e553e0c3f843dff8e6b93d615997aa947567
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:46:12 +0100
Commit message:
version bump
Package: ClustIRR
Commit: a4409a5065cce89b095465d791641f581cc73923
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:45:22 +0100
Commit message:
Commit: a4409a5065cce89b095465d791641f581cc73923
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:45:22 +0100
Commit message:
Last bugfix
Package: ClustIRR
Commit: 618a465357270e0f5f8873e894cf1b05983fc1e0
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:24:12 +0100
Commit message:
Commit: 618a465357270e0f5f8873e894cf1b05983fc1e0
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:24:12 +0100
Commit message:
first round of bugfixes
Package: ClustIRR
Commit: 93d47c6ebfa69a386bde86935661a3f6c0cf6d63
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:10:47 +0100
Commit message:
Commit: 93d47c6ebfa69a386bde86935661a3f6c0cf6d63
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:10:47 +0100
Commit message:
moved function
Package: ClustIRR
Commit: 9a2e722b5f5a25dec55f5711d7e37d4afd8b4ccc
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:07:53 +0100
Commit message:
Commit: 9a2e722b5f5a25dec55f5711d7e37d4afd8b4ccc
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:07:53 +0100
Commit message:
same changes about core region added in the intergraph computation
Package: ClustIRR
Commit: 86984b3d6c463d288f6ec8cebb18186b6da61cad
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 14:17:04 +0100
Commit message:
Commit: 86984b3d6c463d288f6ec8cebb18186b6da61cad
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 14:17:04 +0100
Commit message:
more clear description of global_clustering
Package: ClustIRR
Commit: c0b9df1a2ef0bd977ee843079d867e6a2a7b12bf
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 14:12:31 +0100
Commit message:
Commit: c0b9df1a2ef0bd977ee843079d867e6a2a7b12bf
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 14:12:31 +0100
Commit message:
4th column added to get global -> cweight -> core weight
Package: ClustIRR
Commit: 4e15fd5b4bc65c7a1b47b4e69cf9c4abd219fcde
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 13:54:17 +0100
Commit message:
Commit: 4e15fd5b4bc65c7a1b47b4e69cf9c4abd219fcde
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 13:54:17 +0100
Commit message:
adding global clustering of the core
Package: ClustIRR
Commit: 52014f5aa63e3f1fff21ae15fb040746c235dd46
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-15 17:19:47 +0100
Commit message:
Commit: 52014f5aa63e3f1fff21ae15fb040746c235dd46
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-15 17:19:47 +0100
Commit message:
80->90% similarity global threshold
Package: ClustIRR
Commit: 352d8dc71bb9e48c70499e9b4bd90f326b7c97a8
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-15 14:03:19 +0100
Commit message:
Commit: 352d8dc71bb9e48c70499e9b4bd90f326b7c97a8
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-15 14:03:19 +0100
Commit message:
fixes of minor issues, documentation and namespaces
Package: ClustIRR
Commit: 7c443a66091f82d366987b543bc94433e6061ae7
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-15 11:38:29 +0100
Commit message:
Commit: 7c443a66091f82d366987b543bc94433e6061ae7
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-15 11:38:29 +0100
Commit message:
vignette updated
Package: ClustIRR
Commit: 710c72829bb27b9236bc8e30f2de6d29b406ddfc
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-15 10:33:42 +0100
Commit message:
Commit: 710c72829bb27b9236bc8e30f2de6d29b406ddfc
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-15 10:33:42 +0100
Commit message:
problem with global graph removed
Package: ClustIRR
Commit: da9bd21fa71f74e2442774b5b3be3467b18667aa
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-13 12:08:51 +0100
Commit message:
Commit: da9bd21fa71f74e2442774b5b3be3467b18667aa
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-13 12:08:51 +0100
Commit message:
graph new attributes
Package: ClustIRR
Commit: f31da369df806aee1aeb6ebf870e7a4d7c70e4db
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-10 11:54:13 +0100
Commit message:
Commit: f31da369df806aee1aeb6ebf870e7a4d7c70e4db
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-10 11:54:13 +0100
Commit message:
minor adjustments of weight scaling, making global and local comparable
Package: ClustIRR
Commit: e070410909284197ec2f38cfa62444d5687d23d7
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-10 11:44:18 +0100
Commit message:
Commit: e070410909284197ec2f38cfa62444d5687d23d7
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-10 11:44:18 +0100
Commit message:
more bugfixes and optimizations
Package: ClustIRR
Commit: 1c2fc8bd6f5ba0ee689c0460978c18071f61f69d
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-10 10:37:51 +0100
Commit message:
Commit: 1c2fc8bd6f5ba0ee689c0460978c18071f61f69d
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-10 10:37:51 +0100
Commit message:
minor plotting bugfixes
Package: ClustIRR
Commit: 2d79eec284680b0cfce71f21ce94cb1828a0e94b
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-10 00:14:23 +0100
