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GIT Logs

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

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Package: circRNAprofiler
Commit: 5100cb8ab6e98b37c5a3fe4739b15083c95195f5
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-06-06 13:38:33 +0200
Commit message:

 From Version 1.3.3 to Version 1.3.4
 
Package: circRNAprofiler
Commit: e2ba05bbe4322a8c0a7ef5d43d1630ff5da3e3fe
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-06-06 13:38:05 +0200
Commit message:

 improved code
 
Package: circRNAprofiler
Commit: 73a22e9a77444316fccff59a2bcab765b9cb5b7f
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-06-06 13:36:46 +0200
Commit message:

 updated image data ebicat37 and abicat38 to data ebicat_37 and ebicat_38
 
Package: cn.mops
Commit: 44e77a81d75aa2aa92245fe4e079cbe849464d5e
Author: gpovysil <gpovysil@gmail.com>
Date: 2020-06-06 07:30:17 -0400
Commit message:

 fixed bug

Signed-off-by: gpovysil <gpovysil@gmail.com>
 
Package: seqsetvis
Commit: 6529135d366a474a17006362787fa373ea5debfa
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-06-05 23:49:07 -0400
Commit message:

 v bump 1.9.5
bugfix for strand sensity bam fetch overlapping stranded qgr
added error if qgr id duplicated.
 
Package: PCAtools
Commit: 39b0666ab8561671f34beba0b5f03ca32a906ab6
Author: Kevin Blighe <kblighe@CLINICALBIO.dlink.com>
Date: 2020-06-05 21:18:00 -0300
Commit message:

 Change pairsplot default
 
Package: PCAtools
Commit: a76ab63418a061515895339ccb4aedbb6214952e
Author: Kevin Blighe <23179755+kevinblighe@users.noreply.github.com>
Date: 2020-06-01 13:27:34 -0300
Commit message:

 Merge pull request #22 from LTLA/master

Added draft of random matrix methods for choosing PCs. 
Package: PCAtools
Commit: 98ee8326eb341fc94ba0c6c3259518d7f6e1f7de
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-31 17:49:52 -0700
Commit message:

 Updated NAMESPACE, added documentation.
 
Package: PCAtools
Commit: 98e9e1af7e066794a5b17a8a1340dd3734f63931
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-31 17:48:07 -0700
Commit message:

 Slightly more correct Gavish-Donoho implementation.
Added effective limit on variance to attributes.
 
Package: PCAtools
Commit: fc57bf5460ba6b91d4220c415aac83af8d69cb50
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-31 17:37:40 -0700
Commit message:

 Added draft of random matrix methods for choosing PCs, closes #9.
 
Package: pcaExplorer
Commit: b1fb39d589f19fb9176c782bd8791a20ce20ff89
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-06-06 00:06:50 +0200
Commit message:

 Version bump - 2.15.2, fixed double name
 
Package: pcaExplorer
Commit: 2271daf1a285a47c66c9cf751f0cfd1537f6bab3
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-06-06 00:04:33 +0200
Commit message:

 fixed double naming
 
Package: pcaExplorer
Commit: 5cb37fbea2d75cba74fd4c378d5a81e05c3f4664
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-06-02 12:34:33 +0200
Commit message:

 rerendered docs - last time local
 
Package: pcaExplorer
Commit: e06eea5f3cdb8f9d62b55d4ab1a544745ae0b143
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-06-02 12:19:46 +0200
Commit message:

 removing appveyor continuous integration
 
Package: pcaExplorer
Commit: 8c4566b9f0c9e96975debcf4188c2a8eef8a8613
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2020-06-02 12:09:13 +0200
Commit message:

 removing circleCI continuous integration
 
Package: seqsetvis
Commit: bb2b0a6543fcf6eee06a3f4782aa1c7b9762858d
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-06-05 17:06:25 -0400
Commit message:

 v bump 1.9.4 bugfix - n_region_splits limited to lenght of qgr
 
Package: ggcyto
Commit: cbe0be9dadba3e9bf75466d0b287d1a7c9165054
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-06-05 13:00:36 -0700
Commit message:

 Merge branch 'master' into devel
 
Package: ggcyto
Commit: 2285f3db52551252eab63becab749a579bc9eeb9
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-04-28 16:59:45 -0700
Commit message:

 Merge branch 'ggsave_autoplot'
 
Package: ggcyto
Commit: 6907613d2619b89fa5dbb8b40e4949f355b88e03
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2020-04-27 18:53:41 +0000
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_11 branch
 
Package: ggcyto
Commit: 476a6acd17656f7bb0be70e0d312df40da164b6e
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2020-04-27 18:53:41 +0000
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
 
Package: ggcyto
Commit: 425d2aec40530bb51926af772786e4f23f3b5edd
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-04-23 14:21:13 -0700
Commit message:

 Make ggsave work for ggcyto_GatingLayout objects
 
Package: CytoML
Commit: 6c9cfb561fd44c8dc5cd79d0804be47e87fc5ca1
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-06-05 12:59:52 -0700
Commit message:

 Merge branch 'master' into devel
 
Package: CytoML
Commit: 0cbf349ea528cbe227ec05d559774f01a94fff71
Author: Greg Finak <greg.finak@gmail.com>
Date: 2020-06-04 10:11:34 -0700
Commit message:

 Update README.md 
Package: CytoML
Commit: 030d243167299b725822e76b180fa3b23dfba195
Author: Greg Finak <gfinak@fredhutch.org>
Date: 2020-06-04 09:45:00 -0700
Commit message:

 Merge branch 'master' of github.com:RGLab/cytoml
 
Package: CytoML
Commit: 0b3666b92bcbc830b097600fb9e6c7d92e073917
Author: Greg Finak <gfinak@fredhutch.org>
Date: 2020-06-04 09:44:55 -0700
Commit message:

 update issue template
 
Package: openCyto
Commit: 6664bc01e4fe305cf00dc2e0d144e1598aaaa66e
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-06-05 12:58:38 -0700
Commit message:

 Merge branch 'master' into devel
 
Package: openCyto
Commit: 20bcae7e28376260a28b5d13438793a76dc51aa3
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-06-04 15:14:58 -0700
Commit message:

 Merge branch 'master' of https://github.com/RGLab/openCyto
 
Package: openCyto
Commit: 05aa1946fe67177c41024a25de53f3873a48a3af
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-06-04 15:14:47 -0700
Commit message:

 drop deprecated autostart arg in vignette
 
Package: openCyto
Commit: cd6e409a94bb1cb44497599fe42a504ba91d8db0
Author: Greg Finak <greg.finak@gmail.com>
Date: 2020-06-04 10:11:02 -0700
Commit message:

 Update README.md 
Package: openCyto
Commit: d9058ec67a1d3442e1bf0a9f3e3af8a608d735ae
Author: Greg Finak <greg.finak@gmail.com>
Date: 2020-06-04 10:08:31 -0700
Commit message:

 Update README.md 
Package: openCyto
Commit: fda5091d3ef02829971c91844e64e5b5ba6ac3bf
Author: Greg Finak <gfinak@fredhutch.org>
Date: 2020-06-04 09:40:13 -0700
Commit message:

 update bug report template
 
Package: openCyto
Commit: 9b664d28ef72249d7366ac0606a9df58d3a84994
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-04-30 18:36:39 -0700
Commit message:

 Add support for gate_quad_ methods in templates and gs_add_gating_method
 
Package: openCyto
Commit: 1e5aa13d6dea18618c71673e089915a018a793ef
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2020-04-27 18:37:01 +0000
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_11 branch
 
Package: openCyto
Commit: f2ad074f3a4ef45e69196d1cbf2b8a3fdeb87c6e
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2020-04-27 18:37:01 +0000
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
 
Package: flowWorkspace
Commit: ab021dda86ecd0d56cc54a058db302d6ca4f66ca
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-06-05 12:54:54 -0700
Commit message:

 Merge branch 'master' into devel
 
Package: flowWorkspace
Commit: 7c2d921132113576b2ca08907aab9d4732fccf61
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-06-04 21:22:16 -0700
Commit message:

 document gs_pop_add logical vectors as gates
 
Package: flowWorkspace
Commit: 3a36c31574131ef2433e3de688640bbc04838055
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-06-04 13:30:40 -0700
Commit message:

 add optional 'tmp' argument to convert_legacy_gs to customize the working dir during converting when the default system temp is full
 
Package: flowWorkspace
Commit: e7a3fb936e01f4916abe2c5eb13b0006a240a502
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-06-04 12:09:09 -0700
Commit message:

 guard against segfault for the edge case of empty cytoset
 
Package: flowWorkspace
Commit: 2cb94e5dbfa3fdee5eb30e0174972845a851da9f
Author: Greg Finak <greg.finak@gmail.com>
Date: 2020-06-04 10:10:36 -0700
Commit message:

 Update README.md 
Package: flowWorkspace
Commit: 7252627066a0730b4151f4150a62ecdea9c62b1d
Author: Greg Finak <greg.finak@gmail.com>
Date: 2020-06-04 10:07:44 -0700
Commit message:

 Update README.md 
Package: flowWorkspace
Commit: 3845614f993377dc392908c7526163fc4cde75b5
Author: Greg Finak <gfinak@fredhutch.org>
Date: 2020-06-04 09:43:51 -0700
Commit message:

 Merge branch 'master' of github.com:RGLab/flowWorkspace
 
Package: flowWorkspace
Commit: 274cc1547505fd3c70c3ac374e137708d92b6600
Author: Greg Finak <gfinak@fredhutch.org>
Date: 2020-06-04 09:43:44 -0700
Commit message:

 update issue template
 
Package: flowWorkspace
Commit: f8b11c7e2e09702642a2cb47c4a1649c37c39b00
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-06-03 14:50:22 -0700
Commit message:

 Merge branch 'master' of github.com:RGLab/flowWorkspace
 
Package: flowWorkspace
Commit: 89170e3432a2c05a0371af1391773236c976b856
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-06-03 14:50:17 -0700
Commit message:

 bump
 
Package: flowWorkspace
Commit: b020723ff8d9f937736b1e523cdb166ab1d1cb79
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-06-03 14:49:44 -0700
Commit message:

 add test case for RGLab/cytolib#36
 
Package: flowCore
Commit: bbe5736cc64740e12f274e9ca5387e2f9c874c41
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-06-05 12:53:25 -0700
Commit message:

