Bioconductor - Packages: GIT Log

Home
Developers
Packages: GIT Log

Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active. The following are the git logs.

GIT Logs

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

This list is also available as an RSS feed (master branch), and RSS feed (release branch)

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

Source Code & Build Reports »

Source code is stored in Git.

Software packages are built and checked nightly. Build reports:

Development Version »

Bioconductor packages under development:

Analysis software packages.
Illustrative experiment data packages

Developer Resources:

GIT Log