Commit message:
Commit: 2d79eec284680b0cfce71f21ce94cb1828a0e94b
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-10 00:14:23 +0100
Commit message:
bugfix and graph joining fixed
Package: ClustIRR
Commit: 30e1d908351420192336eb83c6ba860412ecbe78
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-09 20:53:13 +0100
Commit message:
Commit: 30e1d908351420192336eb83c6ba860412ecbe78
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-09 20:53:13 +0100
Commit message:
joining graph fixing
Package: ClustIRR
Commit: 46171b8c9c5432676796397a3d87acd289adda4f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-09 15:10:11 +0100
Commit message:
Commit: 46171b8c9c5432676796397a3d87acd289adda4f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-09 15:10:11 +0100
Commit message:
weight -> -b62
Package: ClustIRR
Commit: e5f430564fea88e8c8ad6f834b0f1f3f92fd7944
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-09 12:19:30 +0100
Commit message:
Commit: e5f430564fea88e8c8ad6f834b0f1f3f92fd7944
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-09 12:19:30 +0100
Commit message:
minor mistake redone check
Package: ClustIRR
Commit: 66fbbf61d0f8c4c674520310cee1a76fefe39ff5
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-09 12:15:23 +0100
Commit message:
Commit: 66fbbf61d0f8c4c674520310cee1a76fefe39ff5
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-09 12:15:23 +0100
Commit message:
updated global_pairs input and a new (hopefully smarter) global clustering strategy
Package: ClustIRR
Commit: 375ac7f747c31a8ff194d5019db8da051b1bea0a
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-22 12:35:08 +0100
Commit message:
Commit: 375ac7f747c31a8ff194d5019db8da051b1bea0a
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-22 12:35:08 +0100
Commit message:
speedup, cores reconsidered
Package: ClustIRR
Commit: 8b5ab8ee140881042310799e583d54429a5ab684
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-21 15:34:43 +0100
Commit message:
Commit: 8b5ab8ee140881042310799e583d54429a5ab684
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-21 15:34:43 +0100
Commit message:
speedup
Package: ClustIRR
Commit: 5587fb284c7529c3765ddf8703e19c64a5ca4b87
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-21 12:32:10 +0100
Commit message:
Commit: 5587fb284c7529c3765ddf8703e19c64a5ca4b87
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-21 12:32:10 +0100
Commit message:
bugfix
Package: ClustIRR
Commit: 13a1aed38375ec174c8465a051771906aedb0238
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-21 12:20:03 +0100
Commit message:
Commit: 13a1aed38375ec174c8465a051771906aedb0238
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-21 12:20:03 +0100
Commit message:
get_graph and get_joint_graph fixes and doc update
Package: ClustIRR
Commit: b116317bc041cae7361f891ebcbc3e7317a483b8
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-21 12:19:29 +0100
Commit message:
Commit: b116317bc041cae7361f891ebcbc3e7317a483b8
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-21 12:19:29 +0100
Commit message:
version bump
Package: ClustIRR
Commit: 170f18e38ac0ba5c49031d2edd814930de81ad69
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-19 10:41:20 +0100
Commit message:
Commit: 170f18e38ac0ba5c49031d2edd814930de81ad69
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-19 10:41:20 +0100
Commit message:
get joint graph message updates
Package: ClustIRR
Commit: 01e4e60952c3d129567f0eafb73ffaa4b8f1c46b
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-17 22:53:25 +0100
Commit message:
Commit: 01e4e60952c3d129567f0eafb73ffaa4b8f1c46b
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-17 22:53:25 +0100
Commit message:
update last chapter
Package: ClustIRR
Commit: 607bf2d91325f14a85e9359a7448fc6249cd9d14
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-17 22:53:16 +0100
Commit message:
Commit: 607bf2d91325f14a85e9359a7448fc6249cd9d14
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-17 22:53:16 +0100
Commit message:
small bugfix, if df_e has no values
Package: ClustIRR
Commit: f1ea24417a28dd4b827ed6856b698af14aff6560
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-17 22:28:44 +0100
Commit message:
Commit: f1ea24417a28dd4b827ed6856b698af14aff6560
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-17 22:28:44 +0100
Commit message:
bump
Package: ClustIRR
Commit: 1b897b517d4ce94aacf9cdd0d1bb1e6efba8d737
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-17 22:28:29 +0100
Commit message:
Commit: 1b897b517d4ce94aacf9cdd0d1bb1e6efba8d737
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-17 22:28:29 +0100
Commit message:
update vignette intro
Package: ClustIRR
Commit: 07338c0cdd66a48c79388ed8114929479e497763
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-16 09:05:51 +0100
Commit message:
Commit: 07338c0cdd66a48c79388ed8114929479e497763
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-16 09:05:51 +0100
Commit message:
bugfix, tests next
Package: ClustIRR
Commit: 285460084d439b300025b17521393c9e5da0083f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-16 09:00:37 +0100