 Merge branch 'master' into devel
 
Package: flowCore
Commit: 61bdc041375857a24784d6a46d927707c40a7b49
Author: Mike Jiang <wenxin.jiang@gmail.com>
Date: 2020-06-03 20:31:27 -0700
Commit message:

 Merge pull request #190 from itskathylam/patch-1

Update README.md 
Package: flowCore
Commit: 2a70aa83685ba91d56aac34eb85844e43c71d191
Author: Mike Jiang <wenxin.jiang@gmail.com>
Date: 2020-06-03 20:30:20 -0700
Commit message:

 Update README.md 
Package: flowCore
Commit: 9f412c6df8b52c4edb5c81a54c65c429f757dc83
Author: Kathy Lam <itskathylam@gmail.com>
Date: 2020-06-03 17:37:55 -0700
Commit message:

 Update README.md 

"trunk" branch no longer exists; provide an example of using a commit SHA 
Package: flowCore
Commit: 3116d8dc8b174a239520652a8f2b14c6e3dd4683
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-06-02 12:07:37 -0700
Commit message:

 Add decompensate method for compensation object
 
Package: flowCore
Commit: 6739f46cdf976192325133e4191fd7f0d6aa2dad
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-29 14:00:02 -0700
Commit message:

 #189: Make rectangleGate upper bounds inclusive, matching flowWorkspace behavior
 
Package: flowCore
Commit: 933e8fca7a4a5f9600a3109db5d65a4e0e0261e8
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-14 12:04:21 -0700
Commit message:

 populate keywords in flowFrame constructor by write/read FCS routines
 
Package: flowCore
Commit: a81ec1a84f851fc5f0fe4e711d10c68505647aac
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-07 13:26:37 -0700
Commit message:

 update test case. #187
 
Package: flowCore
Commit: 09aac52ffb085bdc20bd40dae3b024fbd85e0fd2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-07 13:24:08 -0700
Commit message:

 Merge branch 'master' of github.com:RGLab/flowCore
 
Package: flowCore
Commit: 654f0c36e61ebc197bd79501761318e174c67cf7
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-07 13:23:41 -0700
Commit message:

 bump the computed(from data) range value for the missing PnR keywords. #187
 
Package: flowCore
Commit: b7e0574ec048e32f5350dcefb5ff434eff602413
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2020-04-27 18:14:14 +0000
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_11 branch
 
Package: flowCore
Commit: a1779b4620824157a8c7c0316799cbaf85f525d6
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2020-04-27 18:14:14 +0000
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
 
Package: flowCore
Commit: 163a4abd8a58cc69c872da99d7d90a828ccf238d
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-04-28 09:06:34 -0700
Commit message:

 pkgdown update after author fix
 
Package: flowCore
Commit: a53292d0d8ed14fc8ba39795583e01651f191d9f
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-04-28 09:02:37 -0700
Commit message:

 Fix author
 
Package: cytolib
Commit: d232ca84e0c2e8ce3aa26f9149a9bcfd234f321d
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-06-05 12:48:06 -0700
Commit message:

 Merge branch 'master' into devel
 
Package: cytolib
Commit: f96a01e7a4993d81f43707bb935d6bf6d2cef5ec
Author: Greg Finak <greg.finak@gmail.com>
Date: 2020-06-04 10:10:17 -0700
Commit message:

 Update README.md 
Package: cytolib
Commit: da72c971ef794479335b289ae66074b03a4bf52e
Author: Greg Finak <greg.finak@gmail.com>
Date: 2020-06-04 10:09:27 -0700
Commit message:

 Update README.md 
Package: cytolib
Commit: 210714a0d4c2487d5428c4a956717279a2157194
Author: Greg Finak <gfinak@fredhutch.org>
Date: 2020-06-04 09:46:02 -0700
Commit message:

 update issue template
 
Package: cytolib
Commit: f7a505f1b5f134e8c6a9c560a07dcbb1dd35d4fa
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-06-03 14:48:09 -0700
Commit message:

 Merge branch 'master' of github.com:RGLab/cytolib
 
Package: cytolib
Commit: e764cd7d0ee53d0d0f3abd3719056068b193d4f2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-06-03 14:47:54 -0700
Commit message:

 bump
 
Package: cytolib
Commit: 16705e1ebd6baf3ae3db1d237b46b2185119ab1a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-06-03 14:47:17 -0700
Commit message:

 fix #36
 
Package: cytolib
Commit: 2bfb1ce274fe84192ef3b852cc956c419dcbf20f
Author: Greg Finak <greg.finak@gmail.com>
Date: 2020-06-01 11:36:31 -0700
Commit message:

 Update LICENSE 
Package: cytolib
Commit: ee6bb4bfe10e90796367002d165ab9711fdf2463
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-20 17:41:00 -0700
Commit message:

 bump
 
Package: cytolib
Commit: d02503918cc751c5435b4e5861060dcfc673b737
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-20 17:24:55 -0700
Commit message:

 add option skip_faulty_node to gating
 
Package: cytolib
Commit: 86940834379a8e6d2b2b2cf4746aeefa40b6fff1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-14 16:33:25 -0700
Commit message:

 bump
 
Package: cytolib
Commit: a8285c03c07182075ac4879eae58ccca4efe82cc
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-14 15:32:10 -0700
Commit message:

 add recursive version of removeNode()
 
Package: trena
Commit: bac0feb823cc2e1a3afdf31c60d628dcf0d56300
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2020-06-05 12:35:14 -0700
Commit message:

 removed flare from imports
 
Package: trena
Commit: 59852f3f15bce9f49e36006b46b0c5901c59070a
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2020-06-05 12:34:21 -0700
Commit message:

 merge
 
Package: trena
Commit: 957502fc13c4041c7256c5fb430d4c68138a511b
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2020-04-02 18:49:50 -0700
Commit message:

 added arabidopsis genome
 
Package: trena
Commit: 0acbcbe1ae852e0bebcbd3fba24e59d44abf6209
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2020-04-02 10:18:33 -0700
Commit message:

 simplify installation
 
Package: trena
Commit: b292d41129800d455f2a562df1e46855882a8224
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2020-03-17 15:08:39 -0700
Commit message:

 old change
 
Package: trena
Commit: 6690db2f5817a6d87720a0d80d7a84b00d63c402
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2020-03-17 14:32:41 -0700
Commit message:

 not sure
 
Package: cleaver
Commit: 67636497bca8e3a40dcac33bbee97074dbcfe862
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2020-06-05 21:29:25 +0200
Commit message:

 doc: fix typo in cleavage rule for glutamyl endopeptidase
 
Package: OmnipathR
Commit: baec2372932c3f35e7331216136fb4c994e4e204
Author: Alberto Valdeolivas <alvaldeolivas@gmail.com>
Date: 2020-06-05 20:49:59 +0200
Commit message:

 Fix error in dorothea confidence levels parameter

Fix error with dorothea confidence levels parameter
 
Package: GSCA
Commit: cf61fd379a91cf24aace7781501d783036b52cea
Author: Zhicheng Ji <zhichengji@Zhichengs-MacBook-Pro.local>
Date: 2020-06-05 14:49:14 -0400
Commit message:

 My informative commit message
 
Package: variancePartition
Commit: 1ca7b7cd2011e802a7fcd77938722991bdeeec16
Author: GabrielHoffman <gabrielhoffman@typhon.local>
Date: 2020-06-05 12:58:16 -0400
Commit message:

 restore
 
Package: dittoSeq
Commit: bd6c177aae852ee2ba9d1c28f31ac765db420015
Author: dtm2451 <Daniel.Bunis@ucsf.edu>
Date: 2020-06-04 17:27:25 -0700
Commit message:

 NEWS update & Version Bump
 
Package: dittoSeq
Commit: 7ccf452364a7724bb8fda9ab40d52657b221920a
Author: dtm2451 <Daniel.Bunis@ucsf.edu>
Date: 2020-06-04 17:26:23 -0700
Commit message:

 Ignore DimPlot add-ons meant for discrete data when data is numeric

Add tests that check if these are ignored when needed.

Also updates the `.msg_ifV()` internal function to simply `.msg_if()`, and moves it to 'utils.R'
 
Package: dittoSeq
Commit: 9a4194f4b85e292215c96b26815cbeefae058ea3
Author: dtm2451 <Daniel.Bunis@ucsf.edu>
Date: 2020-06-04 16:38:45 -0700
Commit message:

 Bug fix: Allow expression grabbing across visualizations (ultimately via `gene()`) from non-default assays of Seurat objects.
 
Package: dittoSeq
Commit: 454ebbd82d3640f2d760e6b63a1d8f05f3b6ab83
Author: dtm2451 <Daniel.Bunis@ucsf.edu>
Date: 2020-05-26 12:15:10 -0700
Commit message:

 Updated `importDemux()` documentation

Reorganized the details & multi-lane sections to hopefully make the documentaation clearer and easier to follow.
 
Package: dittoSeq
Commit: a1a94c8942f51f006290216ea76e13467b68d189
Author: dtm2451 <Daniel.Bunis@ucsf.edu>
Date: 2020-05-26 12:13:13 -0700
Commit message:

 Updated logo

also adjusted the README's  formatting in general & Demuxlet Tools section
 
Package: GenomicScores
Commit: 678ac4f6fcf821d7a9d8f6b0f4358d5b129a1b89
Author: [rcastelo] <[robert.castelo@upf.edu]>
Date: 2020-06-05 19:00:56 +0200
Commit message:

 Fixed bug caused by a change in gwascat.
 
