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GIT Logs

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

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Package: ExpressionAtlas
Commit: dbb99596d468e785eb006dfc2cc0af00127ee0ec
Author: Pedro Madrigal <8195212+pmb59@users.noreply.github.com>
Date: 2022-05-17 21:31:29 +0100
Commit message:

 enforce R (>= 4.2.0) 
Package: CoreGx
Commit: a72fc91e397bfb9364939c7c4edab99e95f31123
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-17 14:41:40 -0400
Commit message:

 Finished updating NEWS.md
 
Package: CoreGx
Commit: 995885aeb551188bb95ba9d1fd9383b49c383d67
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-17 14:40:31 -0400
Commit message:

 Increment package version for Bioc push; updating NEWS.md
 
Package: CoreGx
Commit: 87c0cf85e9587b0c46a3fdef9cab9a116b2ec213
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2022-05-17 14:23:20 -0400
Commit message:

 Merge pull request #144 from bhklab/fix_reformat_data

y to frac needs to be run before truncation 
Package: CoreGx
Commit: 89ae3527fc5aba1a3790670d838298390a4ae4af
Author: Petr Smirnov <psmirnov2000@gmail.com>
Date: 2022-05-17 11:07:52 -0400
Commit message:

 y to frac needs to be run before truncation
 
Package: gemma.R
Commit: 4d4ea50d73207499f4a9b75edb3493ad34b382d7
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2022-05-17 10:29:08 -0700
Commit message:

 backwards compatibility for older R versions
 
Package: goSorensen
Commit: c457e64c8d9c5bec4d8af7d26152778e3964c2f7
Author: Pablo Flores <pablojfm1988@gmail.com>
Date: 2022-05-17 12:22:49 -0500
Commit message:

 Change version to 0.99.1
 
Package: scDDboost
Commit: 3e6bcae7a0f754d8af86e742c32f976ffa81d32b
Author: xiuyuma <ma79@wisc.edu>
Date: 2022-05-17 13:23:07 -0400
Commit message:

 bump ver
 
Package: fastseg
Commit: bb3019e562c9bad706111ae26b9010db3cea0ab5
Author: Alexander Blume <alex.gos90@gmail.com>
Date: 2022-05-17 19:14:40 +0200
Commit message:

 Change of Maintainer
 
Package: scDDboost
Commit: cd6e447a1ad30b23b20c5ad2fddf7f4a3e9bf2de
Author: xiuyuma <ma79@wisc.edu>
Date: 2022-05-17 13:22:23 -0400
Commit message:

 add blank space
 
Package: gemma.R
Commit: 18c2b0f865116f036e8d604b661b28e34d34e640
Author: OganM <ogan.mancarci@gmail.com>
Date: 2022-05-17 10:07:20 -0700
Commit message:

 nth time's the charm
 
Package: gemma.R
Commit: e00b202ef1f7e03200cd42ef404c0c57b6a49e8c
Author: OganM <ogan.mancarci@gmail.com>
Date: 2022-05-17 09:58:38 -0700
Commit message:

 fix registration
 
Package: gemma.R
Commit: 4b9683a5acf34af2c954e149e2a4bc0a61315ebf
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2022-05-17 09:47:47 -0700
Commit message:

 version bump for push
 
Package: gemma.R
Commit: 281ed09a34317ae1abe1c03a6bbd8e28a24941ee
Author: OganM <ogan.mancarci@gmail.com>
Date: 2022-05-17 09:28:36 -0700
Commit message:

 merge upstream
 
Package: gemma.R
Commit: f34d8eeee9e117049fedf9dbdd1d85f30d55e45a
Author: OganM <ogan.mancarci@gmail.com>
Date: 2022-05-17 09:25:12 -0700
Commit message:

 version bump
 
Package: nnSVG
Commit: 88baee07989b2cee46b5758d1e62d0d6d21cedb2
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-17 11:06:54 -0400
Commit message:

 GitHub installation instructions on readme
 
Package: zellkonverter
Commit: 45e77827d8371ed7dfc4ced17fa0032f767bea6a
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2022-05-17 16:44:09 +0200
Commit message:

 Merge branch 'RELEASE_3_15'

* RELEASE_3_15:
  Fix bug in long tests
 
Package: zellkonverter
Commit: 5f819f34c3da7da09c00157efe58be242da665d3
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2022-05-17 16:42:00 +0200
Commit message:

 Fix bug in long tests
 
Package: lineagespot
Commit: 33bbec4aad83158501306c2f514c0c97064ebae8
Author: aspaor <aspasiaor@hotmail.com>
Date: 2022-05-17 16:59:35 +0300
Commit message:

 update maintainer
 
Package: lineagespot
Commit: ee6b545dd52c1b639c4b2bb3716a272f10ecbe29
Author: aspaor <aspasiaor@hotmail.com>
Date: 2022-05-17 16:29:42 +0300
Commit message:

 Update DESCRIPTION
 
Package: cfDNAPro
Commit: 0c0fad0d3a9d5345438bf48d50490e667fa6979b
Author: haichao <wanghaichao2014@gmail.com>
Date: 2022-05-17 11:41:51 +0100
Commit message:

 debug README.md

 
Package: tripr
Commit: 06d1020c93a7a1d10e029040d4fd2ae345fb5200
Author: aspaor <aspasiaor@hotmail.com>
Date: 2022-05-17 13:39:45 +0300
Commit message:

 Change maintainer
 
Package: cfDNAPro
Commit: 954af1b1431d4c4ed1d160c4b950cf8bb2432057
Author: haichao <wanghaichao2014@gmail.com>
Date: 2022-05-17 10:58:25 +0100
Commit message:

 bump up z 

 
Package: STRINGdb
Commit: 46ab9d6de86c290ecf6b84492faa866d05a50b91
Author: Damian Szklarczyk <damian.szk@gmail.com>
Date: 2022-05-17 11:56:59 +0200
Commit message:

 unitTest bugfix
 
Package: cfDNAPro
Commit: 8322e5477113d861294633e65191c996157d8909
Author: haichao <wanghaichao2014@gmail.com>
Date: 2022-05-17 10:51:20 +0100
Commit message:

 debug and modified introductions

 
Package: oncoscanR
Commit: 8124b2aba02f009fbffdabd642250ff789b30bcf
Author: Yann Christinat <yann.christinat@hcuge.ch>
Date: 2022-05-17 11:28:26 +0200
Commit message:

 Extended vignette and corrected build warnings/notes

 
Package: reconsi
Commit: b2a094a82112d7ce716bde5a0af2375b8a14b902
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2022-05-17 11:27:19 +0200
Commit message:

 Explicityl load vandeputte data
 
Package: reconsi
Commit: 86eaae45b050c4e794b5279d02104598f9717309
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2022-05-17 11:11:00 +0200
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/reconsi
 
Package: reconsi
Commit: 092b803f0767b9c38a39a6a8582f7583d21f8729
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2022-05-17 11:10:23 +0200
Commit message:

 load data in vignette
 
Package: pengls
Commit: 55abde32c036a17e295f2f8b6c28431de99c06cd
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2022-05-17 11:03:31 +0200
Commit message:

 Solved conflict

Merge branch 'master' of git.bioconductor.org:packages/pengls

# Conflicts:
#	DESCRIPTION
 
Package: pengls
Commit: 69531c98024a0d5e39afecd7a79548527b112fab
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2022-05-17 11:01:13 +0200
Commit message:

 Update decsription file
 
Package: biomaRt
Commit: 3bbbecb7309ed936303692e7a4e1e9792ba119cc
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-05-17 10:10:50 +0200
Commit message:

 Merge pull request #65 from LiNk-NY/master

fix partial argument matching and bfcremove error 
Package: biomaRt
Commit: ae57984ee60fb0f965493a8facb6a6d607442e26
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-05-16 20:19:34 -0400
Commit message:

 bug fix: add bfc to bfcremove call
 
Package: biomaRt
Commit: c436e3b86d296651244ae51111e14f9541512f7e
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-05-16 20:19:07 -0400
Commit message:

 use length.out argument avoid partial matching warning
 
Package: biomaRt
Commit: eb4b89c2b408789fb22739a8181f142950c432d1
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-05-10 08:58:27 +0200
Commit message:

 Allow alternative host to be provided to useEnsembl (#64)
 
Package: nnSVG
Commit: a851058035cffe8535f52488c878d02eb23f4b0f
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-17 01:36:08 -0400
Commit message:

 update NEWS
 
Package: nnSVG
Commit: 96872cf1ea5ae2210ccc8d564efb911ab5595c4d
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-17 01:35:21 -0400
Commit message:

 version
 
Package: nnSVG
Commit: 3ff8e71ebe9849ee10dd4f9b9fb5d96c384013f6
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-17 01:34:57 -0400
Commit message:

 keep rownames for non-SPE inputs
 
Package: nnSVG
Commit: 1c945f52b620eab3ce118a9580957e32a835c2e5
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-17 00:28:12 -0400
Commit message:

 version
 
Package: nnSVG
Commit: 67ff6dd5afba711aebf1aae5b6df5c00660061c8
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-17 00:27:59 -0400
Commit message:

 update readme to mention non-SPE inputs
 
Package: nnSVG
Commit: c95f90066c6610352009e9e1320cb23a648e5939
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-17 00:26:10 -0400
Commit message:

 update vignette to mention non-SPE inputs
 
Package: nnSVG
Commit: 8180f90211f60e438d23086fb5c4360ebdaf403a
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-17 00:25:37 -0400
Commit message:

 wording
 
Package: nnSVG
Commit: 98d12d98ee17ede7c8089ead2d4f2a3057b30d2c
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-17 00:16:04 -0400
Commit message:

 update NEWS
 
Package: nnSVG
Commit: c313686642d2a8614e8eeb9aeadc068cd9616b83
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-17 00:15:22 -0400
Commit message:

 enable non-SpatialExperiment inputs
 
Package: nnSVG
Commit: ae3bc3f4ed18d31537be2f039199df23f0daea34
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-16 23:16:57 -0400
Commit message:

 wording
 
Package: nnSVG
Commit: bcd8284bd73e3552d72ec22f540729afae60ce09
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-16 23:14:27 -0400
Commit message:

 fix Rbuildignore for png image
 
Package: nnSVG
Commit: 1cf2e2481653c33bdc8356b6bda52a3435042075
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-16 23:10:34 -0400
Commit message:

 readme formatting
 
Package: nnSVG
Commit: 46ff7c7e49d76c8f8c5041878de1f0ac4459d1be
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-16 23:02:11 -0400
Commit message:

 add outputs and plot to workflow
 
Package: nnSVG
Commit: 620be5f2222c17ee57a19341d5302da814dd272d
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-16 22:43:58 -0400
Commit message:

 formatting
 
Package: nnSVG
Commit: 8916986ddf85745e9466aeefa5699dc886f602ee
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-16 22:42:47 -0400
Commit message:

 rearrange sections
 
Package: nnSVG
Commit: d0123346f55dddf9f9a45eb2d10acbb16408b3fa
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-16 22:40:46 -0400
Commit message:

 add short example workflow to readme
 
Package: nnSVG
Commit: d3e307d076956053bfde346e49c2e8edaf6a8b26
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-16 22:24:27 -0400
Commit message:

 update readme
 
Package: scPipe
Commit: a55a6af4647aaf18817adf1af2e3f56254f9b906
Author: Shians <registertonysu@gmail.com>
Date: 2022-05-17 11:21:26 +1000
Commit message:

 Version bump
 
Package: scPipe
Commit: 238e62c1ac1ff926bea7bf610bdd2283405dcf98
Author: Shians <registertonysu@gmail.com>
Date: 2022-05-17 11:16:01 +1000
Commit message:

 Spellcheck
 
Package: scPipe
Commit: fa83df2cc08ea6981643f8d23797d7496b58cf64
Author: Shians <registertonysu@gmail.com>
Date: 2022-05-17 11:10:51 +1000
Commit message:

 Spellcheck
 
Package: ggmsa
Commit: 83e7aa2b301b0da3c3367293a2eab754b5b315d4
Author: nyzhoulang <nyzhoulang@163.com>
Date: 2022-05-17 09:06:53 +0800
Commit message:

 calling  for the examples on ggmsa
 
Package: ggmsa
Commit: 5eebccf9afb737e878f2671a04516849499afce3
Author: nyzhoulang <nyzhoulang@163.com>
Date: 2022-05-17 09:05:33 +0800
Commit message:

 bump version to 1.3.3
 
Package: ggmsa
Commit: 388f14a4a886684881029dabb7c7106ac18fa3b5
Author: nyzhoulang <nyzhoulang@163.com>
Date: 2022-05-17 09:05:10 +0800
Commit message:

 add bioc update
 
Package: ggmsa
Commit: 9a6ef7d06651a115399fec84e88112d999c79060
Author: nyzhoulang <nyzhoulang@163.com>
Date: 2022-05-13 21:45:03 +0800
Commit message:

 update README fig
 
Package: ggmsa
Commit: ea82e32834abfbc1e19532eaf1b08f43edda1a56
Author: nyzhoulang <nyzhoulang@163.com>
Date: 2022-05-13 21:17:12 +0800
Commit message:

 bugfix: geom_msaBar conservation layer incorrectly aligned
 
Package: ggmsa
Commit: 9edf3301b3e44c876f8bc7536b37d507211a28c0
Author: nyzhoulang <nyzhoulang@163.com>
Date: 2022-05-13 21:16:45 +0800
Commit message:

 bump dev version to 1.3.2
 
Package: scPipe
Commit: 8a4998cd61a6edf964e1d56c68ffdc4b3a25b591
Author: Shians <registertonysu@gmail.com>
Date: 2022-05-17 11:02:04 +1000
Commit message:

 BiocCheck fixes
 
Package: scPipe
Commit: 28f446351b0819ab4bf1e341e42a41a88886e285
Author: Shians <registertonysu@gmail.com>
Date: 2022-04-29 16:25:31 +1000
Commit message:

 Merge branch 'master' of https://github.com/LuyiTian/scPipe
 
Package: scPipe
Commit: 016bc799aeff59b1eec7091263a694ca4ab6e9a0
Author: Shians <registertonysu@gmail.com>
Date: 2022-04-29 16:07:38 +1000
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/scPipe
 
Package: scPipe
Commit: ddb95d33620ec0c62312ac09ca63519e071dc778
Author: Luyi Tian <tlytiger@hotmail.com>
Date: 2022-04-23 02:15:06 +1000
Commit message:

 Update DESCRIPTION
 
Package: scPipe
Commit: 6d39d4fcc7c6c690a628df2474f50f5bde4d7599
Author: Luyi Tian <tlytiger@hotmail.com>
Date: 2022-04-23 02:10:12 +1000
Commit message:

 Merge pull request #144 from shaniAmare/master

scATAC-Seq preprocessing functionality update 
Package: scPipe
Commit: 12dbc757b56955fee93b5c9feb431066a0c2dc41
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2022-04-22 14:21:26 +1000
Commit message:

 Merge pull request #26 from philyang07/master

 
Package: scPipe
Commit: ce45f86188bb32944c6daa766226cf035854e5c8
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2022-04-22 14:18:17 +1000
Commit message:

 Minor fix to sc_atac_pipeline
 
Package: scPipe
Commit: 332126766ce6875c4fb794ff725a4e2302d1a6cc
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-04-22 13:49:23 +1000
Commit message:

 Merge branch 'master' of github.com:shaniAmare/scPipe into luyi_merge
 
Package: scPipe
Commit: 7e2563e7fc21011b28c91d81310c032575dec6be
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2022-04-21 17:50:03 +1000
Commit message:

 Merge pull request #25 from OliverVoogd/master

 
Package: scPipe
Commit: 645bc6de68b2970c63b2e5e0aa2bd3ecef3ddc60
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2022-04-21 16:17:54 +1000
Commit message:

 Merge branch 'shaniAmare-master'
Merge conflicts from outdated local with Shani master
 
Package: scPipe
Commit: 4e764291cdadd6628242d63fc50c8a389abf01be
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2022-04-21 16:17:04 +1000
Commit message:

 merge conflicts
 
Package: scPipe
Commit: aa27a233bcdb1bebc4fee600379ba0eeac9b9bf5
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2022-04-21 16:08:43 +1000
Commit message:

 optional arg to not perform reverse complement matching
 
Package: scPipe
Commit: a4e6d70af7a10c3682b985e415162967696d6837
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2022-04-18 17:52:50 +1000
Commit message:

 repo error, restore files
 
Package: scPipe
Commit: 2101b3c69c0155521aacd4d09cbddbf8400bcd3a
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2022-04-18 16:18:50 +1000
Commit message:

 Added compressed annotation files, updated vignette to include sc_atac_pipeline
 
Package: scPipe
Commit: c537cdc22d09bbda5f04afc77457bafee49473c4
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-04-17 23:35:13 +1000
Commit message:

 Removed unnecessary files in extdata
 
Package: scPipe
Commit: 51e892a1e429c034fa37a1c16cfbd47324e94766
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-04-17 23:27:29 +1000
Commit message:

 Resolved further conflicts
 
Package: scPipe
Commit: 1dfedf0ba20e2a23c892202456ccc362ff771aa9
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-04-17 23:16:57 +1000
Commit message:

 Resolved conflicts
 
Package: scPipe
Commit: 06b1eed6b6093279daec120239057c8652fc7cdf
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-04-17 22:44:11 +1000
Commit message:

 Updated annotation url, updated DESCRIPTION file with couple of dependencies
 
Package: scPipe
Commit: a990c0f742d82c40b8154aa8a773537ecbb846da
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-04-17 16:30:48 +1000
Commit message:

 Merge branch 'master' of github.com:philyang07/scPipe
 
Package: scPipe
Commit: affeb8668ca310a3e1a14417b5803e4063d6f256
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-04-17 16:30:30 +1000
Commit message:

 Removed annotation files from repo
 
Package: scPipe
Commit: 2732db527a7c12c88448a67101db00cc9883088a
Author: Phil Yang <48355111+philyang07@users.noreply.github.com>
Date: 2022-04-17 16:29:35 +1000
Commit message:

 Delete inst/extdata/annotations directory 
Package: scPipe
Commit: 65b6cfcc14856fdcfc476de6454f328d5cb58acb
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-04-17 16:29:01 +1000
Commit message:

 Stopped storing annotation files in repo, now downloads into extdata/annotations
 
Package: scPipe
Commit: a77b0b917928a266813535128a79e6141de128bf
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2022-04-12 14:22:04 +1000
Commit message:

 Merge pull request #24 from philyang07/master

Updated plots and demultiplexing functionality 
Package: scPipe
Commit: 8475974b8345c86fe7c77c933298a852a798c701
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-04-10 20:20:46 +1000
Commit message:

 Removed ggpubr dependency for plots
 
Package: scPipe
Commit: 4a8c9fa67f92211830b06d6841c0285525bc9117
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-04-10 13:06:18 +1000
Commit message:

 Changed trim_barcode stats file approx reads name, minor change to rmd report
 
Package: scPipe
Commit: f568fc7b18fa72adc05b938b42f51faa21b3ba53
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2022-04-09 20:33:42 +1000
Commit message:

 Made small changes to plots, now concatentate partial/completematching barcode reads
 
Package: scPipe
Commit: 9cdd6df6e9d79c70175bbc37c46f1b30f3e692ac
Author: Shani Amarasinghe <amarasinghe.s@vc7-shared.hpc.wehi.edu.au>
Date: 2022-04-08 12:33:21 +1000
Commit message:

 8apr2022 | remove ggpubr and seqinr dependencies
 
Package: scPipe
Commit: 65b9fc4bcb769201363cb696c6ee2acc6b1a1835
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2022-04-06 22:42:22 +1000
Commit message:

 Merge branch 'master' of github.com:shaniAmare/scPipe into tasks/demux_plot
 
Package: scPipe
Commit: e737cb289077e9c8db5b7e4bc4273d1aef45e495
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2022-04-04 20:05:16 +1000
Commit message:

 Merge pull request #23 from OliverVoogd/master

atac_trim_barcode fastq approach new outputs 
Package: scPipe
Commit: 1ff43e3c91deaafecd952a3a50024be474383d75
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2022-04-04 19:17:36 +1000
Commit message:

 atac_trim_barcode fastq approach outputs to full, partial and no match barcode files
 
Package: scPipe
Commit: f84e7e13043c28c733ef5e61c9bb3d05ec3df622
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2022-04-04 12:29:59 +1000
Commit message:

 Merge pull request #22 from OliverVoogd/master

trimbarcode csv approach R1 & R2 matches -  thanks Oliver. 
Package: scPipe
Commit: e635847b4dd6e6df30b55b25c24ca724cd2dea74
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2022-04-04 11:21:16 +1000
Commit message:

 resolved barcode error correction bugs
 
Package: scPipe
Commit: fd8474e982c98978f5d7f277daac3516dec79e9b
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2022-04-02 23:44:01 +1100
Commit message:

 Added demux plot functionality for csv barcode method
 
Package: scPipe
Commit: b56740dd8c7672ae9098c5e06204f8832f2e263a
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-04-01 23:48:59 +1100
Commit message:

 Merge branch 'master' of https://github.com/OliverVoogd/scPipe into tasks/demux_plot
 
Package: scPipe
Commit: 5ac9f8704ff2993a642c78947f3633bed3fb2294
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-04-01 23:31:48 +1100
Commit message:

 Added examples to functions
 
Package: scPipe
Commit: 10b08c1043f10bc3b980fbd85ec3c597ff8aec0a
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2022-04-01 17:06:57 +1100
Commit message:

 error correction
 
Package: scPipe
Commit: 2b1281c600353ecdc928e2abbea84256279f2891
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2022-03-30 15:27:40 +1100
Commit message:

 Merge branch 'master' of github.com:OliverVoogd/scPipe
merge minor changes into local repo
 
Package: scPipe
Commit: 0730be850980ccbf10140ae90a99556ae1f8f6dc
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2022-03-30 15:26:48 +1100
Commit message:

 minor typo 2
 
Package: scPipe
Commit: 75ae87ea4a71681e297674f74f9cd75afc28d97a
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2022-03-30 15:24:16 +1100
Commit message:

 minor typo
 
Package: scPipe
Commit: 07469c69e69995f3a6c47fe2c252ae00ca810e34
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2022-03-30 15:23:45 +1100
Commit message:

 barcode error correction using valid barcode file INPROGRESS
 
Package: scPipe
Commit: 47231d3b7a219a5d4fcc258ac6724e3607c32928
Author: OliverVoogd <51314988+OliverVoogd@users.noreply.github.com>
Date: 2022-03-28 12:41:01 +1100
Commit message:

 Update trimbarcode.cpp

fixed variable name errores in trimbarcodes 
Package: scPipe
Commit: cf15850803a415d6ba7a9772ccced6ef8d72a8cd
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2022-03-24 20:31:59 +1100
Commit message:

 adjusted trim_barcode csv to output both reads to the same output file
 
Package: scPipe
Commit: 9bc018f9f09cb9ad854459f9b36ee7dc7136a00c
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-03-15 13:10:27 +1100
Commit message:

 updated report with fixed headings and new/updated plots
 
Package: scPipe
Commit: 2a980369ce93a945f17e42e442f005d1e75f23a8
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2022-03-11 14:04:46 +1100
Commit message:

 Merge pull request #21 from OliverVoogd/master

Updated sc_atac_create_fragments 
Package: scPipe
Commit: 6aa12c8d2b4d7891d1c1a1efa238eae784de86db
Author: Luyi Tian <tlytiger@hotmail.com>
Date: 2022-03-09 11:36:19 +1100
Commit message:

 Update DESCRIPTION 
Package: scPipe
Commit: e7ebbf44c697b4e49f3f9a9988ee525d6451ed2a
Author: Luyi Tian <tlytiger@hotmail.com>
Date: 2022-03-09 11:35:58 +1100
Commit message:

 Merge pull request #142 from LuyiTian/RELEASE_3_14

Release 3 14 
Package: scPipe
Commit: 28fbfa2b689fbec68a0d1f3cf6f4b5494bf963d0
Author: Luyi Tian <tlytiger@hotmail.com>
Date: 2022-03-09 11:35:43 +1100
Commit message:

 Merge branch 'master' into RELEASE_3_14 
Package: scPipe
Commit: d7b9a87b4579ba201bce39f7d4e0cdb528fabcd5
Author: Luyi Tian <tlytiger@hotmail.com>
Date: 2022-03-09 11:31:25 +1100
Commit message:

 Update DESCRIPTION 
Package: scPipe
Commit: e1ef1058938f6c79925e226273ee72acebde1f96
Author: Luyi Tian <tlytiger@hotmail.com>
Date: 2022-03-09 11:31:04 +1100
Commit message:

 Update report_template.Rmd 
Package: scPipe
Commit: 24f8ece02e2955935c46f2cefab6d09d95aee03d
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2022-02-24 16:46:02 +1100
Commit message:

 Updated barcode selection parameters, fixed minor namespace error with sparseMatrix() call in bam tagging function
 
Package: scPipe
Commit: ca3b3c5d40385ce118dca98e2e8e0333e296bbd6
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-02-11 13:47:03 +1100
Commit message:

 replcaed sc_atac_create_fragments with sc_atac_fragments
 
Package: scPipe
Commit: 7a9f3282588dc3f465288a205f90da83d7513327
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-02-11 13:17:03 +1100
Commit message:

 Merge branch 'master' of https://github.com/OliverVoogd/scPipe into tasks/test_oliver_fragments
 
Package: scPipe
Commit: 7a8aa26cc058f1cf7c828fc4bdc87be2de4901e9
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2022-02-11 13:16:52 +1100
Commit message:

 Updated vignette workflow image
 
Package: scPipe
Commit: 44fafc55758d3d37a0c5ade77d5082abefed23be
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-12-21 15:10:41 +1100
Commit message:

 fixed issue created through merge
 
Package: scPipe
Commit: 030a5a2e196aa105d83baddc14e877a7b87e5c66
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-12-18 16:22:09 +1100
Commit message:

 fixed barcode mapping statistics plot
 
Package: scPipe
Commit: d5af318b502898451069ef0b19872424d2a3c069
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-12-18 15:55:50 +1100
Commit message:

 fixed more bugs with duplicate removal failure handling
 
Package: scPipe
Commit: a84f7944629ae6b97cc0e6b55abebeb3205171b5
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-12-18 15:23:28 +1100
Commit message:

 fixed bam tagging function locating issues, fixed samtools installation detection errors for duplicate removal
 
Package: scPipe
Commit: 41eb0572e01c80e4efd5e77c48509e86fe1afef8
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-12-14 13:30:05 +1100
Commit message:

 merge conflicts
 
Package: scPipe
Commit: c50deed8a99df299e2b3c6343f0d878530c2c2db
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-12-14 13:21:37 +1100
Commit message:

 new fragments function
 
Package: scPipe
Commit: b04b04ed5ca639a5a478fdf333624a888ba4a8e4
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-11-29 15:50:49 +1100
Commit message:

 Merge pull request #20 from philyang07/master

 
Package: scPipe
Commit: bb7e8fd55b74cd94776eeece9472140efa37fb2a
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-11-22 12:20:04 +1100
Commit message:

 resolved BiocCheck errors for a few package dependencies, renamed  new fragments function
 
Package: scPipe
Commit: f8986e58fb9370410bab2269876f9706734353a2
Author: OliverVoogd <51314988+OliverVoogd@users.noreply.github.com>
Date: 2021-11-22 11:24:39 +1100
Commit message:

 Merge branch 'shaniAmare:master' into master
 
Package: scPipe
Commit: 28acdba9891d131252f126913f5fce25ab7d50b1
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-11-19 15:10:24 +1100
Commit message:

 implemented thread locked outputfeil instead of temp output rewrite
 
Package: scPipe
Commit: 247c252c0ddacf6d94ed58536a95b31b79203b22
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-10-19 17:03:45 +1100
Commit message:

 testthat functions for fragmentThread
 
Package: scPipe
Commit: 781a180e882fef234ade348c074edb082ea2448b
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-10-18 04:40:24 +1100
Commit message:

 Merge branch 'master' of github.com:philyang07/scPipe

Need to do it before pushing
 
Package: scPipe
Commit: aa2f19d707b91e89529abb846ef333ad79f7ba6f
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-10-18 04:39:42 +1100
Commit message:

 added plot for cellular alignment statistics to rmd report
 
Package: scPipe
Commit: 7b3e7a61a284310bfd78834fa6bbd549470caf4b
Author: Phil Yang <48355111+philyang07@users.noreply.github.com>
Date: 2021-10-15 19:31:37 +1100
Commit message:

 Merge pull request #5 from philyang07/tasks/windowed_feature_counting

Tasks/windowed feature counting 
Package: scPipe
Commit: 3bdeb03ae22d5e222264b196afde63b280289e58
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-10-15 19:30:28 +1100
Commit message:

 windowed approach for feature counting and alignment stats per barcode generation
 
Package: scPipe
Commit: 5bf49d46b38bfdad06e769c33ad22b0548d6d28c
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-10-03 22:48:19 +1100
Commit message:

 implemented windowing for feature counting
 
Package: scPipe
Commit: e842e332a1bda7e3e9371d7cad66223b254cfbff
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-09-29 12:57:49 +1000
Commit message:

 fragment tests
 
Package: scPipe
Commit: 2337e27691a955726de67e965034486fb732b556
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-09-26 09:55:25 +1000
Commit message:

 writing to file
 
Package: scPipe
Commit: d73dd1469f0a3325523e5379f9c890cc2f69e69d
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-09-18 23:44:19 +1000
Commit message:

 created small test datasets using chr21 and updated pipeline test function documentation
 
Package: scPipe
Commit: 5442505243bcfcfd63cd9e3579edcc3e92d3d1d2
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-09-07 16:10:49 +1000
Commit message:

 samtools bam loading
 
Package: scPipe
Commit: 09c9eee0a3f26ae8f6d3a5b11cd4478afcff5305
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-08-22 15:47:58 +1000
Commit message:

 fragments cpp function using multithreading (in progress)
 
Package: scPipe
Commit: cde1acdad1daee40447076fe6451263514abbf3b
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-07-22 17:52:05 +1000
Commit message:

 Merge pull request #19 from OliverVoogd/master

 
Package: scPipe
Commit: 7448bea13be1eb9944c4fb05107fcd56da0fd51f
Author: OliverVoogd <51314988+OliverVoogd@users.noreply.github.com>
Date: 2021-07-22 17:00:36 +1000
Commit message:

 Merge branch 'shaniAmare:master' into master
 
Package: scPipe
Commit: a76936610a24c7e1cfec7589618895a7bbaf10c3
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-07-22 16:54:53 +1000
Commit message:

 fixed unused variable warning
 
Package: scPipe
Commit: 546f89559a731d08a3c0cb7a44dd11540698a555
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-07-22 16:37:01 +1000
Commit message:

 removed warnings for int comparison
 
Package: scPipe
Commit: 88ee1e9ed0118465e40307d1f2c19f84d78669d1
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-07-20 19:36:26 +1000
Commit message:

 Merge pull request #18 from philyang07/master

fixed sc_align function  
Package: scPipe
Commit: fc8fb956ef9a283d30c53812f0e36953fc97b350
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-07-20 19:17:17 +1000
Commit message:

 Merge https://github.com/shaniAmare/scPipe
 
Package: scPipe
Commit: 342b47ca8f7d90dff58c2516c72ac92819d3f6e3
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-07-20 19:16:39 +1000
Commit message:

 minor fix to aligning function
 
Package: scPipe
Commit: 3bc6f1eeb9e32e818aa76e5ae570640a9c4d4696
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-07-20 19:10:19 +1000
Commit message:

 fixed sc_aligning and replaced sc_atac_aligning
 
Package: scPipe
Commit: 6e9d81b11a0ac40e3ba36ff9fb5fea3ae42c97c8
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-07-20 15:08:34 +1000
Commit message:

 Merge pull request #17 from philyang07/master

 
Package: scPipe
Commit: c4536e012eb675abe03a565c0bd2c2bbcf4ef7f3
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-07-19 20:56:26 +1000
Commit message:

 minor change to vignette tutorial
 
Package: scPipe
Commit: e8fa6bc3749097fab1e7db31e639e562ae29877f
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-07-19 20:35:08 +1000
Commit message:

 used small test files for sc_atac_pipeline_quicktest()
 
Package: scPipe
Commit: cf629a496e4e2f4daac1ae240ee2b1f648e00d89
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-07-19 19:57:22 +1000
Commit message:

 minor documentation fix
 
Package: scPipe
Commit: 08a292717090298817cf04a8a487390b3c717a51
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-07-19 19:56:21 +1000
Commit message:

 minor documentation fix
 
Package: scPipe
Commit: cee180626c92c6473385a30b351e3e93f0349a1f
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-07-19 19:50:25 +1000
Commit message:

 merged updated repo from Shani
 
Package: scPipe
Commit: f0aaa33fa09b23b9e7268cf0a2b5a8b6027ec935
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-07-19 19:43:50 +1000
Commit message:

 changed organisation of data files, made filter cell calling method default in case others fail
 
Package: scPipe
Commit: 47480e3a5bc52a11a0a8508151ab53fc71c5fedb
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-07-19 19:20:39 +1000
Commit message:

 Merge pull request #16 from OliverVoogd/master

 
Package: scPipe
Commit: daa4c8d87ea3af52d32d67a3551c4258c8b28ff0
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-07-19 17:03:41 +1000
Commit message:

 removed warnings for unused kseq.h functions
 
Package: scPipe
Commit: bf68ab9dd9ea0d8b5586c925510651c652c9ab2d
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-07-13 16:05:30 +1000
Commit message:

 add end<- and start<- to feature counting imports
 
Package: scPipe
Commit: b13ffc48cfa113d59afb5d6685a42890b1d5495d
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-07-13 15:30:25 +1000
Commit message:

 updated NAMESPACE and updated tutorial to not use here library
 
Package: scPipe
Commit: bd01f7de7e889919e94b514579fe76a9d93b9228
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-07-13 15:00:55 +1000
Commit message:

 importing strand from BiocGenerics
 
Package: scPipe
Commit: 6b13302f802c087b648ef03e4732e2cc701717c4
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-07-13 14:47:13 +1000
Commit message:

 added convenience testing function of whole pipeline
 
Package: scPipe
Commit: 2be17c9edd238c2ca36a4ecb828401091195f4c5
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-07-13 13:30:18 +1000
Commit message:

 fixed imports, imported dplyr, tidyr
in feature counting function since many of their functions are used
 
Package: scPipe
Commit: 67a928bf43882e56792c45974d24e04db494316c
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-07-13 12:58:51 +1000
Commit message:

 added tibble prefix to tibble function
 
Package: scPipe
Commit: 576ff6cddca0c23b4c30f0bb2dd5aaec8a980bde
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-07-13 12:43:55 +1000
Commit message:

 fixed some missing library specifications for functions
 
Package: scPipe
Commit: fe53fe4e53322dec2153307407d3d14bff36b6b8
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-07-13 11:28:40 +1000
Commit message:

 fixed syntactical error in DESCRIPTION file for authors
 
Package: scPipe
Commit: 9f72007cf9e0e10007142c1bd814b12e28755a48
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-07-12 13:21:33 +1000
Commit message:

 fixed path to trimbarcode_stats_filename in rmd html report
 
Package: scPipe
Commit: aac57495a15c69f7929fd38c0921ef2e84f2b5a4
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-07-09 18:15:11 +1000
Commit message:

 updated DESCRIPTION with ATAC-seq module dependencies, updated authors, added duplicate removal stats to HTML report
 
Package: scPipe
Commit: 29ebf3f19ad58dbb3d5520ad2f9780e2c074df64
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-07-07 15:05:24 +1000
Commit message:

 delay plot generation for demultiplexing to report generation
 
Package: scPipe
Commit: 04f8f4881ae8b322fb73ca42b9ca0de8111aacaa
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-07-07 13:50:03 +1000
Commit message:

 remove report file from R subdirectory
 
Package: scPipe
Commit: ad58f9acc4f75f7bc75bc1a991519dfeaa499567
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-07-07 13:46:54 +1000
Commit message:

 updated description to include data.table, added additional arguments for cell calling
 
Package: scPipe
Commit: 958fe912c270faa19f06e9b2ce04a2e196666130
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-07-07 12:46:23 +1000
Commit message:

 removed here() for locating the report skeleton rmd file
 
Package: scPipe
Commit: ca6be48cee15552a6abba98cb0e39e6116e6bde0
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-07-06 16:33:02 +1000
Commit message:

 edited function roxygen imports etc.
 
Package: scPipe
Commit: d9a4e614a78c643bcfc86850b0e08d717e5026e5
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-07-02 12:04:42 +1000
Commit message:

 changes to report, tutorials
 
Package: scPipe
Commit: 22dad6923d7c7b9db3dbe47e0b342b68ce8ae1d0
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-06-29 15:23:07 +1000
Commit message:

 added convenience pipeline running function, added new arguments for annotation files to feature counting, refactoring of output folders, general cleaning up of code
 
Package: scPipe
Commit: f01641e4bc17f8449a4d4b7c6d399dd12b094016
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-06-23 02:04:51 +1000
Commit message:

 rendered all plots for report, barcode read count plot fixed, aesthetic changes to report
 
Package: scPipe
Commit: 7fdf90c0a80bf62d0d40fc2f02f68ae634011512
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-06-21 21:29:12 +1000
Commit message:

 fixed sce creating functionality and associated generic functions
 
Package: scPipe
Commit: 8d6e17966557ffd1d6cad9b9525e0d49da0171a4
Author: Phil Yang <yang.p@vc7-shared.hpc.wehi.edu.au>
Date: 2021-06-20 00:56:48 +1000
Commit message:

 gerge branch 'shaniAmare-master' into devel
 
Package: scPipe
Commit: 8a037ffafd2f3ec8ee0008c7981f418ee4177eab
Author: Phil Yang <yang.p@vc7-shared.hpc.wehi.edu.au>
Date: 2021-06-20 00:50:57 +1000
Commit message:

 resolved merge conflicts with bam tagging, feature counting and cell calling
 
Package: scPipe
Commit: edcfaf0847b9d388881a59a23eb2fb968f046078
Author: Phil Yang <yang.p@slurm-login01.hpc.wehi.edu.au>
Date: 2021-06-16 03:11:14 +1000
Commit message:

 feat: implemented cellranger and filter cell-calling methods, significant refactoring to cell calling
 
Package: scPipe
Commit: ec798b013898da3ce599e25881e0b993b4add402
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-06-05 15:46:22 +1000
Commit message:

 Merge pull request #15 from OliverVoogd/master

graph generation for sc_atac_bam_tagging and test cases 
Package: scPipe
Commit: 77c612753a6bde7395539beb76236867b4cead86
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-06-01 11:45:46 +1000
Commit message:

 testing for Trie ds
 
Package: scPipe
Commit: ae7b15a447e1d5a0f1f2d88e5210132a86f01fdb
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-06-01 10:53:40 +1000
Commit message:

 removed debug code
 
Package: scPipe
Commit: 23889d4de24943f7cdca691a93e6d0585f9415b5
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-06-01 10:47:32 +1000
Commit message:

 graph generation for sc_atac_bam_tagging and test cases for cpp code and check barcode reads
 
Package: scPipe
Commit: 37a6a03979b12bc26428fdf2cc84c1fba20af3f2
Author: Phil Yang <yang.p@vc7-shared.hpc.wehi.edu.au>
Date: 2021-05-17 09:33:04 +1000
Commit message:

 feat: added new qc plots with fragment file into rmd report, refactoring of qc plot and qc_per_bc_file generation (now in feature counting function)
 
Package: scPipe
Commit: e7fef7884865ac12dec7af3f9af8c622cc91ce5d
Author: Phil Yang <yang.p@vc7-shared.hpc.wehi.edu.au>
Date: 2021-05-02 15:15:24 +1000
Commit message:

 changed line 379 to read.table
 
Package: scPipe
Commit: 312360139abf8f59ce3185611df0d622bd7bd50f
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-23 18:59:38 +1000
Commit message:

 Merge pull request #14 from OliverVoogd/master

Memory leak bug fixes, basilisk support for python 
Package: scPipe
Commit: 64327a47e305f8bae3e08ae8011efc7e09b789dc
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-23 18:55:32 +1000
Commit message:

 man sections
 
Package: scPipe
Commit: 38aaf33a6dac9a3536d964e2e4a4ac8b7f0fd960
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-23 17:31:24 +1000
Commit message:

 Merge pull request #13 from hy-Yang/patch-7

Create sc_aligning.R 
Package: scPipe
Commit: 087252690ebe51f0b53262ba18ac088cf871a283
Author: Phil Yang <yang.p@vc7-shared.hpc.wehi.edu.au>
Date: 2021-04-23 13:44:32 +1000
Commit message:

 minor tweak to handling of output bam file in duplicate removal
 
Package: scPipe
Commit: ba016a862f8872a0892e2e809c187295ae67e865
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-16 15:43:59 +1000
Commit message:

 changes to fasta header handling for sc_atac_feature_counting
 
Package: scPipe
Commit: fa137599cb56fab5b3dcc4008ab4db4e63b73313
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-16 14:56:45 +1000
Commit message:

 basilisk for MACS3 python call
 
Package: scPipe
Commit: 5e1976b0485bcf13127ffd4fadb1b5336210e004
Author: OliverVoogd <51314988+OliverVoogd@users.noreply.github.com>
Date: 2021-04-13 17:04:59 +1000
Commit message:

 Merge pull request #2 from OliverVoogd/basilisk

Basilisk 
Package: scPipe
Commit: ae9c1a3829ab969c7130419391fed0d68b8f8111
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-13 16:59:28 +1000
Commit message:

 basilisk documentation fixes
 
Package: scPipe
Commit: 12f931ee8545da05da0419e471a679066e672f2c
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-10 17:05:35 +1000
Commit message:

 basilisk support for sinto
 
Package: scPipe
Commit: a7464faae4db3bcb80a8ee7012b5486d56faa30a
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-10 16:30:51 +1000
Commit message:

 Merge branch 'master' of github.com:shaniAmare/scPipe into basilisk
add support for basilisk.
 