Commit message:
Commit: 285460084d439b300025b17521393c9e5da0083f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-16 09:00:37 +0100
Commit message:
more bugfix
Package: ClustIRR
Commit: 467a6fa37840107859c7a130139813cf2aed047c
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-15 15:56:28 +0100
Commit message:
Commit: 467a6fa37840107859c7a130139813cf2aed047c
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-15 15:56:28 +0100
Commit message:
all bugfixes done except for cols, next
Package: ClustIRR
Commit: 860a00a2497d3f7930cd4a0bf1850a0c35301d1e
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-14 21:48:51 +0100
Commit message:
Commit: 860a00a2497d3f7930cd4a0bf1850a0c35301d1e
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-14 21:48:51 +0100
Commit message:
prelim version, more bugfix come tomorrow in graph-building part
Package: ClustIRR
Commit: 0f08d1a8cb269817c1a1940cfd9744f39ee9a98b
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-14 21:18:17 +0100
Commit message:
Commit: 0f08d1a8cb269817c1a1940cfd9744f39ee9a98b
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-14 21:18:17 +0100
Commit message:
bugfix chain
Package: ClustIRR
Commit: a102fed518b97e6b3f51f05d863519339fabe7a3
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-14 20:10:28 +0100
Commit message:
Commit: a102fed518b97e6b3f51f05d863519339fabe7a3
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-14 20:10:28 +0100
Commit message:
version back to ok
Package: ClustIRR
Commit: 7690b59e52d22ad26151130c1193ace0b3b70d49
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-12-14 20:06:45 +0100
Commit message:
Commit: 7690b59e52d22ad26151130c1193ace0b3b70d49
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-12-14 20:06:45 +0100
Commit message:
version bump
Package: ClustIRR
Commit: 460f0315648a11154cb8c2084408ca34b1026f68
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-12-14 20:05:07 +0100
Commit message:
Commit: 460f0315648a11154cb8c2084408ca34b1026f68
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-12-14 20:05:07 +0100
Commit message:
bugfix and massive speedup for graph joining
Package: ClustIRR
Commit: 04d19b8f1d6397b0d7ba802887c5b363f4b577c8
Author: snaketron <snaketron@users.noreply.github.com>
Date: 2023-12-13 17:09:39 +0100
Commit message:
Commit: 04d19b8f1d6397b0d7ba802887c5b363f4b577c8
Author: snaketron <snaketron@users.noreply.github.com>
Date: 2023-12-13 17:09:39 +0100
Commit message:
Update README.md Fixed reame
Package: ClustIRR
Commit: 081908e07f68fd371c9ebe53de56844d9ccaa2de
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-13 17:04:04 +0100
Commit message:
Commit: 081908e07f68fd371c9ebe53de56844d9ccaa2de
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-13 17:04:04 +0100
Commit message:
updated vignette
Package: ClustIRR
Commit: c5d558a4d3cd595dec5d15d26d6eefe709b2db84
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-13 16:54:59 +0100
Commit message:
Commit: c5d558a4d3cd595dec5d15d26d6eefe709b2db84
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-13 16:54:59 +0100
Commit message:
how to join multiple graphs together
Package: ClustIRR
Commit: d1cfe316f36d0c3c6c66344d41f22cc1d14fdb41
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-08 16:04:24 +0100
Commit message:
Commit: d1cfe316f36d0c3c6c66344d41f22cc1d14fdb41
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-08 16:04:24 +0100
Commit message:
joining many clustirr object now possible
Package: OmnipathR
Commit: 582735943c63e64aeaf52a0cb7ad0733ff4bcbd7
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 13:31:18 +0100
Commit message:
Commit: 582735943c63e64aeaf52a0cb7ad0733ff4bcbd7
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 13:31:18 +0100
Commit message:
Bump version: 3.11.9 → 3.11.10
Package: OmnipathR
Commit: e9ef4a8c3a24b85042c21b6f5f56b5d6ae2c16bd
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 13:31:11 +0100
Commit message:
Commit: e9ef4a8c3a24b85042c21b6f5f56b5d6ae2c16bd
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 13:31:11 +0100
Commit message:
forgot to rebuild the docs after 442cb77
Package: alevinQC
Commit: 9025674817b081d22a6df79317b97eac59bd0617
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 10:19:56 +0100
Commit message:
Commit: 9025674817b081d22a6df79317b97eac59bd0617
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 10:19:56 +0100
Commit message:
Catch messages in unit tests
Package: alevinQC
Commit: 7fb51cc532c08bdeae6251f72760ef33969801cc
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 10:19:43 +0100
Commit message:
Commit: 7fb51cc532c08bdeae6251f72760ef33969801cc
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 10:19:43 +0100
Commit message:
Expand chunk options in template
Package: alevinQC
Commit: be2068eda827093579d3ebe884544aa8fac9fa91
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 10:19:21 +0100
Commit message:
Commit: be2068eda827093579d3ebe884544aa8fac9fa91
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 10:19:21 +0100
Commit message:
Version bump
Package: iCOBRA
Commit: 6a7e2a95ae9c2350cc01409372f5fca74d5e498c