Package: CNVRanger
Commit: 674fd3d34491aeb697c381b601457e2cdbc5dbeb
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2020-06-05 12:12:03 -0400
Commit message:

 update affiliation vinicius
 
Package: OmnipathR
Commit: dd138e4ea5ae4b9ac5f80de4acbdc7aca0bd8576
Author: Alberto Valdeolivas <alvaldeolivas@gmail.com>
Date: 2020-06-05 17:57:30 +0200
Commit message:

 Include warnings for deprecated functions
 
Package: OmnipathR
Commit: 7aff8aca7b9fdf6d2da34a77033d7705033b15dc
Author: Alberto Valdeolivas <alvaldeolivas@gmail.com>
Date: 2020-06-05 12:40:45 +0200
Commit message:

 Fixing errors, warnings and notes from R CMD Check and BiocCheck
 
Package: OmnipathR
Commit: e3155917da4a0630bbd8caf7c0e9c38b6a742094
Author: Alberto Valdeolivas <alvaldeolivas@gmail.com>
Date: 2020-06-05 10:00:28 +0200
Commit message:

 Website
 
Package: OmnipathR
Commit: 8dd10ef31acf65e54d49976ae3d45c6a22bda7f7
Author: Alberto Valdeolivas <alvaldeolivas@gmail.com>
Date: 2020-06-04 19:16:29 +0200
Commit message:

 Delete _pkgdown.yml 
Package: OmnipathR
Commit: 98e06aa3b58ee29ba400e4d98676e3426a698ae3
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-06-02 14:56:49 +0200
Commit message:

 swap_undirected: keep also the original orientation of undirected interactions
 
Package: OmnipathR
Commit: 9fe0ae9bbc449ba2c3e8b30ad2cb6965efd99895
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-29 02:45:29 +0200
Commit message:

 minor adjustments on readme
 
Package: OmnipathR
Commit: 003624bef72a1d5caa9744f736b449e868263330
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-28 04:07:19 +0200
Commit message:

 import_intercell_network: docs updated
 
Package: OmnipathR
Commit: 747421f3d7a4289f8d9442f383fd46379e089a90
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-28 02:36:35 +0200
Commit message:

 fixed: missing argument name `proteins`; some non-vectorized operators
 
Package: OmnipathR
Commit: 75ab2bfe37709f13fad208ec5231735d266bf915
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-28 00:58:57 +0200
Commit message:

 merge conflicts resolved
 
Package: OmnipathR
Commit: c0dc8f38aa10514ac97fda8cfc5c64a8fa1849ae
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-28 00:24:16 +0200
Commit message:

 minor corrections until successful build
 
Package: OmnipathR
Commit: 48f986bfb84241a958a6ead233aac4a866b597a7
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-28 00:23:27 +0200
Commit message:

 vignettes: updated some details, build successful
 
Package: OmnipathR
Commit: e69d9e34f2fa7ddd2d0d7646bcdab39831b1bcbd
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-28 00:22:21 +0200
Commit message:

 updated exports
 
Package: OmnipathR
Commit: 4d76392a9c2e92e570e9123bc173a145df095f80
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 19:41:10 +0200
Commit message:

 replaced nsources, nrefs in print_interacions
 
Package: OmnipathR
Commit: ead21a814c86cfb3c3e7ba71b6f0f411ed11cfb9
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 19:19:52 +0200
Commit message:

 topology and causality in `filter_intercell`
 
Package: OmnipathR
Commit: 313fcc3098bf60d289beca34c42dfa5e53f6697f
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 18:51:41 +0200
Commit message:

 import_intercell_network seems to work
 
Package: OmnipathR
Commit: f5cf423de259a0ef7059cbc6b99f8cc30d6e05f0
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 18:21:00 +0200
Commit message:

 updated imports
 
Package: OmnipathR
Commit: 540bbf27c41ed1288566c501c559282cb581c10e
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 18:13:18 +0200
Commit message:

 updated version
 
Package: OmnipathR
Commit: 35d07dc8b415025b77d55af49529fc0d670f67d4
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 18:11:41 +0200
Commit message:

 removed `filter_format_inter` as its functionality has been delegated to other methods
 
Package: OmnipathR
Commit: d5be84f393781e56e397567579f4db7f3918e0f6
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 18:08:27 +0200
Commit message:

 count_resources/references methods
 
Package: OmnipathR
Commit: 3dd06ed6cb107ea768820895cc12c8b822d9a40d
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 17:36:59 +0200
Commit message:

 added curation_effort to default fields
 
Package: OmnipathR
Commit: 2a10e65556f22db5c96fdcf6dec325059b63ee7b
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 17:35:04 +0200
Commit message:

 updated import_intercell_network drafted
 
Package: OmnipathR
Commit: 6a7b32d6acd3f99372ea9adcc5fe4f119b5d1bfe
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 16:25:03 +0200
Commit message:

 intercell causality and topology options
 
Package: OmnipathR
Commit: 8878e90203978135dece4fa4c2d5aee7485a4420
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 12:46:07 +0200
Commit message:

 option to remove resource labels from references
 
Package: OmnipathR
Commit: 674422733d2b39cd2fd7bfdeb9d2315ba368d781
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 05:36:27 +0200
Commit message:

 omnipath_download handles json
 
Package: OmnipathR
Commit: 1d79abb8d29a8c3bb45a7c7abddd51523e0e1091
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 05:17:56 +0200
Commit message:

 option to provide arguments for omnipath_download
 
Package: OmnipathR
Commit: e8df0b095778f21dabb55c40354bf6423373e8ca
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 05:02:26 +0200
Commit message:

 intercell local filtering & casting boolean vars to R logical
 
Package: OmnipathR
Commit: ca24657f2b7fa8260fcf51ff02dc25067f675835
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 04:27:15 +0200
Commit message:

 import intercell adjusted to new intercell data and new import_omnipath
 
Package: OmnipathR
Commit: c6c80609ee7d918103b7cf99dda2dbba37aae274
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 03:45:19 +0200
Commit message:

 import annotations uses to import_omnipath; always checking correct resource names
 
Package: OmnipathR
Commit: adce164f4186afae2e96a57b47e98cabe2ceed4d
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-27 03:09:01 +0200
Commit message:

 filter_by_resource added to cache loading routine
 
Package: OmnipathR
Commit: be8df27e6275ccbfaeb1a0d4aff5115696e2a82c
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-26 22:05:57 +0200
Commit message:

 refactored import_omnipath_complexes
 
Package: OmnipathR
Commit: af6a6c3be4a1aaec1fed8c2b77d69cfe6b111795
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-26 21:52:51 +0200
Commit message:

 import...interactions methods finished
 
Package: OmnipathR
Commit: 1ad21dc693656c53491ffe0bce99ef9eac7d25d9
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-26 17:41:54 +0200
Commit message:

 removed old dorothea method
 
Package: OmnipathR
Commit: e1c0b12eb3f6c667062558ff064dc190161e7921
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-26 17:37:08 +0200
Commit message:

 renamed arguments updated in docstrings; default fields
 
Package: OmnipathR
Commit: 0c36a08bb57b699d166471bbdf134c8bc3b80b4b
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-26 17:20:55 +0200
Commit message:

 bool arguments can be R logical
 
Package: OmnipathR
Commit: 8391d61c125d7b962306ffdc36cac6517c02150f
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-26 16:53:00 +0200
Commit message:

 query_string reference extended
 
Package: OmnipathR
Commit: 3ed2c4bc03a217440d7397c37e2c3641407b3320
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-26 15:50:51 +0200
Commit message:

 refactoring download methods, vol 4
 
Package: OmnipathR
Commit: eb1095752d9e8d96509317efd49df1bb06515cb7
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-24 00:20:56 +0200
Commit message:

 Signor -> SIGNOR in examples
 
Package: OmnipathR
Commit: 7087e5580cb70bfcc18211cac90840fd24903235
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-21 04:55:12 +0200
Commit message:

 refactoring download methods, vol 3
 
Package: OmnipathR
Commit: 226eda16c15b8dd2adfc5b9294e53c5d52231344
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-21 03:18:59 +0200
Commit message:

 refactoring download methods, vol 3
 
Package: OmnipathR
Commit: 2173bbdf7e3060c01bc67960d010f5b7cf85332c
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-21 03:03:35 +0200
Commit message:

 refactoring download methods, vol 2
 
Package: OmnipathR
Commit: a67b7244def0d98b6fb714eb4d996899fcd8a47b
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-21 01:58:53 +0200
Commit message:

 refactoring download methods, vol 1
 
Package: OmnipathR
Commit: 1f872edfa7c77ab2ecd38500814e2ed071e5d62d
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-20 16:07:03 +0200
Commit message:

 get_resources method for each query type
 
Package: OmnipathR
Commit: 7b8790253e1f4f4c61175eeefca6b3921f3f4b69
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-20 15:28:42 +0200
Commit message:

 new function: get_resources -- gonna replace all `get_..._databases` functions
 
Package: OmnipathR
Commit: 6b0782bff66309af2bfd3914379489bce9e5f01e
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-20 05:08:49 +0200
Commit message:

 code cosmetics incl. consistent names, spacing and doc style
 
Package: OmnipathR
Commit: 948d91f1aeb4f7e7dac5d1f75298116e80f3ab84
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-20 02:51:53 +0200
Commit message:

 cosmetic changes on function headers
 
Package: OmnipathR
Commit: 31ac88e5fb59355a74494aeb260ea3bd3d6c8dc2
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2020-05-20 02:43:19 +0200
Commit message:

 removed trailing spaces
 
Package: OmnipathR
Commit: c974f713e3090626e609ebc7b1b22048a6a03a4f
Author: Alberto Valdeolivas <alvaldeolivas@gmail.com>
Date: 2020-05-18 10:34:06 +0200
Commit message:

 Revert "website"

This reverts commit 6fc327d2e7e36376d687bad2d81cc61b3f2b9636.
 
Package: OmnipathR
Commit: 93cbd83491266fe797095602fcf6ffb5fa778fd2
Author: Alberto Valdeolivas <alvaldeolivas@gmail.com>
Date: 2020-05-18 10:32:42 +0200
Commit message:

 update website in description file
 
Package: OmnipathR
Commit: 6fc327d2e7e36376d687bad2d81cc61b3f2b9636
Author: Alberto Valdeolivas <alvaldeolivas@gmail.com>
Date: 2020-05-18 10:27:40 +0200
Commit message:

 website
 
Package: OmnipathR
Commit: 2e80efb9c4dd7c9fb79ea26a7a72e520c343aee8
Author: Alberto Valdeolivas <alvaldeolivas@gmail.com>
Date: 2020-05-18 10:24:42 +0200
Commit message:

 Website
 
Package: ChIPpeakAnno
Commit: 437a15dfeb84df3938532de9398dc63468811c6b
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2020-06-05 11:01:52 -0400
Commit message:

 use roxygen2 to generate the help file.
move multiple package from Imports to Suggests.
 