Package: scPipe
Commit: 320f031256d59a8ee4ef386730c4b3d0f13c384c
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-10 16:29:04 +1000
Commit message:

 more bug fix attemps
 
Package: scPipe
Commit: ab9b563a9447dd17821335ba64e16cf74471dfff
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-10 16:21:34 +1000
Commit message:

 attempt at bug fix
 
Package: scPipe
Commit: 692fe845d38f449705b78d976c92c65da1d1ed03
Author: hy-Yang <52733913+hy-Yang@users.noreply.github.com>
Date: 2021-04-09 11:34:27 +1000
Commit message:

 Create sc_aligning.R

Added sc_aligning() 
Package: scPipe
Commit: ffaef463499f40a12f42ada1bcad1ac9281de959
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-07 19:47:07 +1000
Commit message:

 add reticulate, remove seqinr
 
Package: scPipe
Commit: 68e29ac06b7a0fc027217b1fcbcdb30b502e818d
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-07 19:32:32 +1000
Commit message:

 fix error in order or GAlignment file creation
 
Package: scPipe
Commit: fe787d58111da33426d54d66b5b1ad9604262e30
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-07 19:00:06 +1000
Commit message:

 fix bug with system.file for extdata()
 
Package: scPipe
Commit: ebca75868a44b316706173b1ae44f317c9fec9bc
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-07 16:54:10 +1000
Commit message:

 minor bug <- to =
 
Package: scPipe
Commit: 6103782b1faed2530a36bea924cad000b6a9c85c
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-07 16:06:27 +1000
Commit message:

 minor bug in roxygen
 
Package: scPipe
Commit: a9f46dbb3b3b91e778d6438a3cadbfbcd5f78f41
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-07 15:28:47 +1000
Commit message:

 minor bugs
 
Package: scPipe
Commit: 72a9ca718f3d9aeacd2b7812c723d0aab74a9ba6
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-07 14:24:12 +1000
Commit message:

 fixes linux bug
 
Package: scPipe
Commit: a0537d36fac5978f7503f0a81debe0eda78e37c5
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-07 11:41:31 +1000
Commit message:

 Merge pull request #12 from OliverVoogd/master

Removal of bc_start and bc_length 
Package: scPipe
Commit: c0170f7934c85afe22a6ecb02274e367cc99f55e
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-07 11:38:46 +1000
Commit message:

 Update zzz.R
 
Package: scPipe
Commit: 553d000cb39e5c13d8fcfb9982078f2c4fb95c2d
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-07 11:30:50 +1000
Commit message:

 Merge branch 'master' of github.com:shaniAmare/scPipe
merge before pull request
 
Package: scPipe
Commit: fd2222803baa9f5678d49388da68cbb833e2df2a
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-07 11:30:00 +1000
Commit message:

 removed bc_start and bc_length
 
Package: scPipe
Commit: 3fb20a0ee074ca09dd406ea90ad1481135bf238f
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-07 11:06:29 +1000
Commit message:

 revert back
 
Package: scPipe
Commit: 790d786b78e10fe7c1f4ecb7e51e059e5be5c9e1
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-07 10:56:36 +1000
Commit message:

 Merge branch 'master' of github.com:shaniAmare/scPipe
attempt to locate crash bug
 
Package: scPipe
Commit: bc249aae08c2a8ff77d45e26086297b903617bcd
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-07 02:01:21 +1000
Commit message:

 minor bug in log report
 
Package: scPipe
Commit: 0fb0b725c6bf8a959b17c7fda649cea6727bae27
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-07 01:47:04 +1000
Commit message:

 fix_chr modifications to feature counting, minor changes to create_sce and tutorial
 
Package: scPipe
Commit: 4cbe9d8011db4ef835336dc91166ec5b9bab46d3
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-06 16:14:35 +1000
Commit message:

 Revert "removed bc_start and bc_length"

This reverts commit 7fab8adf5a58675f8a492411926f81a393e101ef.

revert changes for bc_start which broke build
 
Package: scPipe
Commit: 7fab8adf5a58675f8a492411926f81a393e101ef
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-06 16:00:42 +1000
Commit message:

 removed bc_start and bc_length
 
Package: scPipe
Commit: cd9b0abf7a10f4d100ea9399b6c0b7fc1e02feb2
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-06 15:51:31 +1000
Commit message:

 Update scPipe_atac_tutorial.Rmd
 
Package: scPipe
Commit: 9eb95853b31c54abb0556df5a2a8cfc9b0ace76d
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-06 15:50:57 +1000
Commit message:

 feature counting, cell calling, create sce functions are updated

feature counting, cell calling, create sce functions are updated
 
Package: scPipe
Commit: 12bfa7bc2a4cb791eb6ed6bf90254074c1baa2c9
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-06 14:42:42 +1000
Commit message:

 type
 
Package: scPipe
Commit: fd78393eff3179e8b03c976e77a6b7a275712e0f
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-06 14:34:05 +1000
Commit message:

 warning fixes
 
Package: scPipe
Commit: 6901bd937e5716eca44d48f2864c3066198000e8
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-04 01:58:11 +1100
Commit message:

 Update README.md 
Package: scPipe
Commit: 89bccdf4babd2567969439e0903eb42592a58731
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-04 01:52:08 +1100
Commit message:

 Update sc_atac_feature_counting.R

Correcting the shift for Tn5 cut site
 
Package: scPipe
Commit: ae7cb7515bd3116188f771895c15559c865f48da
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-04 01:21:38 +1100
Commit message:

 some more aesthetics
 
Package: scPipe
Commit: 4b2982d84b4678f962cb17ef7902e66852291a10
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-04 01:00:58 +1100
Commit message:

 Merge pull request #6 from OliverVoogd/newtrimbarcode

Newtrimbarcode 
Package: scPipe
Commit: ea4d188fb9f32ac6a41ce6ecdd41941871c756b5
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-04 01:00:14 +1100
Commit message:

 Merge branch 'master' into newtrimbarcode 
Package: scPipe
Commit: ad825a8c567cfb6db8c699fd189039235ba189f6
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-04 00:53:52 +1100
Commit message:

 aesthetic changes
 
Package: scPipe
Commit: c47c7b28fcf8cc008d831fa997a11e0280c3a5b2
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-04 00:43:18 +1100
Commit message:

 multiple changes to sc_atac_cell_calling()

emptydrops() fdr set to 001
emptydrops() lower parameter set to 1
NAMESPACE is modified to get @philyang07's edits
cell-called matrix to return to sc_atac_feature_counting function
clean up sc_atac_bam_tagging()
 
Package: scPipe
Commit: d99b692102cfd3df33f69eacd012eea8c2d62a1a
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-02 17:17:41 +1100
Commit message:

 removal of old testing code for iterations
 
Package: scPipe
Commit: 6c069d5a89a27608dd7728963907e6133939f55f
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-04-02 16:43:34 +1100
Commit message:

 fixed csv approach, now matches correctly in a reasonable time frame
 
Package: scPipe
Commit: f9d8f7af4b937bf15b00d0894f4567c5f74c0934
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-01 14:50:57 +1100
Commit message:

 Update sc_atac_cell_calling.R
 
Package: scPipe
Commit: bb299627be0b543e444284d2473c4b0f9d1c94f4
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-01 14:44:49 +1100
Commit message:

 cell calling function modified
 
Package: scPipe
Commit: ce11cc431bbadad203cf8e2ee684c05ad1128d06
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-04-01 01:12:44 +1100
Commit message:

 major upgrades to functionality, three new functions

macs3 for peak calling; sinto for fragment file; remove duplicates using samtools; multiple upgrades in aligning,, report generation and feature counting functions
 
Package: scPipe
Commit: 522f5b7719bc1f60a61b365d58f7cdf72d862a3a
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-03-30 15:52:37 +1100
Commit message:

 refactor fastq_to_csv trimming method
 
Package: scPipe
Commit: 135f519dda071ad880a6f26f6eb87fa520a864c9
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-03-29 15:12:39 +1100
Commit message:

 Update README.md 
Package: scPipe
Commit: 75d1dedf57b626d3e33567b47a55b7f2e1f82942
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-03-29 15:02:55 +1100
Commit message:

 Update README.md 
Package: scPipe
Commit: a67885a93cc83a018359725efe781e7cc75949ee
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-03-29 14:59:29 +1100
Commit message:

 Update sc_atac_call_peaks.R
 
Package: scPipe
Commit: 599d9a0d2ff2fe72d1fefac3fe3c8020bbc651b2
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-03-29 14:46:51 +1100
Commit message:

 update readme
 
Package: scPipe
Commit: d4dbd1f0a0471501cb34d582514fbbc92f6d83f0
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-03-26 15:20:44 +1100
Commit message:

 initial commit
 
Package: scPipe
Commit: 037db4346dce816ef330bf4d3addfcb1c13d7620
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-03-26 14:13:28 +1100
Commit message:

 new branch commit
 
Package: scPipe
Commit: c460e0a4b27bbb7334b993eee7659c040c3d2b8b
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-03-26 13:43:58 +1100
Commit message:

 small modification
 
Package: scPipe
Commit: 99b50621db66032d8252272043ee55aaf6a736a3
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-03-23 17:05:19 +1100
Commit message:

 report_gen changes
 
Package: scPipe
Commit: 9e05f758196d47f3d999201bae4635c618c843ff
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-02-23 12:34:54 +1100
Commit message:

 Merge pull request #4 from philyang07/devel

Changed peak calling function to use MACSr, and determine effective genome size via reference genome or use user-specified value 
Package: scPipe
Commit: c9de818a4451dc8c347956cd12eb712cd519c005
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-02-23 12:31:44 +1100
Commit message:

 update README, vignette and advaned aligning functions
 
Package: scPipe
Commit: 454453ab2a25e4bb53ccd6b599aa8daef4d75938
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-02-22 18:22:56 +1100
Commit message:

 user continue & warning fix
 
Package: scPipe
Commit: be157bbd86742301191e0b656651c4ef3b8c4a8b
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-02-22 16:39:23 +1100
Commit message:

 minor warning fixes
 
Package: scPipe
Commit: ab222e06f7aa3e1ab67b20d36b2b5d63d2e90270
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-02-18 17:50:13 +1100
Commit message:

 feat: updated .onAttach() function to check for samtools and R version for MACSr
 
Package: scPipe
Commit: 10834db009afe4e27dbc6058cff92595331620be
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-02-18 12:11:36 +1100
Commit message:

 changed string to char utils
 
Package: scPipe
Commit: 4200f6604336b1f94d7f67157e384866775c4f81
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-02-17 17:59:43 +1100
Commit message:

 refactor: remove function call at the end of peak calling script
 
Package: scPipe
Commit: 734c419f05dbfcbd1ba4f647bffbec0253243bda
Author: Phil Yang <yang.p@slurm-login02.hpc.wehi.edu.au>
Date: 2021-02-17 17:55:02 +1100
Commit message:

 feat: peak calling with MACSr, effective genome size determined by genome file size
 
Package: scPipe
Commit: 1ef2ddd1e2d826ede76cc0947b76fde6e4a876fd
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-02-16 16:11:36 +1100
Commit message:

 minor warning fixes
 
Package: scPipe
Commit: da3a3c24f0fc74bd484854d198df6a9b25521527
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-02-09 14:51:01 +1100
Commit message:

 fix bam file paths
 
Package: scPipe
Commit: a89c4d696ca086dc6400893aafab032b862d850e
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-02-09 12:16:11 +1100
Commit message:

 Merge pull request #3 from OliverVoogd/master

Small typo fixes 
Package: scPipe
Commit: 4ad27c9ab40c5758a8018a44355231138724ce8d
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-02-09 12:09:39 +1100
Commit message:

 sc_atac_check_qual typo fix
 
Package: scPipe
Commit: 1e911ced9c27d763b660e58f8dc3f5cb7aaf97d1
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-02-09 11:52:02 +1100
Commit message:

 Merge branch 'master' of github.com:shaniAmare/scPipe
merge remote changes
 
Package: scPipe
Commit: a191b2f3f83a70e11a20de828fd871ad3d32da59
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-02-09 11:42:25 +1100
Commit message:

 fix file path issues
 
Package: scPipe
Commit: 5d132301ed29ef140f2ffd67a65c4cd8bd101406
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-02-08 21:32:17 +1100
Commit message:

 Delete .DS_Store 
Package: scPipe
Commit: 751b259223750f9801d05dc9035d86ce167ee6c8
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-02-08 21:32:03 +1100
Commit message:

 Delete .DS_Store 
Package: scPipe
Commit: 271a1fffad41fcb73007949241062b8d7bbb9bdc
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-02-08 21:31:48 +1100
Commit message:

 Delete .DS_Store 
Package: scPipe
Commit: edfbab68df488f3f655e9a6dee3bb3df5ae89879
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-02-08 21:01:27 +1100
Commit message:

 Add files via upload 
Package: scPipe
Commit: a8c7888ec210cb9021d9d48594da2e672b616a7c
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-02-08 15:50:29 +1100
Commit message:

 Delete .DS_Store 
Package: scPipe
Commit: 384dcec61e47a76bf33d98fdd39551d0ded8e4b8
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-02-08 15:45:09 +1100
Commit message:

 Delete stats_file_trimbarcode.txt 
Package: scPipe
Commit: 2585beb7ecda50232166729595e6c9033d5d7fed
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-02-08 15:44:57 +1100
Commit message:

 Delete log_file.txt 
Package: scPipe
Commit: a5034d2089ef03c1959b0cb06b8edf8cfa458d3d
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-02-08 14:18:53 +1100
Commit message:

 bad check_barcode_start_position call
 
Package: scPipe
Commit: 2e3eda7ed83a33c9521e104c5a69690129565839
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-02-08 14:08:16 +1100
Commit message:

 Merge pull request #2 from OliverVoogd/master

Issue #44 Check for out of bounds indices 
Package: scPipe
Commit: f34e2b0cc52177278ab62b15c4c788ee4af79ef9
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-02-08 14:03:35 +1100
Commit message:

 Issue #44 range check for sc_atac
 
Package: scPipe
Commit: 2aea95d3262828f693583ce60ea40500078a0f12
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-02-08 12:13:45 +1100
Commit message:

 Merge branch 'master' of github.com:shaniAmare/scPipe
merge upstream into local branch
 
Package: scPipe
Commit: 9d4a09b01f9e5d1f4b3fe6181fc643994eb7b83e
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-01-30 11:11:33 +1100
Commit message:

 typo
 
Package: scPipe
Commit: a01f29e49dff6e243119c86f06c75606729b53b5
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-01-30 11:10:49 +1100
Commit message:

 minor fix
 
Package: scPipe
Commit: d9a0d70915b01757fd9d2bec54cfcda52a1f31e3
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-01-30 11:10:02 +1100
Commit message:

 Revert "trimbarcode check of read length"

This reverts commit c0e7b1e5a6dc0985df488f1395af0dd2d093181e.
 
Package: scPipe
Commit: c0e7b1e5a6dc0985df488f1395af0dd2d093181e
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-01-30 11:07:28 +1100
Commit message:

 trimbarcode check of read length
 
Package: scPipe
Commit: e10a6703406358c7618aefcda82c232020cc27c0
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-01-30 11:03:23 +1100
Commit message:

 Merge branch 'master' of github.com:OliverVoogd/scPipe
merge master to local
 
Package: scPipe
Commit: f6f2251d3512d4cc720ea56937a8cc02eb5a3d9c
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-01-30 11:01:37 +1100
Commit message:

 trimbarcode check for barcode beyond read
 
Package: scPipe
Commit: f86aa15b7bc5ffa61c1fb4e4da26a858f65c43e9
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-01-28 15:19:16 +1100
Commit message:

 Merge pull request #1 from OliverVoogd/master

Subset testing for correct barcode start position 
Package: scPipe
Commit: b9b87a826f90de2243c20a63dd23abf15ad3e03f
Author: OliverVoogd <51314988+OliverVoogd@users.noreply.github.com>
Date: 2021-01-28 14:45:17 +1100
Commit message:

 Merge branch 'master' into master 
Package: scPipe
Commit: 02798955be39637c722acf292a38d69ba346dacb
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-01-28 14:38:02 +1100
Commit message:

 header for resizearray
 
Package: scPipe
Commit: ae3eced410bbfcd6bd6439425616a363caccfb9f
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-01-28 14:22:30 +1100
Commit message:

 header files and final testing
 
Package: scPipe
Commit: 970eacce3801830ae4d5a2cd246b540cbb1dff5e
Author: Shani Amarasinghe <43805905+shaniAmare@users.noreply.github.com>
Date: 2021-01-18 14:38:00 +1100
Commit message:

 files for peak calling tests 
Package: scPipe
Commit: 3a8a7fd8b752299295563a994ab34a8b79b2d0f9
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2020-12-24 01:28:32 +1100
Commit message:

 stat file name change, new function for report and SCE object creation
 
Package: scPipe
Commit: 3fe2039024fd0b2d2ff5851378bb90e43d082663
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2020-12-21 13:54:42 +1100
Commit message:

 testing and printing
 
Package: scPipe
Commit: 6c7d86a98e3fe7472e187dea70f50bcb0d28ecf7
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2020-12-17 19:51:45 +1100
Commit message:

 working verification
 
Package: scPipe
Commit: 6d90a2c681bab629bd84078c1bcef6b45557b81a
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2020-12-15 14:20:40 +1100
Commit message:

 minor typos, bug fixes, structure fixes, consistency fixes, new data files
 
Package: scPipe
Commit: 34dadcef17f6deee740efcd3b0c71ae27d3ab5c3
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2020-12-12 10:09:30 +1100
Commit message:

 trie clean up
 
Package: scPipe
Commit: 10ce0ec0d34c9674f164ec7526d3c61417847b75
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2020-12-11 21:35:56 +1100
Commit message:

 basic single index searching
 
Package: scPipe
Commit: e421a674b7b4408966317d0a5a5335bed3f5f479
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2020-12-11 20:42:31 +1100
Commit message:

 cpp barcode reading
 
Package: scPipe
Commit: bda38999b3cc3f1fab5844a3e939595e9242b29e
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2020-12-07 19:15:42 +1100
Commit message:

 new matrix formation, log files, messages, timers, qc checks
 
Package: scPipe
Commit: 0729aacd0e184b500d08a18349e0a4d6b53e501d
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2020-12-06 01:41:58 +1100
Commit message:

 correct matrix format and sparse matrix format
 
Package: scPipe
Commit: eea8805171c86b9740ecc77e08c2180644b154f9
Author: shaniAmare <43805905+shaniAmare@users.noreply.github.com>
Date: 2020-12-05 23:30:03 +1100
Commit message:

 scpipe atac-seq extension functions
 
Package: GenomicFeatures
Commit: 6d0be8eeee782a1f4266756f39b0938b04a18a0a
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-05-16 20:37:32 -0400
Commit message:

 version bump 1.49.3
 
Package: GenomicFeatures
Commit: 0fdbd2b65b39751e04185c017402f0c6857939bb
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-05-16 20:34:57 -0400
Commit message:

 check for mirrors in host input
 
Package: benchdamic
Commit: 32ef7bc1061f6c7502d978325076bcea5128e5a9
Author: Matteo Calgaro <mcalgaro93@gmail.com>
Date: 2022-05-16 22:11:01 +0200
Commit message:

 Improved vignette with more authors, references, and figure captions
 
Package: GenomicFeatures
Commit: 55c136ce19426c445b6c29c6e29ab68ae392d182
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-05-16 11:32:46 -0400
Commit message:

 version bump 1.49.2
 
Package: GenomicFeatures
Commit: d45c72c722f74781510f138282abdd2774a84b55
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-05-16 11:32:22 -0400
Commit message:

 useEnsemblGenomes in examples and makeTxDbFromBiomart
 
Package: MungeSumstats
Commit: fb9ffb681d2e85e7ebdb13ccfb67aab976a6c431
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2022-05-16 15:40:05 +0100
Commit message:

 fix R CMD Rd2pdf error
 
Package: DExMA
Commit: e1ccbb83e12c8a56455bc9fae35bf22df4eac64c
Author: Juananvg <juanantoniovillatorogarcia@gmail.com>
Date: 2022-05-16 14:05:26 +0200
Commit message:

 Removing seeCov function
 
Package: DExMA
Commit: b687264582d04194426f113af798defad2c0c287
Author: Juananvg <juanantoniovillatorogarcia@gmail.com>
Date: 2022-05-16 14:04:23 +0200
Commit message:

 Functions improvement and ACAT method added
 
Package: VAExprs
Commit: 1d0bdf4606e2649534c086e953ada31962a2a265
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2022-05-16 20:35:58 +0900
Commit message:

 update
 
Package: VAExprs
Commit: a0af6c204a7359455e3751329152550c282701e2
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2022-05-16 20:31:49 +0900
Commit message:

 update
 
Package: miaSim
Commit: 2a679346629042ed98cb76be96a52514393b0769
Author: YagmurSimsekk <yagmur.simsek@hsrw.org>
Date: 2022-05-16 13:50:32 +0300
Commit message:

 changes
 
Package: miaSim
Commit: 4fc249a942ba27bc98651144b83ea7b80dd365fe
Author: YagmurSimsekk <yagmur.simsek@hsrw.org>
Date: 2022-05-16 10:47:47 +0200
Commit message:

 Merge pull request #32 from microbiome/devel

matrix to assay 
Package: miaSim
Commit: 1c3007ed27e2651b14d03bbd21f84aa267465a52
Author: YagmurSimsekk <yagmur.simsek@hsrw.org>
Date: 2022-03-31 01:12:00 +0545
Commit message:

 input change
 
Package: miaSim
Commit: 9065eae4ae36d02394c3fa48d1b192e274d32648
Author: YagmurSimsekk <yagmur.simsek@hsrw.org>
Date: 2022-03-31 01:01:32 +0545
Commit message:

 vignette fix 2
 
Package: miaSim
Commit: 32d109d9fbee966b6fb75ba0c8b1d5a12749aa5d
Author: YagmurSimsekk <yagmur.simsek@hsrw.org>
Date: 2022-03-31 00:37:22 +0545
Commit message:

 vignette fix
 
Package: miaSim
Commit: d75f6de9a64339d2bdf456e5e78e9eccf552a624
Author: YagmurSimsekk <yagmur.simsek@hsrw.org>
Date: 2022-03-30 23:52:28 +0545
Commit message:

 vignette
 
Package: miaSim
Commit: 343332e38b91a8e3140e9771b593e1a41ebac876
Author: YagmurSimsekk <yagmur.simsek@hsrw.org>
Date: 2022-03-30 23:06:11 +0545
Commit message:

 matrix to assay
 
Package: miaSim
Commit: b7e998347a4071132937cb2298651ff67dd93f2c
Author: Leo Lahti <leo.lahti@iki.fi>
Date: 2022-03-29 20:28:49 +0300
Commit message:

 Update miaSim.Rmd 
Package: ExpressionAtlas
Commit: a1060780ddc60b4ea81c52c465bb958613edfcc3
Author: Pedro Madrigal <8195212+pmb59@users.noreply.github.com>
Date: 2022-05-16 10:29:53 +0100
Commit message:

 improve level of strictness when comparing a computation to a reference value in the tests (#10)

* Update DESCRIPTION

* Update test_functions.R 
Package: stJoincount
Commit: afae8a4cce04b7f7347a43f5565e2105ec3409b0
Author: Nina-Song <songjiar@usc.edu>
Date: 2022-05-15 23:38:09 -0700
Commit message:

 fixed merge issues
 
Package: stJoincount
Commit: 17d34b17ee9c99c198e18cc04770d0ddc3cf8092
Author: Nina-Song <songjiar@usc.edu>
Date: 2022-05-15 23:28:57 -0700
Commit message:

 merge remote
 
Package: stJoincount
Commit: 72e4f03bc1a0cd82cd2c8e6c3ecf814f3794c27c
Author: Nina-Song <songjiar@usc.edu>
Date: 2022-05-15 23:24:10 -0700
Commit message:

 fixed issues for local merge
 
Package: stJoincount
Commit: 19f0e1f83951439ee1ead824c87c5a9582926bd3
Author: Nina-Song <songjiar@usc.edu>
Date: 2022-05-15 23:19:34 -0700
Commit message:

 merged
 
Package: stJoincount
Commit: 63eaf2dccf74b964a300d21205e02b047622bc2a
Author: Nina-Song <songjiar@usc.edu>
Date: 2022-05-15 23:10:06 -0700
Commit message:

 First try
 
Package: stJoincount
Commit: 6a8292349b6fe3e1889f95b9c0f3150768d810c9
Author: Nina-Song <songjiar@usc.edu>
Date: 2022-05-15 23:06:56 -0700
Commit message:

 First try
 
Package: stJoincount
Commit: 10f837a70c084e2f955dfa4e258fd3880a54ef0b
Author: rania-bassi <104520420+rania-bassi@users.noreply.github.com>
Date: 2022-05-11 10:22:45 -0700
Commit message:

 Update README.md 
Package: stJoincount
Commit: 228c280a74fe7ee39ea5417a3524cdfd3dbb22b8
Author: Nina-Song <69836560+Nina-Song@users.noreply.github.com>
Date: 2022-05-11 09:36:37 -0700
Commit message:

 Merge pull request #5 from Nina-Song/rania-bassi-readme-edits

Update README.md 
Package: stJoincount
Commit: 84b4ac9953acfc27814fc9139efcc54ee7f1cb36
Author: rania-bassi <104520420+rania-bassi@users.noreply.github.com>
Date: 2022-05-10 15:12:57 -0700
Commit message:

 Update README.md 
Package: stJoincount
Commit: c85574e87922ea6cbad67196c3cdc57c6bc165f2
Author: Nina-Song <songjiar@usc.edu>
Date: 2022-05-10 00:44:28 -0700
Commit message:

 updating for bioC requirement
 
Package: stJoincount
Commit: 240e78f75b88ec67d75dce267451a6b77abcf300
Author: Nina-Song <69836560+Nina-Song@users.noreply.github.com>
Date: 2022-05-03 15:23:17 -0700
Commit message:

 Update README.md 
Package: stJoincount
Commit: ea6e669a757cf7cc5391f70e78e781975f396b5b
Author: Nina-Song <69836560+Nina-Song@users.noreply.github.com>
Date: 2022-05-03 09:38:55 -0700
Commit message:

 Update stJoincount-vignette.Rmd 
Package: stJoincount
Commit: d0fdee8abc966112eb3ca7f3b14a5d2e5fec154f
Author: Nina-Song <69836560+Nina-Song@users.noreply.github.com>
Date: 2022-05-03 09:27:42 -0700
Commit message:

 Update NEWS.md 
Package: stJoincount
Commit: c6ac6c9452c707bfe4070e2cde5ff5d2fa4d384f
Author: Nina-Song <69836560+Nina-Song@users.noreply.github.com>
Date: 2022-05-03 01:09:13 -0700
Commit message:

 Update DESCRIPTION 
Package: stJoincount
Commit: 6332bcc5b3e40f12f1535271291fe5f22dec9cc7
Author: Nina-Song <69836560+Nina-Song@users.noreply.github.com>
Date: 2022-05-03 01:02:23 -0700
Commit message:

 Update DESCRIPTION 
Package: stJoincount
Commit: e572aab79622fb4e4fd2ad1ae0b8ac785ea1fc5e
Author: Nina-Song <69836560+Nina-Song@users.noreply.github.com>
Date: 2022-05-03 01:00:57 -0700
Commit message:

 Update DESCRIPTION 
Package: stJoincount
Commit: b42fdba26ce268c79d3dc4fb67db8f7aaa71a3bc
Author: Nina-Song <69836560+Nina-Song@users.noreply.github.com>
Date: 2022-05-03 00:25:39 -0700
Commit message:

 Update DESCRIPTION 
Package: stJoincount
Commit: 44eb0d1b261ff4d89dbefb3ddb406416515dda09
Author: Nina-Song <69836560+Nina-Song@users.noreply.github.com>
Date: 2022-05-03 00:22:24 -0700
Commit message:

 Update README.md 
Package: stJoincount
Commit: 9e0543370a68d9e28a169c30e4f90e174201c889
Author: Nina-Song <69836560+Nina-Song@users.noreply.github.com>
Date: 2022-05-03 00:19:35 -0700
Commit message:

 Update README.md 
Package: stJoincount
Commit: 0438c9fbaa7866b64e7b1f2059cb7e26102da816
Author: Nina-Song <songjiar@usc.edu>
Date: 2022-05-02 23:32:11 -0700
Commit message:

 test2
 
Package: stJoincount
Commit: 931ac26b7a19a35320021f47789799aa7ea103a0
Author: Nina-Song <songjiar@usc.edu>
Date: 2022-05-02 23:25:54 -0700
Commit message:

 adding examples for README
 
Package: monaLisa
Commit: 189e345ba71fcf2cdeae094a283b1cdc70e954de
Author: Michael Stadler <stadler.michael@gmail.com>
Date: 2022-05-16 07:59:53 +0200
Commit message:

 Merge pull request #59 from fmicompbio/bioc-actions

Use Bioc actions, change to devel 
Package: monaLisa
Commit: c4b9b5b984429bb65c25d3bc3c60172d85c922eb
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2022-05-13 13:47:55 +0200
Commit message:

 Update citation text version
 
Package: monaLisa
Commit: c0f3f5e21be05d4fff2d34803961d93332c9d810
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2022-05-13 13:42:59 +0200
Commit message:

 Update citation details
 
Package: monaLisa
Commit: 4663d2239a5962f7c7e25ac10ec23b8fb40ce494
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2022-05-13 13:14:30 +0200
Commit message:

 Use Bioc actions, change to devel
 
Package: exomePeak2
Commit: 330d8d8527fc6ed0f3664ccbe0280a8aef3c8760
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-16 12:14:31 +0800
Commit message:

 Update Vignette_V_2.00.Rmd
 
Package: exomePeak2
Commit: 956d1c5c7e324dd47800d8d15ba74d7e34cf24a8
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-16 12:04:45 +0800
Commit message:

 Update Vignette_V_2.00.Rmd
 
Package: exomePeak2
Commit: f0e6c36ee802628d55a802eec2ba263deb9eeb27
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-16 12:01:48 +0800
Commit message:

 Update Vignette_V_2.00.Rmd
 
Package: exomePeak2
Commit: 5af7ca238b36beb5011d56b21fbd7022038fd3e4
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-16 11:56:59 +0800
Commit message:

 documentation update
 
Package: exomePeak2
Commit: 910a7a11300a70495494cd45156fd70edd821314
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-16 11:40:44 +0800
Commit message:

 fix na values is BED score
 
Package: exomePeak2
Commit: 0f454c325bd902f3b949132e2dc86253dd21ade7
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-13 14:25:00 +0800
Commit message:

 Update Vignette_V_2.00.Rmd
 
Package: exomePeak2
Commit: 4cb1edd2d7cd8c1a0470976b493a96f4302cec35
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-13 14:22:31 +0800
Commit message:

 Update Vignette_V_2.00.Rmd
 
Package: exomePeak2
Commit: 48c4bb23dbc537f4a8a5a4a7a1addd49bb82974c
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-13 13:47:37 +0800
Commit message:

 Update Vignette_V_2.00.Rmd
 
Package: exomePeak2
Commit: 048f607465efbd6bc3f97eec002dbd07b65e566d
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-13 13:45:51 +0800
Commit message:

 Update Vignette_V_2.00.Rmd
 
Package: exomePeak2
Commit: b6c419f686ca781b7f6f3ea72ced93cb827eed2c
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-13 13:45:02 +0800
Commit message:

 Update Vignette_V_2.00.Rmd
 
Package: exomePeak2
Commit: 5de9aaea7f385686445c1003aa1f852579958e87
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-13 13:40:26 +0800
Commit message:

 Update Vignette_V_2.00.Rmd
 
Package: exomePeak2
Commit: b8eba648ed8ba54204018407d5f15eb0bc1c4dcd
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-13 13:38:49 +0800
Commit message:

 Update Vignette_V_2.00.Rmd
 
Package: exomePeak2
Commit: dd63d68f08baf0980d03bc2f09ff5707421d7b31
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-13 13:35:55 +0800
Commit message:

 Update Vignette_V_2.00.Rmd
 
Package: exomePeak2
Commit: f64806af4a8d5fbb2f55f7a8ebb8a5a6202b9762
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-13 13:31:39 +0800
Commit message:

 Update Vignette_V_2.00.Rmd
 
Package: exomePeak2
Commit: 4309dc8143efcd9ddd1dc999acddce94181f4d05
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-12 22:11:09 +0800
Commit message:

 update document
 
Package: exomePeak2
Commit: 2276b01aefcffdcba0255859716ab09aa3d7ceb5
Author: zw_xjtlu <Zhen.wei10@icloud.com>
Date: 2022-05-07 03:12:16 +0800
Commit message:

 Update exomePeak2.Rd
 
Package: FLAMES
Commit: 3ddad9b50ba6c45d675b21416f8be199dd22f5bd
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2022-05-16 12:37:58 +1000
Commit message:

 Merge branch 'master' of github.com:OliverVoogd/FLAMES
merge windows changes with local
 
Package: FLAMES
Commit: 2a2a405a4731392b90106b9d1c1e537666dfe6c7
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2022-05-16 12:37:03 +1000
Commit message:

 version bump
 
Package: FLAMES
Commit: 247d926837ebcdecad7f8f20cfbefa66978fe51a
Author: Oliver Voogd <51314988+OliverVoogd@users.noreply.github.com>
Date: 2022-05-13 19:29:49 +1000
Commit message:

 updated makevars.win to build src/ subfolders
 
Package: FLAMES
Commit: cc4e611ed5721a80b1f8932957260cbd0c89963e
Author: Oliver Voogd <51314988+OliverVoogd@users.noreply.github.com>
Date: 2022-05-13 19:03:47 +1000
Commit message:

 minor typos
 
Package: Rsubread
Commit: 6dfe5348b71726052eee4585b613af117d5efc21
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2022-05-16 12:06:35 +1000
Commit message:

 Fixed a bug in cellCounts about deleting a temporary file in Windows. A new version was released.
 
Package: ccImpute
Commit: a9758b93b8711bdb203e601aaab9809c153db36b
Author: Marcin Malec <mamalec@iu.edu>
Date: 2022-05-15 14:31:44 -0400
Commit message:

 Change the lineq solver
 
Package: fastreeR
Commit: 78fa5f8fb1af1a7f8e2c6b1e22ebe4b3ba4be44a
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2022-05-15 20:27:24 +0200
Commit message:

 Update possibly corrupted samples.vcf.gz
 
Package: chimeraviz
Commit: 79c6fbc93c08689cf2d9680bcadea765a8bb40a9
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2022-05-15 19:40:54 +0200
Commit message:

 Add citation
 
Package: cfDNAPro
Commit: 801d60c5225d1b609b99699dd8f4266f77ecc80e
Author: haichao <wanghaichao2014@gmail.com>
Date: 2022-05-15 18:27:41 +0100
Commit message:

 major updates: added curated readBam function

and some internal functions 
Package: STexampleData
Commit: d0a38abfbc54467c3d138f865347a2efad692c9b
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-15 12:39:54 -0400
Commit message:

 version
 
Package: STexampleData
Commit: ffc818ae809ba05e28e28ba2ab97cc201260d3aa
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2022-05-15 12:39:41 -0400
Commit message:

 update EHub IDs in vignette
 
Package: limma
Commit: 5c64b4c640cc80bffb9859e92a9b29cab10ffda0
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2022-05-15 11:31:06 +1000
Commit message:

 limma 3.53.2

- lmFit() now checks explicitly for NAs in the design matrix.
 
Package: imageHTS
Commit: a04668cbae7b5138e141b6a6b69070340e46f7f1
Author: Joseph Barry <jbarry@alnylam.com>
Date: 2022-05-14 14:15:48 -0400
Commit message:

 remote query in vignette not performed to avoid error on subset of servers
 
Package: STRINGdb
Commit: 9605acc4a3965baa8b5b975c91cb57336d650167
Author: Damian Szklarczyk <damian.szk@gmail.com>
Date: 2022-05-14 15:18:19 +0200
Commit message:

 bugfix: comma added
 
Package: goSorensen
Commit: 42b8b6d4d56fd9b3ce56b2d61f59c69b1423a008
Author: Pablo Flores <pablojfm1988@gmail.com>
Date: 2022-05-13 08:07:56 -0500
Commit message:

 changes
 
Package: SNPRelate
Commit: 614483611147a7743ecc7a8033628e373b9bbc65
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2022-05-13 16:29:39 -0500
Commit message:

 fix a portable issue
 
Package: gemma.R
Commit: 34768b387f9a45192bebf94b8e66bee1e68528b5
Author: yavyx <javiercastilloar@gmail.com>
Date: 2022-05-13 13:37:54 -0700
Commit message:

 bumped to version 0.99.4
 
Package: gemma.R
Commit: d4e573e85c237e7bfacee6e1faa819ed411ebc01
Author: yavyx <javiercastilloar@gmail.com>
Date: 2022-05-13 13:31:46 -0700
Commit message:

 made Ogan maintainer
 
Package: gemma.R
Commit: 5720d496e6143ef2efbfa8cf228d53c9822da7c9
Author: yavyx <javiercastilloar@gmail.com>
Date: 2022-05-11 17:28:19 -0700
Commit message:

 Merge branch 'master' of github.com:PavlidisLab/gemma.R
 
Package: gemma.R
Commit: a231c56dcb65b53638195463bfe04e15b09a8f99
Author: B. Ogan Mancarcı <ogan.mancarcii@gmail.com>
Date: 2022-05-10 15:33:48 -0700
Commit message:

 Merge pull request #21 from oganm/persistent_cache

persistent caching with memoise 
Package: gemma.R
Commit: d8847f5d814d0603ad366c39814566111c0a4cab
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2022-05-10 15:25:57 -0700
Commit message:

 test fix
 
Package: gemma.R
Commit: 39460774451297b300b28d629fad39a2fa1ceabf
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2022-05-10 15:25:25 -0700
Commit message:

 test fix
 
Package: gemma.R
Commit: e3fae4155c2ca96918436c304b8676592f156092
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2022-05-10 15:21:10 -0700
Commit message:

 minor
 
Package: gemma.R
Commit: f2291c9d4cf00eb75ad60cf56e2cfbe6736c9f6d
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2022-05-10 15:19:07 -0700
Commit message:

 vignette building touches
 
Package: gemma.R
Commit: d2ce503b01474ed70c6c23cf02d082d41ad99139
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2022-05-10 15:11:22 -0700
Commit message:

 add caching details to the vignette
 
Package: gemma.R
Commit: 1de6b0ee7524c36b10e73f6b5e34cef8f2a58300
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2022-05-10 14:59:53 -0700
Commit message:

 memoisation test
 
Package: gemma.R
Commit: 925b8166d16fb86b9baeb67ce5dff2a88ff22b8e
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2022-05-10 14:51:47 -0700
Commit message:

 force cache creation
 
Package: gemma.R
Commit: 28f641f43d8107c05948fb2abfe005cf05f9d20f
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2022-05-04 14:44:44 -0700
Commit message:

 replace requirement
 
Package: gemma.R
Commit: 9e6ffee4fb782a91ece2e045f50ecca2e0826f3a
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2022-05-04 14:43:21 -0700
Commit message:

 obey https://contributions.bioconductor.org/data.html#other-data
 
Package: gemma.R
Commit: eb4d70b5b6d2511c04599195a41d142d949fab26
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2022-05-04 14:27:13 -0700
Commit message:

 new dependency
 
Package: gemma.R
Commit: b1a2507668652ca89a8c40c6af81a2cb036c4eaf
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2022-05-04 14:15:45 -0700
Commit message:

 persistent caching with memoise
 
Package: OSCA.basic
Commit: bdde7e5c75d904e2cefe53f1bebf3747a631dfb1
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-05-13 13:26:04 -0700
Commit message:

 Depends on package mbkmeans

mbkmeans is needed for the call to

  scran::clusterCells(..., BLUSPARAM=MbkmeansParam(...)))
 