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:57:47 +0100
Commit message:
Commit: 6a7e2a95ae9c2350cc01409372f5fca74d5e498c
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:57:47 +0100
Commit message:
Merge pull request #7 from csoneson/fix-gha Replace deprecated tidyverse functions
Package: iCOBRA
Commit: f1a2cc118bfa96d62d3a04a7f3e2356a02312c7d
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:41:28 +0100
Commit message:
Commit: f1a2cc118bfa96d62d3a04a7f3e2356a02312c7d
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:41:28 +0100
Commit message:
Update results (rounding differences)
Package: iCOBRA
Commit: a095ab12baa26b7ea7f06b1e511deaf94b4ca1ed
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:40:16 +0100
Commit message:
Commit: a095ab12baa26b7ea7f06b1e511deaf94b4ca1ed
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:40:16 +0100
Commit message:
Catch expected warnings in tests
Package: iCOBRA
Commit: 748753413afebb9f7a16f0ddc6112caaad56e6a7
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:39:57 +0100
Commit message:
Commit: 748753413afebb9f7a16f0ddc6112caaad56e6a7
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:39:57 +0100
Commit message:
Replace deprecated aes_string, use linewidth instead of size
Package: iCOBRA
Commit: d67fa73fa2e3e3d07b34ee217511bbb2ebb159c2
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:29:34 +0100
Commit message:
Commit: d67fa73fa2e3e3d07b34ee217511bbb2ebb159c2
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:29:34 +0100
Commit message:
Add warning expectation to test_app
Package: iCOBRA
Commit: c081586ae0add1ecabe60b0ea857d415301d72ac
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:27:49 +0100
Commit message:
Commit: c081586ae0add1ecabe60b0ea857d415301d72ac
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:27:49 +0100
Commit message:
Add tests for get_keeplevels
Package: iCOBRA
Commit: 0bb29754142654906f99c1361a8d662c893ecad5
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:09:23 +0100
Commit message:
Commit: 0bb29754142654906f99c1361a8d662c893ecad5
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:09:23 +0100
Commit message:
Replace deprecated dplyr functions
Package: iCOBRA
Commit: 58784a9f5c1df190be10033ea50d330e354bc479
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:06:48 +0100
Commit message:
Commit: 58784a9f5c1df190be10033ea50d330e354bc479
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:06:48 +0100
Commit message:
Bump version
Package: EpiTxDb
Commit: 821fd21d97be545a3570d216c33350a2e2a41c80
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-24 01:48:14 +0100
Commit message:
Commit: 821fd21d97be545a3570d216c33350a2e2a41c80
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-24 01:48:14 +0100
Commit message:
Fixed making EpiTxDb from RMBase
Package: EpiTxDb
Commit: 8129305e62d75a0902532909f46b949d57e88634
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-24 01:47:13 +0100
Commit message:
Commit: 8129305e62d75a0902532909f46b949d57e88634
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-24 01:47:13 +0100
Commit message:
Update DESCRIPTION
Package: EpiTxDb
Commit: 34638d4904babb40994a7786bb93d162a10f0d5c
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-24 01:23:07 +0100
Commit message:
Commit: 34638d4904babb40994a7786bb93d162a10f0d5c
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-24 01:23:07 +0100
Commit message:
Fixed RMBase loading and update RMBase data dictionary
Package: EpiTxDb
Commit: 461e99a357e852e050d3c63a6fcfb31ff116332f
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:22:16 +0100
Commit message:
Commit: 461e99a357e852e050d3c63a6fcfb31ff116332f
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:22:16 +0100
Commit message:
reversed order of importing txdbmaker and GenomicFeatures
Package: EpiTxDb
Commit: 1419ef691740a13ca7593d3fb80310bfd34141f9
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-18 22:22:09 +0100
Commit message:
Commit: 1419ef691740a13ca7593d3fb80310bfd34141f9
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-18 22:22:09 +0100
Commit message:
Update README.md
Package: tRNA
Commit: 2cc567ee5095164308b5e1a97a2a4ca4c9eabdf6
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-24 01:46:09 +0100
Commit message:
Commit: 2cc567ee5095164308b5e1a97a2a4ca4c9eabdf6
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-24 01:46:09 +0100
Commit message:
Fixed warning from upstream ggplot2 chnages
Package: tRNA
Commit: 2e08d8bc66e9186c6e1c1aacea5f577d63b1db6c
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:12:29 +0100
Commit message:
Commit: 2e08d8bc66e9186c6e1c1aacea5f577d63b1db6c
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:12:29 +0100
Commit message:
Update README.md
Package: alabaster.ranges
Commit: 773a02a93c50bfe2554ce094e6b1fe9bee497fbc
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-03-23 17:03:15 -0700
Commit message:
Commit: 773a02a93c50bfe2554ce094e6b1fe9bee497fbc
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-03-23 17:03:15 -0700
Commit message:
Added badges to the README.