Package: variancePartition
Commit: fe3ec6d4eba7d9766eb7533c1252719dc32cc9e4
Author: GabrielHoffman <gabrielhoffman@typhon.local>
Date: 2020-06-05 11:02:20 -0400
Commit message:

 bump version
 
Package: variancePartition
Commit: 317dcf635b5f5a9f64d8ad34457b87c4ecf07f18
Author: GabrielHoffman <gabrielhoffman@typhon.local>
Date: 2020-06-05 10:56:27 -0400
Commit message:

 1.18.3
 
Package: variancePartition
Commit: 7ebe755a8d69c517c7fe1a496cb0bf92ec960ece
Author: GabrielHoffman <gabrielhoffman@typhon.local>
Date: 2020-06-05 08:48:19 -0400
Commit message:

 add documentation
 
Package: variancePartition
Commit: 83cff001c67f4a6c551a80b17c823d2f29f01f37
Author: GabrielHoffman <gabrielhoffman@typhon.local>
Date: 2020-06-03 12:23:54 -0400
Commit message:

 droplevels
 
Package: variancePartition
Commit: 1065feea34ad77ec22d8bd98a1e66d4b80c6c395
Author: GabrielHoffman <gabrielhoffman@typhon.local>
Date: 2020-06-03 11:18:06 -0400
Commit message:

 Add eBayesFMT
 
Package: gwascat
Commit: b56757cd7a119d281c2f70b239691da1816f5254
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2020-06-05 09:27:36 -0400
Commit message:

 lift over the snpchip 6.0 coordinates for compatibility with gwascat
 
Package: ensemblVEP
Commit: 8dbf70a9b4ca2ac1590f0a9a780cee3fbffc2059
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-06-05 08:33:50 -0400
Commit message:

 Updates for version 100
 
Package: tximport
Commit: 66028f3b01696f8103afdedaf2bec421ec5eabb6
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2020-06-05 07:24:55 -0400
Commit message:

 add dims for sparse and CFA=scaledTPM
 
Package: circRNAprofiler
Commit: 001eafc31f455b4f1492809ce9b7f5bd21285727
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-06-05 11:09:29 +0200
Commit message:

 From version 1.3.2 to Version 1.3.3
 
Package: circRNAprofiler
Commit: ba1b4a5656af192e1eb00a709b659303d4e22bf3
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-06-05 11:09:06 +0200
Commit message:

 update doc
 
Package: DepecheR
Commit: 4933bfcbecc411371d3b74a9383f59af23f357f0
Author: Jakob Theorell <jakob.theorell@ki.se>
Date: 2020-06-05 09:26:07 +0100
Commit message:

 Intro of samplingSubset to depeche, plus bug fixes and minor changes to example and vinjette text.
 
Package: adSplit
Commit: 4069672eb069af9b7c0436f8c135b21efc4a164a
Author: Claudio Lottaz <claudio.lottaz@ur.de>
Date: 2020-06-05 10:09:27 +0200
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/adSplit
 
Package: adSplit
Commit: 7f0f0291e18cb749d8248c7229a5c2b432c25bdc
Author: Claudio Lottaz <claudio.lottaz@ur.de>
Date: 2020-06-05 10:07:19 +0200
Commit message:

 fix URL
 
Package: OrderedList
Commit: fe392e6756870ca848748f78cf889ba4fac7d881
Author: Claudio Lottaz <claudio.lottaz@ur.de>
Date: 2020-06-05 09:32:41 +0200
Commit message:

 fix URL
 
Package: DepecheR
Commit: 96a1ef6599761ea037f523d0d0e233ec710b8ccf
Author: Jakob Theorell <jakob.theorell@ki.se>
Date: 2020-05-18 14:52:18 +0100
Commit message:

 First major overhaul since the introduction of groupStatPlot.
 
Package: EnhancedVolcano
Commit: 62717699098d1b43f4240f181722275eca66659b
Author: Kevin Blighe <kblighe@CLINICALBIO.dlink.com>
Date: 2020-06-05 00:10:53 -0300
Commit message:

 Vignette update
 
Package: CNVRanger
Commit: 14d54531eb7c592b2e9cd452d84f0d57e5f0389f
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2020-06-04 22:23:49 -0400
Commit message:

 vignette: update affiliation + email vinicius
 
Package: CellBench
Commit: 7282a9defd16d7f792039bc4798432532b00599b
Author: Shians <registertonysu@gmail.com>
Date: 2020-06-05 12:17:03 +1000
Commit message:

 Version bump to match upstream
 
Package: CellBench
Commit: 800dcd1d1e38456e6ee77a7bb422eff01cc38881
Author: Shians <registertonysu@gmail.com>
Date: 2020-06-05 12:16:46 +1000
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/CellBench
 
Package: CellBench
Commit: d755314aec19da82b5aaaeb8f69979f7cc855daf
Author: Shians <registertonysu@gmail.com>
Date: 2020-06-05 12:16:24 +1000
Commit message:

 Merge branch 'RELEASE_3_11' of git.bioconductor.org:packages/CellBench
 
Package: CellBench
Commit: 46e64bed9f737955d5af151ab4e62364184d9dca
Author: Shians <registertonysu@gmail.com>
Date: 2020-06-05 12:14:37 +1000
Commit message:

 Explicitly setting factor levels in tests
 
Package: GenomicAlignments
Commit: c0159088517e3319ba13073f09ed588ae9d103de
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-04 17:48:26 -0700
Commit message:

 minor edit
 
Package: GenomicAlignments
Commit: 04bb1cb82b7586edc3498fae81be928258133c0a
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-04 17:44:32 -0700
Commit message:

 bump IRanges version requirement
 
Package: GenomicRanges
Commit: 251691c8b9b07e1b1867b8a4a039e0c9aea5e5e7
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-04 17:43:15 -0700
Commit message:

 bump IRanges version requirement
 
Package: IRanges
Commit: c96eae89639a63a4a90604851e80701fa5703527
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-04 17:41:29 -0700
Commit message:

 version bump
 
Package: IRanges
Commit: c7fe90ee05d71d34ea2a3bd1ffef3a8c8b1a9ab6
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-04 15:18:18 -0700
Commit message:

 coverage() now supports 'method="naive"'

This is in addition to the already supported methods "sort" and "hash".
This new method is a slower version of the "hash" method that has the
advantage of avoiding floating point artefacts in the no-coverage regions
of the numeric-Rle object returned by coverage() when the weights are
supplied as a numeric vector of type 'double'.
 
Package: GenomicAlignments
Commit: 1d7a8a01da9a35a16f3fa21e5bf1ac0bce3fd333
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-04 17:34:00 -0700
Commit message:

 resync with GenomicRanges 1.41.4 and IRanges 2.23.7
 
Package: GenomicRanges
Commit: 6afd09fb479dd14fb7db328e9ea430f25cbeb24b
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-04 17:30:59 -0700
Commit message:

 coverage() methods now supports 'method="naive"'

This is in addition to the already supported methods "sort" and "hash".
This new method is a slower version of the "hash" method that has the
advantage of avoiding floating point artefacts in the no-coverage regions
of the numeric-Rle object returned by coverage() when the weights are
supplied as a numeric vector of type 'double'.
 
Package: motifStack
Commit: fadf1e48a349b35bf9b24f902e76ac0271a3ebb0
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2020-06-04 19:34:03 -0400
Commit message:

 change grImport, grImport2 and MotIV to Suggests.
use roxygen2 to generate help files.
 
Package: csaw
Commit: 5b83117160aa72b3df9efd1e19538d7625377f87
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-04 14:19:55 -0700
Commit message:

 Bumped version and date.
 
Package: csaw
Commit: d5db95c29f4825e99970b760e2a2b1a3ce774597
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-04 14:17:27 -0700
Commit message:

 Cleaned up documentation for the cluster-level stats.
 
Package: MOMA
Commit: 852825b00474055b076b3564698c6d02fe8fdeb0
Author: sunny jones <sunnyjjones@gmail.com>
Date: 2020-06-04 16:54:19 -0400
Commit message:

 bug fix: issue with rownames on tibble for oncoPrint plots
 
Package: CNVRanger
Commit: 0a9e4e5ffede338f918913a53ff173ea527cf27b
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2020-06-04 15:39:44 -0400
Commit message:

 cnvEQTL: support window=NULL for genome-wide testing
 
Package: CNVRanger
Commit: debdcf2b9e7e23662d4751ea88d440bb4d9570fe
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2020-06-04 15:39:34 -0400
Commit message:

 cnvEQTL: support window=NULL for genome-wide testing
 
Package: seqsetvis
Commit: a24330c0cdb3ad5ca255218bc6dc6986b94b95ce
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-06-04 14:58:28 -0400
Commit message:

 rm digest::digest from test
 
Package: circRNAprofiler
Commit: 374e0a9739b2cc2e82c84fcd329f17188951002c
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-06-04 20:05:23 +0200
Commit message:

 From Version 1.3.1 to Version 1.3.2
 
Package: circRNAprofiler
Commit: 1e25a64197b8f833659359f542e7780ac3ec24a7
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-06-04 18:24:38 +0200
Commit message:

 From Version 1.3.0 to Version 1.3.1
 
Package: circRNAprofiler
Commit: 2d009eaab53a12dd7001b7e3fdb1fd3a0a578d02
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-06-04 18:24:20 +0200
Commit message:

 update doc
 
Package: circRNAprofiler
Commit: bcc86da903d1a54de05ec370020910ca01d7887e
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-06-04 15:46:55 +0200
Commit message:

 From Version 1.2.6 to Version 1.3.0
 
Package: circRNAprofiler
Commit: bc7ea11f044a3dfc35730527a90dc5a66089d1fa
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-06-03 13:20:28 +0200
Commit message:

 From Version 1.2.4 to Version 1.2.6
 
Package: circRNAprofiler
Commit: e53f88dc77ce6f770d6c796093aa43af08949382
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-06-03 13:20:17 +0200
Commit message:

 update vignettes
 
Package: circRNAprofiler
Commit: c11257ba639be2cb2ac7f713c0421258ab481a6e
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-06-03 11:11:47 +0200
Commit message:

 Fixed bugs due to dplyr 1.0.0 breaking changes.
 