Package: DSS
Commit: 91eb17c2542836f79d8446634f3e9ad8dd1b194f
Author: Hao Wu <hao.wu@emory.edu>
Date: 2022-05-13 15:58:12 -0400
Commit message:

 fix parallel computing problem on windows
 
Package: ScreenR
Commit: 46fb449155b7aa01d70dae3fa754b41352db0f5b
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 21:48:00 +0200
Commit message:

 push to github I hope last time
 
Package: ScreenR
Commit: 97fe7de909e285bed595111fe49b90e66c6bdcfc
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 21:39:15 +0200
Commit message:

 .Rd
 
Package: ScreenR
Commit: 48ac62205dce194edd0d05d0b98e68251775f9ba
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 21:37:23 +0200
Commit message:

 riesco a risolvere sto problema dei lower?
 
Package: ScreenR
Commit: 041c5d02ed3d4e7d9f8584da3fbcd637a5d7b7c8
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 21:25:22 +0200
Commit message:

 cose strane
 
Package: cellxgenedp
Commit: 192b76923d16f2a2f32abc3e7a4130f9f16f81c8
Author: Kayla-Morrell <kayla.morrell@roswellpark.org>
Date: 2022-05-13 14:29:34 -0400
Commit message:

 Change to reorder tabs for shiny app

- closes #5
 
Package: TCGAbiolinks
Commit: b1588c7e0709f0f3a1e9ccc1dcd3b70acbe7f055
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2022-05-13 15:03:22 -0400
Commit message:

 Updating
 
Package: AnVILPublish
Commit: 12c54304b265a10d7364d79fb6e99ab32498a369
Author: Kayla-Morrell <kayla.morrell@roswellpark.org>
Date: 2022-05-13 14:14:30 -0400
Commit message:

 Changes for creating both ipynb and rmd notebooks

- add Kayla as ctb
 
Package: ScreenR
Commit: bab7ead83029122728bb71e63c08aef36d70bc1b
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 20:26:15 +0200
Commit message:

 to LOWERCASE
 
Package: ScreenR
Commit: 9fc2c2801eec5ccc2e0cefa098e9d5ba2dbc4c6b
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 20:21:12 +0200
Commit message:

 to lowercase
 
Package: ScreenR
Commit: d2d40f595457c3f2888ada5e685a0b83cf72e838
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 19:52:54 +0200
Commit message:

 new version on bioconductor
 
Package: AnVIL
Commit: f1144eefad218bb59e6c81fbdb83909ba2569605
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-05-13 14:08:33 -0400
Commit message:

 deprecate install() & friends; add Kayla as author

- BiocManager::install() now knows about binary repositories
 
Package: ScreenR
Commit: c9623049f84e702198f744ed60556a866264e844
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 19:40:56 +0200
Commit message:

 t bioo
 
Package: ScreenR
Commit: f0a28cdd5bc46409dad157750b90fc25e4a67bf9
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 19:34:18 +0200
Commit message:

 resolv the bioc error?
 
Package: biscuiteer
Commit: f91db0a86cd873bd39e0a558ef8ecf12cf9fe977
Author: Jacob Morrison <Jacob.Morrison@vai.org>
Date: 2022-05-12 14:19:03 -0400
Commit message:

 Update version and add Suggests BiocStyle
 
Package: biscuiteer
Commit: 8e56c5cb1671e26c3c437da05f0742c9563b79eb
Author: Jacob Morrison <Jacob.Morrison@vai.org>
Date: 2022-05-12 14:18:40 -0400
Commit message:

 fix another edge case or two in readEpibed
 
Package: biscuiteer
Commit: 0b15863746b8d4a4c309ad7bd511b0250d6d1e73
Author: Jacob Morrison <Jacob.Morrison@vai.org>
Date: 2022-05-11 11:31:20 -0400
Commit message:

 Fix RLE ending with letter

When the RLE string ends with a letter (say only 1 base is filtered at
the end of the read), then the inverse.rle function would break. This
catches when this occurs and properly adds a 1 to the lengths vector.
 
Package: biscuiteer
Commit: ad8c3e6833781f49d9376f1f233ac593ad99bebb
Author: Jacob Morrison <Jacob.Morrison@vai.org>
Date: 2022-05-11 10:53:54 -0400
Commit message:

 Fix case where starts match but ends don't

When collapsing to fragments, there is an edge case where the starts
matched, but the ends didn't. If end(r2) > end(r1), then this is still
considered a proper pair. However, if end(r2) < end(r1), then we can
treat this in the same way as if end(r2) == end(r1).
 
Package: MungeSumstats
Commit: 7feb5d53891f4404744c5f498f89968eb04c5ed6
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2022-05-13 18:22:44 +0100
Commit message:

 Push upstream Bioc
 
Package: MungeSumstats
Commit: 4e394c91fcacce4a1302a3e32c282db0ab9242a8
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-13 13:34:20 +0100
Commit message:

 Trigger GHA
 
Package: MungeSumstats
Commit: d914efd7e6cb904105b81355145211710c05c10e
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-13 13:32:52 +0100
Commit message:

 Set version: 1.5.1 [skip ci]
 
Package: MungeSumstats
Commit: 1bd025f23478b587ac5ecd06747e2f557ce26e1d
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-13 13:14:37 +0100
Commit message:

 Merge branch 'master' of https://github.com/neurogenomics/MungeSumstats
 
Package: MungeSumstats
Commit: 42819772724a38b18a21a3e66720dac0923e46f7
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-13 12:31:01 +0100
Commit message:

 Add tilewidth as an option
 
Package: MungeSumstats
Commit: ef92deda2245965d6cd38c35907604e4053422a5
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-10 00:40:40 +0100
Commit message:

 vectorizee RSID preprocessing [skip ci]
 
Package: MungeSumstats
Commit: 734a9d510095cab7a232ebc20fec3e9fbcb9e2c1
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-09 23:28:11 +0100
Commit message:

 Add messages to load_ref_genome_data [skip ci]
 
Package: MungeSumstats
Commit: 319721bd55c2e8fbe3d4e7f1a208a63469142584
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-09 23:18:07 +0100
Commit message:

 Add messages to load_ref_genome_data [skip ci]
 
Package: MungeSumstats
Commit: 93f9376687348e3ded22b7dc8127d91dec457418
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-09 20:45:53 +0100
Commit message:

 Add messages to load_ref_genome_data [skip ci]
 
Package: MungeSumstats
Commit: 6d6d9c4f3e13bb8509a8d16a4ed6bbef4790f959
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-09 20:45:39 +0100
Commit message:

 Add messages to load_ref_genome_data
 
Package: MungeSumstats
Commit: 3947603692f6841e6f19eb407706571dd07a5bb6
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-09 19:25:01 +0100
Commit message:

 make n_variants an integer [skip ci]
 
Package: MungeSumstats
Commit: 6a73322b9a8e3f2a85f10019af373d7c9de1cce9
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-09 18:31:20 +0100
Commit message:

 Make Rsamtools a Suggest
 
Package: MungeSumstats
Commit: 335cd54247ed97ab0fa8d11bb27ddb74c70042b5
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-09 18:11:34 +0100
Commit message:

 Push fixes to index_vcf
 
Package: MungeSumstats
Commit: 9b308c36431a490aa0f6bd24fce95c66f409d030
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-07 16:46:29 +0100
Commit message:

 Fix is_tabix
 
Package: MungeSumstats
Commit: f4e038157a31e4f3f0b75a227d272cc5bf95bef4
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-06 22:43:41 +0100
Commit message:

 Dont run remote examples in read_vcf examples
 
Package: MungeSumstats
Commit: 7ee12adf1fa756937aaec704d9328b0e35b7da8c
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-06 22:02:40 +0100
Commit message:

 Fix tests
 
Package: MungeSumstats
Commit: 82d66ce84dd502cd36f03702a1db524b256fffd9
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-06 20:37:09 +0100
Commit message:

 Add backup downloader methods
 
Package: MungeSumstats
Commit: 10884d84fb8d4c45b5a508eab8a3541818aa400d
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-06 20:04:36 +0100
Commit message:

 Omit remote example in read_vcf due to issues on Windows
 
Package: MungeSumstats
Commit: 8408018105c007a7e692a55aa6726d394dd80fc7
Author: bschilder <brian_schilder@alumni.brown.edu>
Date: 2022-05-06 18:07:28 +0000
Commit message:

 Remove defunct functions
 
Package: MungeSumstats
Commit: bb17edbc0f1561f84ff1cb330e64d7a7e9f723b0
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-06 16:58:33 +0100
Commit message:

 Parallelise and optimise read_vcf. Improve vcf2df
 
Package: MungeSumstats
Commit: fc96f1570c378d408088ed02983c69c538cedf31
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-06 13:42:54 +0100
Commit message:

 Parallelize read_vcf
 
Package: MungeSumstats
Commit: d33ed4bef4a8133c42c5a50307f18238d2d4107c
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2022-05-05 11:58:51 +0100
Commit message:

 Bug Fix: Reading in VCFs
 
Package: MungeSumstats
Commit: 468739ce14f719939003ba07e5f3026fc9709ebc
Author: bschilder <brian_schilder@alumni.brown.edu>
Date: 2022-05-04 12:30:29 +0000
Commit message:

 Merge remote
 
Package: MungeSumstats
Commit: b11052fe130d58aaf74a0e128f1f542b57b07887
Author: bschilder <brian_schilder@alumni.brown.edu>
Date: 2022-05-04 12:28:25 +0000
Commit message:

 Rebase with master after all GHA Checks passed 2
 
Package: MungeSumstats
Commit: f471d31cad59ef814b2df9a405290c32faf1dc28
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-03 16:37:27 +0100
Commit message:

 Fix read_vcf
 
Package: MungeSumstats
Commit: 78db803ea3140dc4b8dbff0305c3522a714a5848
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-03 16:30:46 +0100
Commit message:

 Fix read_vcf
 
Package: MungeSumstats
Commit: 0abdf19e3365d03847977ed0f8a189be78565162
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2022-05-03 13:05:57 +0100
Commit message:

 Rebased  using changes made to master
 
Package: ScreenR
Commit: 5e37b7267633063fdca0907c16de205747566329
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 19:10:04 +0200
Commit message:

 push to bioc
 
Package: ScreenR
Commit: af0a2c43d570ddb48d083a8b07b6d13938b9e13c
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 19:01:16 +0200
Commit message:

 removed github old
 
Package: ScreenR
Commit: ad1656569cda7a595b28228042f03fba25144b1c
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 17:39:35 +0200
Commit message:

 pushed to bioconductor
 
Package: ScreenR
Commit: c07c022f12400d8f8a32f760802b12bed9e4ecd4
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 11:50:23 +0200
Commit message:

 credo ho risolto il problema
 
Package: ScreenR
Commit: 2622c350565dff68475828daa69fbf8c5c8948d1
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 12:13:56 +0200
Commit message:

 readme
 
Package: ScreenR
Commit: 0857b7554ea7f6a8a40dd571e67891e6c99c1f6f
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 12:12:09 +0200
Commit message:

 dai salvami
 
Package: ScreenR
Commit: fb0cc84e95850ce27cdf7800328faa941221d518
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-13 10:45:23 +0200
Commit message:

 updated vignette
 
Package: ScreenR
Commit: cc837cc9efb0d3ba9e64c52e2a8a5853a819c28c
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-12 16:15:39 +0200
Commit message:

 all works
 
Package: ScreenR
Commit: 7fa1a3f50d377f1fa7ea99928c03bf3be4063324
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-12 15:47:09 +0200
Commit message:

 mi escono le funzion vecchie
 
Package: ScreenR
Commit: a5f57c34db71490a5b0a733d0d84befe404f8eff
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-11 09:43:39 +0200
Commit message:

 correct the spell of some word
 
Package: ScreenR
Commit: 1e70fedfb9a17a6d74f2f81d5b600f86b296921a
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-11 09:12:15 +0200
Commit message:

 codecov.yml cche git rompe23
 
Package: ScreenR
Commit: d5599b03a82a86aa071b50b082c5839fb9b8442b
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-10 20:35:17 +0200
Commit message:

 boh
 
Package: ScreenR
Commit: 5402517e304ff67b6ae2a9cbddff68432271cf66
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-10 20:30:05 +0200
Commit message:

 built site
 
Package: ScreenR
Commit: 14b36998ffbd263929b2120d2c37ea029f214d6c
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-10 20:24:49 +0200
Commit message:

 added new function fo filter the row which are all zeros, solved some warning with this fuction
 
Package: ScreenR
Commit: 366271254b05679bedc0c255513650f0f978910c
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-05-10 11:42:15 +0200
Commit message:

 other update
 
Package: ScreenR
Commit: 95e2b5b0659687183dbc320f19aa9cd8c2a2a289
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-29 16:07:02 +0200
Commit message:

 removed unused function
 
Package: ScreenR
Commit: 40f2b7538970500220f5ff3df1fec3c3b424eb4b
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-25 15:39:56 +0200
Commit message:

 Finally we have the OOP programming
 
Package: ScreenR
Commit: b63fe038926fe3b3b75134be232d6960b43df503
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-24 19:14:38 +0200
Commit message:

 Other issue
 
Package: ScreenR
Commit: 4f58def29c2a4634f2e0b7491af70cbf99650443
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-24 18:12:04 +0200
Commit message:

 addressing other issue
 
Package: ScreenR
Commit: b928b7d7ed827a9847fac83694d0865d8809a4cd
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-23 20:12:48 +0200
Commit message:

 addressed reviews issue
 
Package: ScreenR
Commit: 6a4e15f75a3078da43f39fc55004a8fcfb715a4e
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-22 12:53:01 +0200
Commit message:

 fixed NAMESPACE
 
Package: ScreenR
Commit: 8b97fcd7d1b8b9f493df81f41037c415526d1159
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-19 11:09:38 +0200
Commit message:

 sito finally
 
Package: ScreenR
Commit: 1b529d2af11c98a394fed3197b85e40efe08e64e
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-19 10:06:40 +0200
Commit message:

 tolto backgrund pipeline e ora sito funziona di nuovo
 
Package: ScreenR
Commit: ae66586692a37593b4d08bb621bf1c4e50ab4b8d
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-19 09:13:23 +0200
Commit message:

 sto sito mi sta facendo impazzire
 
Package: ScreenR
Commit: 40d5d3b0a0e6b52e7b039c57dd69e8a41a869e8e
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-18 10:14:49 +0200
Commit message:

 ci provo
 
Package: ScreenR
Commit: b07960522f09ffa87b3927a55f6143bde1dd7d95
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-18 10:05:11 +0200
Commit message:

 docs/pkgdown.css
 
Package: ScreenR
Commit: ff53ad9ffe4e36df7039a6a0eb7e8a940b3ffe44
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-18 10:01:02 +0200
Commit message:

 css pkgdown
 
Package: ScreenR
Commit: dd9602d3f251c4f5e2a9c0471733795402bd72f8
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-17 21:41:31 +0200
Commit message:

 Set theme jekyll-theme-cayman 
Package: ScreenR
Commit: 6fe4b093cfa06379a243e0366473a06676fad1aa
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-17 21:39:56 +0200
Commit message:

 provo ancora il sito
 
Package: ScreenR
Commit: cc59489c0e43e979aa93d68daaa38f29136f4b34
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-17 21:27:32 +0200
Commit message:

 ho riprovato a rifare il sito
 
Package: ScreenR
Commit: 646e903a08bf80a73e2b05947138a951a7ced3d1
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-17 21:16:26 +0200
Commit message:

 riaggiunti file sito
 
Package: ScreenR
Commit: 705f463c969495c0cec577c7be512fceabe777ec
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-17 20:57:40 +0200
Commit message:

 last commit 1704
 
Package: ScreenR
Commit: b67088a6af507a8effc4a26c7d7b3ebdd606e000
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-17 20:39:59 +0200
Commit message:

  removed .github/SUPPORT.md
 
Package: ScreenR
Commit: 6acdc23357fb750b6bf8f0bc1cfe1889e4215e0b
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-17 20:25:24 +0200
Commit message:

 aa
 
Package: ScreenR
Commit: c92433ec621891a65ed136c947f43f3491d6f554
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-17 20:09:28 +0200
Commit message:

 site ok?
 
Package: ScreenR
Commit: b8cec545f1600f0fafd022b78ef49b903d35ce62
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-17 19:50:34 +0200
Commit message:

 spero sia risolto
 
Package: ScreenR
Commit: fecb96194b7152a6dfd77aba63055965c9d1788e
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-17 19:33:40 +0200
Commit message:

 problem with site
 
Package: ScreenR
Commit: d157a13512a292b3a45be3952666b7ef487519d0
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-17 19:07:38 +0200
Commit message:

 used styler
 
Package: ScreenR
Commit: 6ca88b001b83939b2bcf920af3e114c1f13c08d0
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-17 17:56:43 +0200
Commit message:

 scoperto biocthis
 
Package: ScreenR
Commit: e655ff4964845cca0512101a499975f580a40ef9
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-15 16:51:15 +0200
Commit message:

 Removed lazy data
 
Package: ScreenR
Commit: ad6a582ca867a38bcba04b2e65be45a82486a9d4
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-15 16:29:18 +0200
Commit message:

 Start the revision process modified plot_MDS function removing tolto check_overlap = TRUE and added show_elements = TRUE to plot_common
 
Package: ScreenR
Commit: 860275eaddab4b6ab66d8f7628053aa86ed455f4
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-13 11:02:05 +0200
Commit message:

 added new logo
 
Package: ScreenR
Commit: d5a4f7558712fa509f494a70dd8f49c134285642
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-12 22:05:42 +0200
Commit message:

 Update README.md 
Package: ScreenR
Commit: f75bdf3211cbd105e330f5bcd335398a3336dbea
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-12 22:05:01 +0200
Commit message:

 modified site
 
Package: ScreenR
Commit: fcfec19bb1ab2225538367081043fb9d26fe90b1
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-12 21:21:12 +0200
Commit message:

 aggiunte github action
 
Package: ScreenR
Commit: 35afaf59abc78f761baabfa0d986460ad87d2523
Author: Emanuel Soda <emanuelsoda@gmail.com>
Date: 2022-04-12 17:38:16 +0200
Commit message:

 tried some blog stuff
 
Package: ATACCoGAPS
Commit: dc8ebf00e8fb7dd5bd4dc32922bdf00666e573d1
Author: rossinerbe <rossinerbe@gmail.com>
Date: 2022-05-13 12:46:15 -0400
Commit message:

 changing version
 
Package: ATACCoGAPS
Commit: 6ea5a7aa8ec8f0ba918399a1606cd8e41a28d19e
Author: rossinerbe <rossinerbe@gmail.com>
Date: 2022-05-13 12:45:14 -0400
Commit message:

 fixing minor docs issue
 
Package: VariantAnnotation
Commit: f1f06c68eadc7180dba1a1c9e422c3d1583436f5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-05-13 09:28:31 -0700
Commit message:

 Version bump

Only to trigger rebuilt and propagation of new Windows binary statically
linked to Rhtslib 1.99.3.
 
Package: Rsamtools
Commit: 2b7b0187f03e7b78565459dad5f1458fdcbc73c2
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-05-13 09:24:27 -0700
Commit message:

 Version bump

Only to trigger rebuilt and propagation of new Windows binary statically
linked to Rhtslib 1.99.3.
 
Package: ATACCoGAPS
Commit: 4ed7181f1bdd393a14c791d9741fb3a93a340a4c
Author: rossinerbe <rossinerbe@gmail.com>
Date: 2022-05-13 11:52:31 -0400
Commit message:

 fixing data docs for bioccheck
 
Package: OSCA.multisample
Commit: ded0728be264f03281197747a8a3ac4cc2e0d859
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-05-13 08:13:21 -0700
Commit message:

 update Date
 
Package: OSCA.multisample
Commit: bf25518863031235493d3341689347c98a375067
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-05-13 08:03:41 -0700
Commit message:

 Cluster "1" became cluster "10" after a change in igraph::cluster_louvain()
 
Package: DiffBind
Commit: 6fd31d90a938bc198de7724d6a6acc86fe95080c
Author: Randall Stark <rory.stark@cruk.cam.ac.uk>
Date: 2022-05-13 14:08:58 +0100
Commit message:

 Rhtslib patch, vignette update, roll up bugfix
 
Package: GreyListChIP
Commit: d422095aedd1474292c66e2dc900bc60328e6781
Author: Randall Stark <rory.stark@cruk.cam.ac.uk>
Date: 2022-05-13 13:09:00 +0100
Commit message:

 update NEWS with correct version
 
Package: CNORfeeder
Commit: fa46ebe772b64d62f4c8cf16f37b5fa153d78ece
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-05-13 07:16:53 -0400
Commit message:

 Undeprecate
 
Package: ExpressionAtlas
Commit: 71022eddaa1a5774f07da1032ebded40878a87c7
Author: Pedro Madrigal <8195212+pmb59@users.noreply.github.com>
Date: 2022-05-13 11:00:55 +0100
Commit message:

 add RCurl dependency (#8)

 
Package: REMP
Commit: 9c6b097a51249ed50d3bbe8932f17dacfa971c8e
Author: Yinan Zheng <y-zheng@northwestern.edu>
Date: 2022-05-13 04:55:06 -0500
Commit message:

 REMP 1.21.1 updates
 
Package: scuttle
Commit: d20d1746076753851317ef164ca579cc5a49910c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-05-12 23:26:25 -0700
Commit message:

 Missed a spot for the new Fortran behavior.
 
Package: scuttle
Commit: 6910cfce71916ece4ee13a0153d95f75bd58331b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-05-09 23:42:15 -0700
Commit message:

 Update Lapack calls for new Fortran interface.
 
Package: ggmsa
Commit: 7ac5b0767266bb80ed170c49e1d45fc7d06883c2
Author: Lang Chau <nyzhoulang@163.com>
Date: 2022-05-13 12:32:42 +0800
Commit message:

 update Startup Message
 
Package: ggmsa
Commit: f4efb1ee2afd01d4d10ed271a9e5fa7906866ad0
Author: Lang Chau <nyzhoulang@163.com>
Date: 2022-05-13 12:08:59 +0800
Commit message:

 update version following bioc 3.15
 
Package: ggmsa
Commit: 86a14e58ac2d905d0d6e734bc2875a5760aaafac
Author: Lang Chau <nyzhoulang@163.com>
Date: 2022-05-13 12:01:26 +0800
Commit message:

 merge upstream
 
Package: ggmsa
Commit: 67761f8429fe10cd3a400301731b88b1bda79ca9
Author: Lang Chau <nyzhoulang@163.com>
Date: 2022-05-06 17:17:04 +0800
Commit message:

 added a new feature: assigned color according to position
 
Package: ggmsa
Commit: d17c0f70b17f0abf3ba8e3192c50043e3a5c4d2c
Author: nyzhoulang <nyzhoulang@163.com>
Date: 2022-04-15 22:18:19 +0800
Commit message:

 update NEWS
 
Package: ggmsa
Commit: 6828a9c0911467a31ad4967743a307b5f52393c3
Author: Lang Chau <nyzhoulang@163.com>
Date: 2022-04-12 21:27:55 +0800
Commit message:

 fixed treeMSA_plot
 
Package: ggmsa
Commit: 76fc554408a50471d3822652c90c93894709572b
Author: Lang Chau <nyzhoulang@163.com>
Date: 2022-04-12 19:57:52 +0800
Commit message:

 Support to hide or show all ancestor sequences
 
Package: ggmsa
Commit: a5338c7952a6ddb35f300d72728d76ed5ed5807a
Author: Lang Chau <nyzhoulang@163.com>
Date: 2022-04-12 13:26:56 +0800
Commit message:

 make treeMSA_plot support vector
 
Package: ggmsa
Commit: 23253d413ce65c9f68eb2bec5ae4d59dcd9743fd
Author: Lang Chau <nyzhoulang@163.com>
Date: 2022-04-10 18:17:31 +0800
Commit message:

 update man/
 
Package: ggmsa
Commit: 63ff794dd89fd487b9a492ff5d921a665ed8d720
Author: Lang Chau <nyzhoulang@163.com>
Date: 2022-04-10 18:04:32 +0800
Commit message:

 fixed abbreviations 'DMS'
 
Package: ggmsa
Commit: 9d0d9c7a26c6547c406c7ae9e12a10c25f2fec54
Author: nyzhoulang <nyzhoulang@163.com>
Date: 2022-04-08 12:55:49 +0800
Commit message:

 export treeMSA_plot
 
Package: ggmsa
Commit: 4ff1aa7b84eed0751b9c87b9d72916f1da199244
Author: nyzhoulang <nyzhoulang@163.com>
Date: 2022-04-08 12:49:38 +0800
Commit message:

 added new function treeMsa_plot()
 
Package: ggmsa
Commit: ba9d28ac1c037cf7b203251ba09d2191abc43d49
Author: nyzhoulang <nyzhoulang@163.com>
Date: 2022-04-07 21:09:23 +0800
Commit message:

 add new functions requested by reviewers
 
Package: Rgraphviz
Commit: 7d88d0653e7ffab08350fb86f65ff4746776ad8a
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2022-05-12 19:06:06 -0400
Commit message:

 resoolved merge conflicts
 
Package: Rgraphviz
Commit: 7e28e59a7f6c2c64b197c13e9d0b7f621e4bcc68
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2022-05-12 19:03:06 -0400
Commit message:

 Merge pull request #17 from hpages/master

Quick fix for compilation error on lconway (macOS Monterey, R 4.2.0) 
Package: Rgraphviz
Commit: 7c5996cdfcfc99ecf0f5ebd3d17849b2e67a97cd
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-05-09 21:36:22 -0700
Commit message:

 Quick fix for compilation error on lconway (macOS Monterey, R 4.2.0)
 
Package: crisprDesign
Commit: e836d1c063f5f076e12946a001c810f6f22a8996
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-05-12 14:57:09 -0700
Commit message:

 removed crisprDesignData dependency
 
Package: ATACCoGAPS
Commit: 454b57fef85231d78a2d84348aea640016a80f3a
Author: rossinerbe <rossinerbe@gmail.com>
Date: 2022-05-12 16:31:35 -0400
Commit message:

 update version
 
Package: ATACCoGAPS
Commit: 896d626d3476b9a33aea55abfe934a4e8c067475
Author: rossinerbe <rossinerbe@gmail.com>
Date: 2022-05-12 16:30:27 -0400
Commit message:

 adding docs for data
 
Package: clusterExperiment
Commit: 1e6a99492f7ac4d720ff9e93e3083d9f393bf0d6
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2022-05-12 11:50:32 -0700
Commit message:

 fix error in barplot
 
Package: clusterExperiment
Commit: 407d14be4ba03a56212d8a45d2118eaf5543b5af
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2022-05-12 11:25:13 -0700
Commit message:

 fix error in subsetting for -1
 
Package: Rhdf5lib
Commit: 415421d7e8a0efbf2d8a439b057aab017b0f3e33
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-05-12 20:11:19 +0200
Commit message:

 Merge pull request #46 from grimbough/rhdf5-issue-109

Fix rhdf5 issue 109 

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