Package: alabaster.ranges
Commit: 6e6acfd5108b62d06e5937b4a8cdbca4598c19e3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-01-26 22:54:50 -0800
Commit message:
Commit: 6e6acfd5108b62d06e5937b4a8cdbca4598c19e3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-01-26 22:54:50 -0800
Commit message:
Updated the GitHub action to use BioC image and packages.
Package: IgGeneUsage
Commit: 231b901411698e03b8d4e960f000078c734d3518
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-24 00:12:01 +0100
Commit message:
Commit: 231b901411698e03b8d4e960f000078c734d3518
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-24 00:12:01 +0100
Commit message:
minor checks and version bump
Package: Modstrings
Commit: 603cb4674c0b6ded4c35de2b63d9ee710511112f
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 22:57:57 +0100
Commit message:
Commit: 603cb4674c0b6ded4c35de2b63d9ee710511112f
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 22:57:57 +0100
Commit message:
Update GitHub Action config
Package: Modstrings
Commit: d27b32f6cbbbb49bf043443be91522c73542b646
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 22:56:55 +0100
Commit message:
Commit: d27b32f6cbbbb49bf043443be91522c73542b646
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 22:56:55 +0100
Commit message:
Merge branch 'master' of git.bioconductor.org:packages/Modstrings
Package: Modstrings
Commit: 84fb6b7541e724c6a8cfdd71a3e75699f6242eda
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 23:06:31 +0200
Commit message:
Commit: 84fb6b7541e724c6a8cfdd71a3e75699f6242eda
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 23:06:31 +0200
Commit message:
Update README.md
Package: Modstrings
Commit: 5a73d389a6d0c7bd2aa27b191aaa732cddc4d4f1
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:54:10 +0200
Commit message:
Commit: 5a73d389a6d0c7bd2aa27b191aaa732cddc4d4f1
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:54:10 +0200
Commit message:
Update R-CMD-check.yaml
Package: Modstrings
Commit: 01bc40ab7a09d36d2c32a6750a014f78137575a4
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:25:06 +0200
Commit message:
Commit: 01bc40ab7a09d36d2c32a6750a014f78137575a4
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:25:06 +0200
Commit message:
Update R-CMD-check.yaml
Package: Modstrings
Commit: 18bd46ae67f76bbdbb949f618f40ec780bf5819e
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:22:43 +0200
Commit message:
Commit: 18bd46ae67f76bbdbb949f618f40ec780bf5819e
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:22:43 +0200
Commit message:
update to GitHub actions
Package: Modstrings
Commit: b32a9803d165264980217ffa7a0bd3499a8d6438
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:20:36 +0200
Commit message:
Commit: b32a9803d165264980217ffa7a0bd3499a8d6438
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:20:36 +0200
Commit message:
Update R-CMD-check.yaml
Package: Modstrings
Commit: 503abd0a494bdd8a661b9dd1aec851c24de15fcd
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:16:21 +0200
Commit message:
Commit: 503abd0a494bdd8a661b9dd1aec851c24de15fcd
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:16:21 +0200
Commit message:
Update R-CMD-check.yaml
Package: tRNA
Commit: 12e627b193af2df3cf1211f95bdea16551924e54
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:07:14 +0100
Commit message:
Commit: 12e627b193af2df3cf1211f95bdea16551924e54
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:07:14 +0100
Commit message:
Update GitHub action config
Package: tRNA
Commit: c1705c640019dfe8ff039342216b62d3409c1502
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:06:24 +0100