Package: circRNAprofiler
Commit: 99602fd6607ddc0412d0df8dae04bfe53d61da7c
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-06-02 10:02:49 +0200
Commit message:

 From Version 1.2.3 to Version 1.2.4
 
Package: circRNAprofiler
Commit: c2457c6a868c1bccd88f606135a8c906fede2585
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-06-02 10:02:23 +0200
Commit message:

 update vignettes
 
Package: circRNAprofiler
Commit: 93cca7022c772a1ec309f1b02ec5edb181896990
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-05-29 08:56:20 +0200
Commit message:

 From Version 1.2.2 to Version 1.2.3
 
Package: circRNAprofiler
Commit: 35962f43a54a8ee0cfedecf35c2416a20ce49719
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-05-29 08:55:50 +0200
Commit message:

 fixed roxygen doc for data
 
Package: circRNAprofiler
Commit: cce0e19481f37e3cc841ad79d440b5f0680c020a
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-05-12 14:03:04 +0200
Commit message:

 From Version 1.2.0 to Version 1.2.2
 
Package: circRNAprofiler
Commit: 251224eb7419dffe8314c6d1626545c7b7fad055
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-05-12 14:02:19 +0200
Commit message:

 Updated NEWS
 
Package: circRNAprofiler
Commit: d3aa738f8b89c59f6c965f62be22873956b90d45
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-05-12 13:37:31 +0200
Commit message:

 From Version 1.1.17 to Version 1.2.1
 
Package: circRNAprofiler
Commit: 0c62fead00d15d8d2374ef0a9e958626b4fdbf86
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-05-12 13:35:29 +0200
Commit message:

 Merge branch 'RELEASE_3_11' into develop
 
Package: circRNAprofiler
Commit: e5cdab8adf1f1d153b22d6e6808b4404ed06104e
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-05-12 11:16:59 +0200
Commit message:

 From Version 1.1.16 to Version 1.1.17
 
Package: circRNAprofiler
Commit: 6e1dd9dc33335b8c37f15ad768038bd2a2e9c77e
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-05-12 11:16:39 +0200
Commit message:

 added referece to the paper
 
Package: circRNAprofiler
Commit: 251c5c817d94e7f674c0048c18eb762ca2a10a18
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-04-02 09:59:11 +0200
Commit message:

 From Version 1.1.15 to Version 1.1.16
 
Package: circRNAprofiler
Commit: 034b78f29af6c410c250d947d3180b6fcee1eae7
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-04-02 09:58:38 +0200
Commit message:

 update doc
 
Package: circRNAprofiler
Commit: 1b9359d6d422bc6f47473ac891db0a8dadd3fb6d
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-04-02 09:57:55 +0200
Commit message:

 Added setylim param
 
Package: circRNAprofiler
Commit: 6ecfdb0a6ae8d3169398dd51e8853d8c9fd97cbd
Author: simoc <simo.aufiero@gmail.com>
Date: 2020-04-02 09:57:05 +0200
Commit message:

 added setSeed param for reproducible research
 
Package: circRNAprofiler
Commit: 494bc37488f718cf4b7629cac8668b2d92b4a35d
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-03-11 14:11:53 +0100
Commit message:

 From version 1.1.14 to Version 1.1.15
 
Package: circRNAprofiler
Commit: 4f8398964923488f19d5f0a89b22929b0adac17d
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-03-11 14:11:44 +0100
Commit message:

 update doc
 
Package: circRNAprofiler
Commit: 9934b76c52729f3483a462a07f9a42753237477a
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-03-10 17:43:19 +0100
Commit message:

 Fixed coordinates using gtf file
 
Package: circRNAprofiler
Commit: 8b77536c1622336ea8aead057ba351fed5781088
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-27 16:39:51 +0100
Commit message:

 From version 1.1.13 to Version 1.1.14
 
Package: circRNAprofiler
Commit: 64cae94778e6dbe7318e4283e283853646a8c97a
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-27 16:39:35 +0100
Commit message:

  Detection tools can report sligtly different coordinates. It is now possible to fix the latter using the gtf file.
 
Package: circRNAprofiler
Commit: d71080427de7329dbcf83c5ccafa1b275b64f4c6
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-21 13:24:26 +0100
Commit message:

 From Version 1.1.12 to Version 1.1.13
 
Package: circRNAprofiler
Commit: fd650a8880d2fb3becd3de80585115a3b8c991c6
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-21 13:24:07 +0100
Commit message:

 update man doc
 
Package: circRNAprofiler
Commit: 766ca64d1c65f60b038d3dab162f26c9e22953e5
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-20 12:07:20 +0100
Commit message:

 From Version 1.1.11 o Version 1.1.12
 
Package: circRNAprofiler
Commit: 7fbf2cf4f296af32d69cb076ecf19569e7700f35
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-20 12:07:04 +0100
Commit message:

 typos
 
Package: circRNAprofiler
Commit: 94211ede4322464e7ea9fd63f3ad2ac128ff768a
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-20 10:53:59 +0100
Commit message:

 From Version 1.1.10 to Version 1.1.11
 
Package: circRNAprofiler
Commit: 7cb9be1aa5852fdecf3722ffa502ed650cc8ab31
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-20 10:53:41 +0100
Commit message:

 upadate package vignettes
 
Package: circRNAprofiler
Commit: 8f17334ff60ffc5bfca04e35a984c8120d082f70
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-18 15:11:42 +0100
Commit message:

 From Vesrion 1.1.9 to Version 1.1.10
 
Package: circRNAprofiler
Commit: e9adc7bd01c10d548b5ca03e10f75c8b7b79c8af
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-18 15:11:23 +0100
Commit message:

 typos vignettes
 
Package: circRNAprofiler
Commit: 584a235ab7c29a4de1bcb55789e1cb90b325c2f1
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-18 14:46:23 +0100
Commit message:

 From Version 1.1.8 to Version 1.1.9
 
Package: circRNAprofiler
Commit: c60a3b236ee8ca78134a1d67b049cc43458d7cfe
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-18 14:46:05 +0100
Commit message:

 updated vignettes
 
Package: circRNAprofiler
Commit: d8d0c5ef561e5127c307bbac619ac24c72cc54a4
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-17 08:57:09 +0100
Commit message:

 Version1.1.7 to Version 1.1.8
 
Package: circRNAprofiler
Commit: 08a3df08ae0b41218284eafc425487b05531ba05
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-17 08:56:50 +0100
Commit message:

 typo vignettes
 
Package: circRNAprofiler
Commit: f206a440209752cf245353161d0a162adc285b31
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-02-13 10:39:50 +0100
Commit message:

 updated vignettes
 
Package: circRNAprofiler
Commit: 0d7d2ef964a799ed0f3e1eff50ef36ac0cc98609
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-01-30 13:39:20 +0100
Commit message:

 Version 1.1.6 to Version 1.1.7
 
Package: circRNAprofiler
Commit: 3850c7d4bea89d7d61835906d823a42308fb2cda
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-01-30 13:39:02 +0100
Commit message:

 updated vignettes
 
Package: circRNAprofiler
Commit: 557bfcfe41bb9579124505efc5b4581111cb6c84
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-01-23 16:09:04 +0100
Commit message:

 updated News.md
 
Package: circRNAprofiler
Commit: 297412f4d6f713f1220a09cadd813af748eb3287
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-01-23 16:08:41 +0100
Commit message:

 Version 1.1.5 to Version 1.1.6
 
Package: circRNAprofiler
Commit: 65dc5c7293920524b949defc4db88f6059ec5be9
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-01-09 10:47:43 +0100
Commit message:

 Version 1.1.4 to Version 1.1.5
 
Package: circRNAprofiler
Commit: 5cab931dea21049b33277981d331137192339c39
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-01-09 10:47:20 +0100
Commit message:

 Updated getPlots function. Also motifs found in the background sequences are  now reported in the output.
 
Package: circRNAprofiler
Commit: 7494f81df3da86b4cea7e5890c66c206f7a58b65
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-01-09 10:42:55 +0100
Commit message:

 update vignettes
 
Package: circRNAprofiler
Commit: 315ae74cfec6e231b6ef9d020eba91f46c2b1209
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-01-08 16:40:10 +0100
Commit message:

 Version 1.1.3 to Version 1.1.4
 
Package: circRNAprofiler
Commit: a69e1096f1855a383281073240bd17f76fbaf587
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2020-01-08 16:39:36 +0100
Commit message:

 The function getMotifs did not trimmed properly the BSJ sequences. We now fixed it.
 
Package: circRNAprofiler
Commit: 475680cfe64c02377bc4b3f66ddc4ab2e25d480c
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2019-12-19 12:02:13 +0100
Commit message:

 Version 1.1.2 to Version 1.1.3
 
Package: circRNAprofiler
Commit: 5f20e6b6afd752665dc366c9904170f41a30032e
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2019-12-19 12:01:44 +0100
Commit message:

 Added n param for filteringthe motifs in plotMotifs
Improved  doc in getMotifs
 
Package: circRNAprofiler
Commit: 2d12688897959d0967e68989fd20086a90c1d1e1
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2019-12-19 11:59:22 +0100
Commit message:

 updated vignettes
 
Package: circRNAprofiler
Commit: 8e1ec6b5239f0793fcc25f1ed6b1da58a3132032
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2019-12-13 15:47:48 +0100
Commit message:

 updated vignettes and news doc
 
Package: circRNAprofiler
Commit: dbb71527808c9619499e9686cff19963f720b71e
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2019-12-13 15:47:18 +0100
Commit message:

 updated man doc
 
Package: circRNAprofiler
Commit: 4126b4d0bc7f5b50c5df22943a36df59f16cec03
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2019-12-13 15:46:53 +0100
Commit message:

 Included possibilities to use motifs of RBPs from MEME database
 
Package: circRNAprofiler
Commit: 278e54742978e4eef59ae242350b3ddc6c0fdec1
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2019-12-13 15:44:57 +0100
Commit message:

  In plotMotifs function:
To avoid infinity as a value for fold change, 1 was added to number of occurences
of each motif found in the foreground and background target sequences before
the normalization.
 Added angle param for the rotation angle of the axis labels.
 Added removeNegLog2FC param to remove the RBPs having a negative log2FC.
 In volcanoPlot function:
Added geneSet param that allows to show only specified host gene names.
 