Commit message:
Commit: c1705c640019dfe8ff039342216b62d3409c1502
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:06:24 +0100
Commit message:
Merge branch 'master' of git.bioconductor.org:packages/tRNA
Package: tRNA
Commit: f50bc835e38ea71246b80b605ba91dcf5df24ab0
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-01-17 21:01:28 +0100
Commit message:
Commit: f50bc835e38ea71246b80b605ba91dcf5df24ab0
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-01-17 21:01:28 +0100
Commit message:
Update NEWS
Package: tRNAdbImport
Commit: d86b30d8ab59468a8e4c92bede2e9acd684c6ee2
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:09:56 +0100
Commit message:
Commit: d86b30d8ab59468a8e4c92bede2e9acd684c6ee2
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:09:56 +0100
Commit message:
Update GitHub action config
Package: tRNAscanImport
Commit: 4ac8f8618c22219ad6407dec2b0bf677b20a84f4
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:11:28 +0100
Commit message:
Commit: 4ac8f8618c22219ad6407dec2b0bf677b20a84f4
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:11:28 +0100
Commit message:
Updated GitHub action config
Package: IgGeneUsage
Commit: 8f96632dd7d95f9caaebb28b89b903cbdff1530d
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-23 22:44:09 +0100
Commit message:
Commit: 8f96632dd7d95f9caaebb28b89b903cbdff1530d
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-23 22:44:09 +0100
Commit message:
minor bugfixes
Package: IgGeneUsage
Commit: 1bbb804bf2593f66de608cb5d790abdbefcf545a
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 23:00:25 +0100
Commit message:
Commit: 1bbb804bf2593f66de608cb5d790abdbefcf545a
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 23:00:25 +0100
Commit message:
bugfix in theta
Package: IgGeneUsage
Commit: 6247dc07574a9511e764dd88558fd36a159eb5d1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 17:39:56 +0100
Commit message:
Commit: 6247dc07574a9511e764dd88558fd36a159eb5d1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 17:39:56 +0100
Commit message:
prior alpha ~ normal(-3,3)
Package: IgGeneUsage
Commit: fa486a46da0ee62498fa5144e2e416c7088a5d19
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 15:16:29 +0100
Commit message:
Commit: fa486a46da0ee62498fa5144e2e416c7088a5d19
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 15:16:29 +0100
Commit message:
update rng
Package: IgGeneUsage
Commit: da979c8ae14ac2dc378c4dc424c269f80818a459
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 15:14:15 +0100
Commit message:
Commit: da979c8ae14ac2dc378c4dc424c269f80818a459
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 15:14:15 +0100
Commit message:
improved rng
Package: IgGeneUsage
Commit: 579590413bb7da13575590af5544668e90c3f7e1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 15:14:04 +0100
Commit message:
Commit: 579590413bb7da13575590af5544668e90c3f7e1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 15:14:04 +0100
Commit message:
bump
Package: IgGeneUsage
Commit: a563d95d074ee474e78ee37e252f40752670eec1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 22:20:53 +0100
Commit message:
Commit: a563d95d074ee474e78ee37e252f40752670eec1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 22:20:53 +0100
Commit message:
now with bugfixes
Package: IgGeneUsage
Commit: d07e56909319edf38360884e4b0f46c03127cb9c
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:08:13 +0100
Commit message:
Commit: d07e56909319edf38360884e4b0f46c03127cb9c
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:08:13 +0100
Commit message:
makevars deleted, do we need?
Package: IgGeneUsage
Commit: 0cb285e2e52b2977a6a6953579f6063a688b779f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:07:46 +0100
Commit message:
Commit: 0cb285e2e52b2977a6a6953579f6063a688b779f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:07:46 +0100
Commit message:
vignette and namespace update
Package: IgGeneUsage
Commit: b0fd0998cc70840d7e4e543f82ded06932e21fc3
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:07:28 +0100
Commit message:
Commit: b0fd0998cc70840d7e4e543f82ded06932e21fc3
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:07:28 +0100
Commit message:
update replicates model
Package: IgGeneUsage
Commit: 5152e25a9a1b27cb39f89343ec170e8b6c2be067
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:07:01 +0100
Commit message:
Commit: 5152e25a9a1b27cb39f89343ec170e8b6c2be067
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:07:01 +0100
Commit message:
update replicates model
Package: IgGeneUsage
Commit: ce25381b3e1d7fb2bc115765ab06432df70aafa8
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:06:47 +0100
Commit message:
Commit: ce25381b3e1d7fb2bc115765ab06432df70aafa8
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:06:47 +0100
Commit message:
update replicates model
Package: IgGeneUsage
Commit: afc593796dbd3a2b5cb51b0bb2dfd457cb74b8f9
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:05:59 +0100
Commit message:
Commit: afc593796dbd3a2b5cb51b0bb2dfd457cb74b8f9
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:05:59 +0100
Commit message:
update replicate model
Package: IgGeneUsage
Commit: ee0167f87f86ea37e7873c3ca07fbea525fc5813
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-10 22:25:35 +0100
Commit message:
Commit: ee0167f87f86ea37e7873c3ca07fbea525fc5813
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-10 22:25:35 +0100
Commit message:
model for replicate analysis -> stub
Package: IgGeneUsage
Commit: 2696ac30581353c3a7cf3203c5da392e262b486d
Author: snaketron <snaketron@users.noreply.github.com>
Date: 2024-01-22 09:45:57 +0100
Commit message:
Commit: 2696ac30581353c3a7cf3203c5da392e262b486d
Author: snaketron <snaketron@users.noreply.github.com>
Date: 2024-01-22 09:45:57 +0100
Commit message:
Merge pull request #13 from andrjohns/array-syntax Update deprecated Stan syntax
Package: IgGeneUsage
Commit: cf6b83ba44ad3f2a2a4ccc0b65a1ee5a6616f7bf
Author: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: 2024-01-19 19:07:52 +0200
Commit message:
Commit: cf6b83ba44ad3f2a2a4ccc0b65a1ee5a6616f7bf
Author: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: 2024-01-19 19:07:52 +0200
Commit message:
Update deprecated array syntax
Package: IgGeneUsage
Commit: 288af7a1c44e90701ed467b5cd9187787ba8f0ea
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-22 18:11:41 +0100
Commit message:
Commit: 288af7a1c44e90701ed467b5cd9187787ba8f0ea
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-22 18:11:41 +0100
Commit message:
model simplified
Package: IgGeneUsage
Commit: 812313a18813d9233421f8063c0e82038dd8212c
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-19 20:05:06 +0100
Commit message:
Commit: 812313a18813d9233421f8063c0e82038dd8212c
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-19 20:05:06 +0100
Commit message:
new phi, kappa, ppc, var recovery
Package: IgGeneUsage
Commit: 55b3c037c3193d51aabc20f79869fc1fb443c7d1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-13 16:22:05 +0100
Commit message:
Commit: 55b3c037c3193d51aabc20f79869fc1fb443c7d1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-13 16:22:05 +0100
Commit message:
minor change
Package: IgGeneUsage
Commit: fcb8af905dab7f052241ff7912ce8520d6bc8fcb
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-11-04 14:05:04 +0100
Commit message:
Commit: fcb8af905dab7f052241ff7912ce8520d6bc8fcb
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-11-04 14:05:04 +0100
Commit message:
merge Description with bumped version
Package: IgGeneUsage
Commit: 30e200cac2c09502d41f3527d7f267dc13c040fd
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-04 00:48:11 +0100
Commit message:
Commit: 30e200cac2c09502d41f3527d7f267dc13c040fd
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-04 00:48:11 +0100
Commit message:
pmax fix
Package: IgGeneUsage
Commit: 77cd6a11d3923787aa164b22e703898d1769313d
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-03 15:04:10 +0100
Commit message:
Commit: 77cd6a11d3923787aa164b22e703898d1769313d
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-03 15:04:10 +0100
Commit message:
Minor change in GU model
Package: IgGeneUsage
Commit: 722d417f4bc3f6774292d5062baca079aafad946
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-03 14:37:44 +0100
Commit message:
Commit: 722d417f4bc3f6774292d5062baca079aafad946
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-03 14:37:44 +0100
Commit message:
fix GU model
Package: IgGeneUsage
Commit: d8219065f9b21721a2c116c4fbff7f4f77efa2e2
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-11-03 11:36:27 +0100
Commit message:
Commit: d8219065f9b21721a2c116c4fbff7f4f77efa2e2
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-11-03 11:36:27 +0100
Commit message:
version bump, bugfix in GU analysis
Package: IgGeneUsage
Commit: af66f9dd326edfe41756acbfd7acab17b3164114
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-11-03 09:44:18 +0100