Package: circRNAprofiler
Commit: 836cb5504b4d8185ea38474d2abb0c4c47164099
Author: AMC\saufiero <simo.aufiero@gmail.com>
Date: 2019-12-13 15:33:05 +0100
Commit message:

 Version 1.1.1 to Version 1.1.2
 
Package: circRNAprofiler
Commit: 0e07cf0f3d2a7acec98557ec03836d6b57004d67
Author: Simona Aufiero <simo.aufiero@gmail.com>
Date: 2019-11-17 10:00:27 +0100
Commit message:

 Version: 1.1.0 to Version: 1.1.1
 
Package: circRNAprofiler
Commit: c714829e0a9fd37e38448a4361ebb8ee60af2380
Author: Simona Aufiero <simo.aufiero@gmail.com>
Date: 2019-11-17 09:57:57 +0100
Commit message:

 Version: 1.1.0 to Version: 1.1.1
 
Package: circRNAprofiler
Commit: f57b5d00cd486250e8ee2ceb50ee603430d088d9
Author: LAPTOP-LS60IEJD\simoa <simo.aufiero@gmail.com>
Date: 2019-10-09 11:07:59 +0200
Commit message:

  Version: 0.99.13 to Version: 0.99.14
 
Package: circRNAprofiler
Commit: 6d4615e30347f5f86aa7c56cc9f1bc37cf3c09ad
Author: LAPTOP-LS60IEJD\simoa <simo.aufiero@gmail.com>
Date: 2019-10-09 11:07:45 +0200
Commit message:

 update vignettes
 
Package: BiocSet
Commit: a4b42206fe83d0221cbf5db7683d2c52748aa8d1
Author: Kayla-Morrell <Kayla.Morrell@roswellpark.org>
Date: 2020-06-04 13:27:12 -0400
Commit message:

 Bug fixes to tests

- Due to the new version of GO.db, tests were failing
- Now all tests pass
 
Package: BiocGenerics
Commit: 59d694153ec87e0b3ddd54a5a884be4fcb7e5136
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-04 09:59:02 -0700
Commit message:

 Add man page for as.list() S4 generic
 
Package: CoreGx
Commit: febf598cb579333e8bc1f1c5fdad6ac30b709416
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2020-05-24 17:56:03 -0400
Commit message:

 Update: Merged package still passes BiocCheck
 
Package: CoreGx
Commit: 4323e0c633929454a3fd1a814d91d7e788ad1acf
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2020-05-24 17:51:32 -0400
Commit message:

 Merge: Upstream master to development branch
 
Package: CoreGx
Commit: c90c3d9fd8b4a7ead7ee632cdb527561bab1444a
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2020-05-24 17:47:21 -0400
Commit message:

 Update: Expanded CoreGx vignette, as per reviewers request
 
Package: BiocGenerics
Commit: 77ab03b27978848804c786aa4634522d7b7afb37
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-04 09:33:44 -0700
Commit message:

 Link to normalize() method from MSnbase instead of from scater
 
Package: seqsetvis
Commit: 20deda84be79ae62ee768f64e72c64f964592c8e
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-06-04 11:14:32 -0400
Commit message:

 bugfix for file_paths and file_attribs error if data.table
v bump 1.9.3
 
Package: cn.mops
Commit: 15a1b1939a2b50225d8b08c7333ba03f477a5258
Author: gpovysil <gpovysil@gmail.com>
Date: 2020-06-04 11:09:40 -0400
Commit message:

 fixed sort bug

Signed-off-by: gpovysil <gpovysil@gmail.com>
 
Package: seqsetvis
Commit: 29fe12bf68f63810825ba8093c340c4f1b007c90
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-06-04 10:43:56 -0400
Commit message:

 1.9.2 v bump for build
 
Package: seqsetvis
Commit: 1803a55d40c504b4d7e139f5b8ad80969406118b
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-06-04 10:42:08 -0400
Commit message:

 address warning for R 3.6 dependency
 
Package: seqsetvis
Commit: b01e9f445beb771bf22c657aaf0282c81bacdfd2
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-06-04 10:41:51 -0400
Commit message:

 addressed seq over 1:N NOTE.
 
Package: seqsetvis
Commit: 1902d5d2c3269318bd1c0b7e6e00a2bff1a5ac83
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-06-04 10:37:01 -0400
Commit message:

 address vapply prefer over sapply NOTE
 
Package: seqsetvis
Commit: ba8f5f6be7720b271b4de585fd0b3ed980d6fccd
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-06-04 10:36:42 -0400
Commit message:

 un R_REMOTES_NO_ERROS_FROM_WARNINGS
 
Package: seqsetvis
Commit: 0f51f94b064d6cb99fb48845dc498070b9040881
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-06-04 00:24:08 -0400
Commit message:

 R_REMOTES_NO_ERRORS_FROM_WARNINGS=TRUE
 
Package: mogsa
Commit: db751b7713dbe769c25f57256fb7e8c72c28a13f
Author: Chen <chen.meng@tum.de>
Date: 2020-06-04 15:25:06 +0200
Commit message:

 bug fix pathway name doens't exist anymore
 
Package: FEM
Commit: 7e5dfccd696c3b1db01f24cb5157a651e1f2f49c
Author: ubuntu18.04 <zhenyang@fudan.edu.cn>
Date: 2020-06-04 05:28:56 -0700
Commit message:

 New Version
 
Package: FEM
Commit: 3ae20e56905c10bfca423775663693d7604533ee
Author: ubuntu18.04 <zhenyang@fudan.edu.cn>
Date: 2020-06-04 05:26:58 -0700
Commit message:

 New Version
 
Package: FEM
Commit: 1118cd8cb2cc709552c5bd92226f82ea221fb4cc
Author: ubuntu18.04 <zhenyang@fudan.edu.cn>
Date: 2020-06-04 05:19:20 -0700
Commit message:

 New Version
 
Package: FEM
Commit: 5649211d5dca762c2e2480d2832d173f47b15270
Author: ubuntu18.04 <zhenyang@fudan.edu.cn>
Date: 2020-06-04 04:33:50 -0700
Commit message:

 New Version
 
Package: FEM
Commit: 6c1ba376b3d1a470dd0ed32d7bffafde88d2dfc7
Author: ubuntu18.04 <zhenyang@fudan.edu.cn>
Date: 2020-06-04 03:04:21 -0700
Commit message:

 E
 
Package: FEM
Commit: 4c5128915a1b64aa924c6a8eda2abf8d0c7641e9
Author: ubuntu18.04 <zhenyang@fudan.edu.cn>
Date: 2020-06-04 02:44:38 -0700
Commit message:

 w	modified:   ../DESCRIPTION
 
Package: FEM
Commit: d89854a3cd71c2bc2969affeea0b88fbcdc64d07
Author: ubuntu18.04 <zhenyang@fudan.edu.cn>
Date: 2020-06-04 02:26:18 -0700
Commit message:

 Merge remote-tracking branch 'origin/master'
 
Package: FEM
Commit: 71e3e46a0a09b97dbb214b114e6276dea00076d8
Author: ubuntu18.04 <zhenyang@fudan.edu.cn>
Date: 2020-06-04 02:22:42 -0700
Commit message:

 My informative commit message describing the change
 
Package: FEM
Commit: 3e7455febe89433849b899f234d0d3b48a092a1c
Author: zyangx <54207815+zyangx@users.noreply.github.com>
Date: 2020-06-04 17:14:50 +0800
Commit message:

 Add files via upload 
Package: FEM
Commit: 0ab7cea6d033dd8bff7a5c0b8fa30a397e156caa
Author: zyangx <54207815+zyangx@users.noreply.github.com>
Date: 2020-06-04 17:02:37 +0800
Commit message:

 Delete DoFEMbi.R 
Package: FRASER
Commit: 52107d64b4199f3c1d86e1a4737f58daa47067d6
Author: Christian Mertes <mertes@in.tum.de>
Date: 2020-05-29 18:55:11 -0700
Commit message:

 fix appveyor (#7)

* remove vignette build

* run package update step 
Package: FRASER
Commit: 9c8fa37bb21ae83dd664eaf1f54ef1c68ba8a21b
Author: Ines Scheller <scheller@in.tum.de>
Date: 2020-05-26 14:51:33 +0200
Commit message:

 consistent deltaPsi calculation; update of NEWS
 
Package: FRASER
Commit: 2cedaa63460499ff2279a3c99d0ed6133a508716
Author: Christian Mertes <mertes@in.tum.de>
Date: 2020-05-25 09:52:04 -0700
Commit message:

 adjust to released version numbering 
Package: FRASER
Commit: 2654964734238746d97e7fc6309692b3f91ee08c
Author: Ines Scheller <scheller@in.tum.de>
Date: 2020-05-19 11:42:44 +0200
Commit message:

 fixed remaining pajd typos
 
Package: FRASER
Commit: e1c53ed29f54e572f766b36a7c609a485db09c1b
Author: Ines Scheller <scheller@in.tum.de>
Date: 2020-05-19 10:56:25 +0200
Commit message:

 option to include additional columns from mcols in result table; added column for additional overlapping genes in annotateRanges
 
Package: FRASER
Commit: c1d578010d2581aeb6cd16c198a2f1eb60f45b76
Author: Ines Scheller <scheller@in.tum.de>
Date: 2020-05-13 23:20:21 +0200
Commit message:

 option to exclude non standard chr also from existing count cache
 
Package: FRASER
Commit: 652dbeb7ff9187522dafd35f292de2cba88fbd7d
Author: Ines Scheller <scheller@in.tum.de>
Date: 2020-05-13 23:05:27 +0200
Commit message:

 added option to count only standard chromosomes
 
Package: FRASER
Commit: 00d6708cbf8ae1ff820e3bbe0036295e84e98c0f
Author: Ines Scheller <scheller@in.tum.de>
Date: 2020-05-13 17:46:23 +0200
Commit message:

 fixed typo in padjVals
 
Package: FRASER
Commit: 6fbd981a1384b25071a6e489927b2080a7560be5
Author: Ines Scheller <scheller@in.tum.de>
Date: 2020-05-13 16:36:30 +0200
Commit message:

 ensure sampleIDs returned as character
 
Package: FRASER
Commit: cf9b8232d071ce57c91268e13e78f2f0f495a53c
Author: Christian Mertes <mertes@in.tum.de>
Date: 2020-05-09 19:58:58 +0200
Commit message:

 check for empty split read object
 
Package: FRASER
Commit: 652cda13cf2da70e69f9ba9a1a773e762c8f2f4f
Author: Ines Scheller <scheller@in.tum.de>
Date: 2020-05-04 14:15:05 +0200
Commit message:

 version bump after bug fix
 
Package: FRASER
Commit: 217c50d3fe8cad5c134594decdeea92dec4336d0
Author: Ines Scheller <scheller@in.tum.de>
Date: 2020-05-04 13:30:22 +0200
Commit message:

 Merge remote-tracking branch 'bioconductor/master'
 
Package: FRASER
Commit: 6c2eafc3af8974b9a937c9b01e1ac5a4f32223a0
Author: Ines Scheller <scheller@in.tum.de>
Date: 2020-05-04 11:19:36 +0200
Commit message:

 bug fix: counting read pairs in paired-end mode
 
Package: FRASER
Commit: 8d64f6c9419acd23c78b7f9f960917ca46e4142e
Author: Ines Scheller <scheller@in.tum.de>
Date: 2020-04-28 12:55:16 +0200
Commit message:

 minor fix
 
Package: FRASER
Commit: d17f81752399f1bc2530026fc9d3e59167addb91
Author: Ines Scheller <scheller@in.tum.de>
Date: 2020-04-28 11:10:42 +0200
Commit message:

 bug fix
 
Package: FRASER
Commit: c796038c2dfd642d535c2564d4f90894be22c6de
Author: Ines Scheller <scheller@in.tum.de>
Date: 2020-04-27 15:41:55 +0200
Commit message:

 bug fix: correct strandSpecific counting
 
Package: seqLogo
Commit: b303692857dfaa2cee18c81e52fbcedc4837aee7
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-06-04 07:57:22 +0200
Commit message:

 Added back export methods for plot, summary and show fixing #1
 
Package: scater
Commit: 95bc2ee12b69a17331ae3296dd53bf444710645f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-03 22:13:49 -0700
Commit message:

 Re-export scuttle utilities to ensure scater:: still works.
 
Package: lipidr
Commit: a5ced6d3c9cd7df019f9c5e2221c2acd07280a5d
Author: Ahmed Mohamed <mohamed@kuicr.kyoto-u.ac.jp>
Date: 2020-06-04 14:24:50 +1000
Commit message:

 update roxygen / version pump
 
Package: scuttle
Commit: 7120e64e627f312716b8ea56b2831b67888a266e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-03 20:41:27 -0700
Commit message:

 Renamed quickPerCell subset.fields= to avoid subset= clash.
Bugfix to deprecated pseudo-count argument.
 
Package: seqsetvis
Commit: 5abe96a1954b23cd1c002edfc57dae94210123cd
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-06-04 00:08:41 -0400
Commit message:

 parallelization of GRanges

required fragLens precalc for ssvFetchBam

required file_attribs passthrough to ssvFetchSignal

ssvFetchSignal and ssvFetchBam now use
  .get_file_attribs
  .get_unique_names
 
Package: seqsetvis
Commit: cc7fde7cf23f1839a6c22ff007b1aa484e4e03c9
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-06-03 12:12:28 -0400
Commit message:

 Added n_region_splits to ssvFetchSignal and implemented
 
Package: seqsetvis
Commit: fe44eb2cc1139fd600eacf6f24a91a4931e5ece6
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-06-02 12:26:22 -0400
Commit message:

 bugfix - x mismatch for stranded view calls and odd sample windows
 
Package: seqsetvis
Commit: ba67d91cdf1db87e87058915202b56d624108e5b
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-06-02 10:35:25 -0400
Commit message:

 fix spelling error
 
Package: seqsetvis
Commit: c4f6942cc422ac24ec55bc64b27266ff7b95852c
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-05-04 07:53:16 -0400
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/seqsetvis
1.9
 
Package: seqsetvis
Commit: 15ee70987bc9b369d1023a5e27720619fb9d950b
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2020-05-04 07:51:08 -0400
Commit message:

 travis dep libgsl-dev
 
Package: bsseq
Commit: fd51762ce0b6ce73dc4c87db587dd7674b198193
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2020-06-04 13:06:29 +1000
Commit message:

 Version bump
 
Package: bsseq
Commit: b0c2777f11874c65b1cfe135cc3a38e0ea8c173c
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2020-06-04 13:06:19 +1000
Commit message:

 Another attempt to fix links in Rd files to quieten R CMD check on Windows

- According to Martin, this is the 'simplest solution', which lets the help system resolve the location dynamically (https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016552.html)
 
Package: IRanges
Commit: 783963dc3b5f32e3a5d4ce0dc4dbd93899eaf2b2
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-03 19:17:36 -0700
Commit message:

 Prefix names of all .Call entry points with C_
 
Package: TPP
Commit: 34161f5ff4f5ed4b1629ee3bebe647a8d6f48379
Author: Dorothee Childs <childs@embl.de>
Date: 2020-06-04 02:11:10 +0200
Commit message:

 bump version
 
Package: TPP
Commit: 6acc51558cc0a6336209e2fc96cb9a1cde9667a9
Author: Dorothee Childs <childs@embl.de>
Date: 2020-06-04 02:10:37 +0200
Commit message:

 Fixed more bugs and warnings after update to dplyr v1.0.0.
 
Package: TPP
Commit: 5a2ba246523edfe3325c3636b47fdf44042b2fd0
Author: Dorothee Childs <childs@embl.de>
Date: 2020-06-04 01:35:04 +0200
Commit message:

 bump version
 
Package: TPP
Commit: 0a66bb192b74eb757a866573f31ea2762be4f98f
Author: Dorothee Childs <childs@embl.de>
Date: 2020-06-04 01:13:11 +0200
Commit message:

 Fixed bug and warnings after update to dplyr v1.0.0
 
Package: TPP
Commit: 2bd61dba469177ed9e53e9e6921c137e55ca0fdb
Author: Dorothee Childs <childs@embl.de>
Date: 2020-06-04 00:44:38 +0200
Commit message:

 re-render help files with roxygen 7.1.0
 
Package: breakpointR
Commit: 30030d46633d74c68c6d3a7edfa8824bb04232e6
Author: David Porubsky <david.porubsky@gmail.com>
Date: 2020-06-03 16:12:11 -0700
Commit message:

 Updating package NEWS
 
Package: IRanges
Commit: 710daeef6d03cb94b4e2c85a8efdfcb58502ca93
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-03 14:56:18 -0700
Commit message:

 'git clean -i' needs to see *.o and *.so files
 
Package: OrderedList
Commit: ce633d9d26a06bb7c89894e06fb15ab2e226f5d3
Author: Claudio Lottaz <claudio.lottaz@ur.de>
Date: 2020-06-03 22:48:17 +0200
Commit message:

 fix problem with R 4.0.0
Changes to be committed:
	modified:   DESCRIPTION
	modified:   R/OrderedList.R
	modified:   vignettes/tr_2006_01.Rnw
 
Package: IRanges
Commit: c4653d6151215759aace4be26fa845a1bb41d129
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-03 13:27:48 -0700
Commit message:

 Clarifies floating point precision artefacts returned by coverage()
 
Package: BEARscc
Commit: 3860d2870a07d2ce5fda712d2772a2df415b066d
Author: David Tyler Severson <seversond12@mail.wlu.edu>
Date: 2020-06-02 23:17:57 -0400
Commit message:

 - correcting incorrect merge
 
Package: BEARscc
Commit: 45ba9b48ac88c0b3b25f85dd5c9fca512db0797a
Author: David T. Severson <seversond12@mail.wlu.edu>
Date: 2020-06-02 23:14:19 -0400
Commit message:

 Merge pull request #1 from seversond12/RELEASE_3_11

-update RELEASE version number 
Package: BEARscc
Commit: 1fb831dcc10945b3ad3e8f001a98b777037cf2de
Author: David T. Severson <seversond12@mail.wlu.edu>
Date: 2020-06-02 23:13:29 -0400
Commit message:

 Merge branch 'master' into RELEASE_3_11 
Package: BEARscc
Commit: 771b19ac5443e09087cf320e397dbcd81e487bf3
Author: David Tyler Severson <seversond12@mail.wlu.edu>
Date: 2020-06-02 22:57:00 -0400
Commit message:

 -update RELEASE version number
- fixed bug due to deprecated SingleCellExperiment function isSpike()
	- vignette was altered to reflect change in syntax
	- single function in estimate_noise.R was altered to reflect change in syntax
	- data objects were altered so SingleCellExperiment objects stored in them would reflect updates to SingleCellExperiment package
- adjusted version appropriately for bioconductor bump
 
Package: S4Vectors
Commit: ac986e920ab6f8fed889d4597f529132bfe9eb27
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-03 11:58:39 -0700
Commit message:

 Small tweak to show() method for Rle objects

Now it uses showAsCell() instead of as.character() for more compact
display of the run values of the Rle object and for consistency with
other show() methods (e.g. with method for DataFrame objects).
 