Commit message:
Commit: af66f9dd326edfe41756acbfd7acab17b3164114
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-11-03 09:44:18 +0100
Commit message:
More prior changes
Package: IgGeneUsage
Commit: bf4bc80109515cddf9282e39b2de7eebf0c88a88
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-11-02 12:27:56 +0100
Commit message:
Commit: bf4bc80109515cddf9282e39b2de7eebf0c88a88
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-11-02 12:27:56 +0100
Commit message:
minor prior changes in model
Package: IgGeneUsage
Commit: e36a85c936a1704ca7e08f48c558b959bbb80838
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-11-01 19:43:12 +0100
Commit message:
Commit: e36a85c936a1704ca7e08f48c558b959bbb80838
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-11-01 19:43:12 +0100
Commit message:
model upgrade
Package: IgGeneUsage
Commit: 456b3b5bca132c26bd11593d861c3d4afae1d94f
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-10-30 20:06:51 +0100
Commit message:
Commit: 456b3b5bca132c26bd11593d861c3d4afae1d94f
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-10-30 20:06:51 +0100
Commit message:
version bump
Package: IgGeneUsage
Commit: dd6926a5fd481f1b3ab12926e1e5f627d00992ae
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-10-30 20:06:35 +0100
Commit message:
Commit: dd6926a5fd481f1b3ab12926e1e5f627d00992ae
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-10-30 20:06:35 +0100
Commit message:
minor updates, 1st push after release
Package: IgGeneUsage
Commit: 570c4f1ef72a693c218aab61025cbd8cf523ec59
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-10-30 19:12:09 +0100
Commit message:
Commit: 570c4f1ef72a693c218aab61025cbd8cf523ec59
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-10-30 19:12:09 +0100
Commit message:
first push version 1.16
Package: Biostrings
Commit: d13154e5013363a568d983ff26e483e6c77fb007
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-23 12:57:19 -0700
Commit message:
Commit: d13154e5013363a568d983ff26e483e6c77fb007
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-23 12:57:19 -0700
Commit message:
more cleaning/reorganization of the TODO file
Package: Biostrings
Commit: 41955d99621065a36f910f848b00621ca7bfe89c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-23 12:22:06 -0700
Commit message:
Commit: 41955d99621065a36f910f848b00621ca7bfe89c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-23 12:22:06 -0700
Commit message:
More cleaning/reorganization of the TODO file Some items moved to pwalign's TODO.
Package: pwalign
Commit: 2b7411d477361523de4c3336e0973c7efb81225e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-23 12:15:10 -0700
Commit message:
Commit: 2b7411d477361523de4c3336e0973c7efb81225e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-23 12:15:10 -0700
Commit message:
add TODO file (all items taken from Biostrings's TODO)
Package: tximport
Commit: 7b1fbe4bffc98c21e891a37c5a0e1751a85045ba
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2024-03-23 13:58:58 -0400
Commit message:
Commit: 7b1fbe4bffc98c21e891a37c5a0e1751a85045ba
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2024-03-23 13:58:58 -0400
Commit message:
experimental support for oarfish
Package: OmnipathR
Commit: bbbfae5a6c7341f4c490772555de3e5ac6bb18a5
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:34:37 +0100
Commit message:
Commit: bbbfae5a6c7341f4c490772555de3e5ac6bb18a5
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:34:37 +0100
Commit message:
Bump version: 3.11.8 → 3.11.9
Package: OmnipathR
Commit: 442cb7767bbf54b68efddad4873c63f44e6160e2
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:34:29 +0100
Commit message:
Commit: 442cb7767bbf54b68efddad4873c63f44e6160e2
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:34:29 +0100
Commit message:
`_PACKAGE` sentinel for roxygen: finally getting it right
Package: OmnipathR
Commit: 812514458909a784315e3d01dd85c86429463368
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 14:09:17 +0100
Commit message:
Commit: 812514458909a784315e3d01dd85c86429463368
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 14:09:17 +0100
Commit message:
updated years in code file headers
Package: edgeR
Commit: 8cb63a65c2e65f7e25bfa92b72d26c41a6c3beb7
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2024-03-23 22:21:34 +1100
Commit message:
Commit: 8cb63a65c2e65f7e25bfa92b72d26c41a6c3beb7
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2024-03-23 22:21:34 +1100
Commit message:
edgeR 4.1.19 - voomLmFit will now extract exprs from an eSet object but with a warning message. - voomLmFit.Rd help now refers to SummarizedExperiment rather than ExpressionSet.
Package: ggtreeSpace
Commit: 020060b9e96169a3fdb27e828a709883058eb22f
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-03-23 16:00:42 +0800
Commit message:
Commit: 020060b9e96169a3fdb27e828a709883058eb22f
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-03-23 16:00:42 +0800
Commit message:
for bioc
Package: ggtreeSpace
Commit: 0d0a41ce11ad2dcd0cd41b8b72e2a3b6ddb5eb65
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-03-23 15:58:03 +0800
Commit message:
Commit: 0d0a41ce11ad2dcd0cd41b8b72e2a3b6ddb5eb65
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-03-23 15:58:03 +0800
Commit message:
update vignette and licence