Package: STAN
Commit: b26219562898d8fe99d20e7b8d9d20d6ab10879b
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2020-06-03 15:03:21 -0400
Commit message:

 Bump version with fixed merge conflicts
 
Package: STAN
Commit: 46037e428b60ea79d847c3a20711400afba503df
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2020-06-03 15:00:38 -0400
Commit message:

 Fix bad description file
 
Package: goSTAG
Commit: 906d13bc1337d6ea1d6ea5e6e29a1336a29abba2
Author: Brian Bennett <brian.bennett@nih.gov>
Date: 2020-06-03 14:54:53 -0400
Commit message:

 bug fix: is_a to isa
 
Package: GenomeInfoDb
Commit: 6046929d11fa43db3b12c8398956ac0bd4727f24
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-03 11:21:27 -0700
Commit message:

 Small tweak to internal utility fetch_species_index_from_Ensembl_FTP()
 
Package: breakpointR
Commit: 2586037e4e7e71fcd6e352aab85cf3babbae2c19
Author: David Porubsky <david.porubsky@gmail.com>
Date: 2020-06-03 11:15:39 -0700
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: breakpointR
Commit: f1872c8a1da0e4ca1210e10df4d29f589fba1c14
Author: David Porubsky <david.porubsky@gmail.com>
Date: 2020-06-03 11:14:59 -0700
Commit message:

 Added multi-size bin deltaW calculation
 
Package: breakpointR
Commit: 2f20e1d079fb7b495565f684285c2719ad7b74b0
Author: David Porubsky <david.porubsky@gmail.com>
Date: 2020-04-16 12:33:26 -0700
Commit message:

 Downgrading required R version
 
Package: breakpointR
Commit: 6e2b49381a1b292a06f3884b237840d104dd2296
Author: David Porubsky <david.porubsky@gmail.com>
Date: 2020-04-16 12:08:51 -0700
Commit message:

 Added multi sized deltaW calculation
 
Package: GenomicRanges
Commit: 1d4671fbb8c5f47121c995ceb4dab0740cbf975f
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2020-06-03 13:53:13 -0400
Commit message:

 Fix for .findKNN_all_k tests; added NEWS about findKNN
 
Package: OTUbase
Commit: aa9ae342017135bab08ee9ac822343c29b37105f
Author: Daniel Beck <danlbek@gmail.com>
Date: 2020-06-03 10:50:13 -0700
Commit message:

 Fixed vignette Unicode error
 
Package: SingleR
Commit: c65af47356b4ed2547274716ac54eac0132d0d04
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-03 09:30:41 -0700
Commit message:

 Bumped version and date.
 
Package: SingleR
Commit: 87321c5ea3eb37389286090f9ec24ca13280aff8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-03 09:30:25 -0700
Commit message:

 Migrated imports from scater to scuttle.
 
Package: batchelor
Commit: 115a0f44c70db7c12902d7d6abc42f290a34c703
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-03 09:01:34 -0700
Commit message:

 Bumped version and date.
 
Package: batchelor
Commit: 25c8da174ed866c756d4ef18dfb691711e69579a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-03 09:00:45 -0700
Commit message:

 Switched all imports from scater to scuttle.
 
Package: curatedMetagenomicData
Commit: 7b444742b66a9bc7e0b67c915af9bce143eb0cc3
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2020-06-03 17:57:01 +0200
Commit message:

 version bump for master
 
Package: curatedMetagenomicData
Commit: 012a38a536f5a2d089d39807a461bbc27accc236
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2020-06-03 17:50:01 +0200
Commit message:

 restore inst/commandline/curatedMetagenomicData, closes #163
 
Package: timeOmics
Commit: e02d23eb2c564b0a04015061099f24ca279a118c
Author: AB LabDesk <bodein.antoine@gmail.com>
Date: 2020-06-03 11:33:42 -0400
Commit message:

 Merge upstream
 
Package: timeOmics
Commit: 4862af3a9589f22bb7407fc39ddff7e368252183
Author: AB LabDesk <bodein.antoine@gmail.com>
Date: 2020-06-03 11:27:46 -0400
Commit message:

 version bump
 
Package: timeOmics
Commit: 91ee9a800977164a70dc5e4c25a0b0cf035964bc
Author: AB LabDesk <bodein.antoine@gmail.com>
Date: 2020-06-03 11:12:31 -0400
Commit message:

 fix left_join issue
 
Package: timeOmics
Commit: a055a2a95287eb2f734d17707c06163d739ae61e
Author: AB LabDesk <bodein.antoine@gmail.com>
Date: 2020-06-03 11:01:29 -0400
Commit message:

 fix vignette building error
 
Package: GSVA
Commit: 39765154f53b71aad66ea3e4da9b4b0c5c0fda8f
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2020-06-03 17:23:16 +0200
Commit message:

 Merge branch 'pablo-rodr-bio2-newshinyplots'
 
Package: GSVA
Commit: 10197c62852cad0f9825feb9193693c626275b97
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2020-06-03 12:12:49 +0200
Commit message:

 Added new ecdf plot
 
Package: isomiRs
Commit: 3cf6eac269af53eb6bfb5bd9abfe483ce7a75ff5
Author: Lorena Pantano <lorena.pantano@gmail.com>
Date: 2020-06-03 10:01:10 -0400
Commit message:

 fir n() error
 
Package: isomiRs
Commit: 1e610445b257e43b835e0f1b55612b0b8461c301
Author: Lorena Pantano <lorena.pantano@gmail.com>
Date: 2020-06-03 09:57:09 -0400
Commit message:

 fix n() error
 
Package: isomiRs
Commit: 99fb1ff8ec07d8d8cede00c31c86c6c35b541d78
Author: Lorena Pantano <lorena.pantano@gmail.com>
Date: 2020-05-26 15:20:15 -0400
Commit message:

 fix tibble error
 
Package: shinyTANDEM
Commit: b8a2af94cec8783bce7c299fb4ee8986bb3e9459
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-06-03 10:00:46 -0400
Commit message:

 User requested deprecation
 
Package: OncoSimulR
Commit: f4821fe3ac5206ac136dcba2c3435c4f175a1b5a
Author: ramon diaz-uriarte (at Phelsuma) <rdiaz02@gmail.com>
Date: 2020-06-03 15:57:39 +0200
Commit message:

 2.19.2: Updated ctb: added Magellan and exprTk and clarified contributions
 
Package: DEGreport
Commit: cff5b95364704c2e50c51095f48ababa15de34b3
Author: Lorena Pantano <lorena.pantano@gmail.com>
Date: 2020-06-03 09:54:46 -0400
Commit message:

 fix n() error
 
Package: DEGreport
Commit: 0cbb9c9b246f186b144033bc12729d5a05319ca9
Author: Lorena Pantano <lorena.pantano@gmail.com>
Date: 2020-06-03 09:52:54 -0400
Commit message:

 fix n() error from dplyr
 
Package: rTANDEM
Commit: 13849d9f2f1ce604f078c6431b1d90b743d64f07
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-06-03 09:54:06 -0400
Commit message:

 User Requested Deprecation
 
Package: FEM
Commit: ed48c7fba7c78ce878689c6b91d9a7f149a1fbbd
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2020-06-03 09:44:29 -0400
Commit message:

 Update maintainer in DESCRIPTION file
 
Package: PWMEnrich
Commit: edbeb81902370950241f414e2c69a5539a699a8a
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-06-03 09:27:15 -0400
Commit message:

 User requested deprecation
 
Package: PWMEnrich.Mmusculus.background
Commit: 7b4b28b115b27751f0acd84e38ad47f3c879e50d
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-06-03 09:25:57 -0400
Commit message:

 User requested deprecation
 
Package: PWMEnrich.Hsapiens.background
Commit: 43cd1beca0ff7032fd062fc727a72f676f519e5f
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-06-03 09:25:07 -0400
Commit message:

 User Requested Deprecation
 
Package: PWMEnrich.Dmelanogaster.background
Commit: 259aaf20f833f1afd29f16f5965a097082bc7cbd
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-06-03 09:24:22 -0400
Commit message:

 User requested deprecation
 
Package: Organism.dplyr
Commit: f1ef937aa9683f1383dbe89ee5fa460a3d2644e6
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2020-06-03 09:05:16 -0400
Commit message:

 Finalizer fix and change SE to NSE dplyr functions
 
Package: RnaSeqSampleSizeData
Commit: 3ce8934c723c10d278e4e7dfbd47d0451685e646
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-06-03 08:39:05 -0400
Commit message:

 Package deprecation

  - Unresponsive
  - Software removed in previous release
 
Package: mitoODEdata
Commit: 4c39d79f28483c6ab7f1b166cffb72c858f18b5a
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-06-03 08:37:56 -0400
Commit message:

 Package Deprecation

  - Unresponsive
  - Email bounced
  - Software package already deprecated in previous release
 
Package: FunciSNP.data
Commit: 5ee8f568fa99629f7514dba0841b788bfd1f52a3
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-06-03 08:36:15 -0400
Commit message:

 Package deprecation

  - Unresponsive
 
Package: RNAinteractMAPK
Commit: db496581d1cba920b1904c5d03737b400edf5823
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-06-03 08:35:03 -0400
Commit message:

 Package Deprecation

  - unresponsive
  - undeliverable email
 
Package: Mulder2012
Commit: 2b5cf71577c28da8aaf2f490c4f35008d4edbc47
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-06-03 08:34:00 -0400
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/Mulder2012

Conflicts:
	DESCRIPTION
 
Package: Mulder2012
Commit: a70679c42a644deb52f77dfb71c8eb793e06bf7d
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-06-03 08:33:05 -0400
Commit message:

 Package deprecation

  - unresponsive
  - undelierable email
 
Package: sevenbridges
Commit: c775e8940bf2b8c6250219bfbac78955d7549ef5
Author: Nan Xiao <me@nanx.me>
Date: 2020-06-03 06:20:37 -0400
Commit message:

 v1.19.1
 
Package: DiffLogo
Commit: 4748bd1c81c5fbb5f0442f2e20064af68dc96d21
Author: Hendrik Treutler <hendrik.treutler@gmail.com>
Date: 2020-06-03 10:17:54 +0200
Commit message:

 Version bump
 
Package: DiffLogo
Commit: 445d00409bc5fbb0ac53d572a922d3485a1f8ce6
Author: Hendrik Treutler <hendrik.treutler@gmail.com>
Date: 2020-06-03 10:03:41 +0200
Commit message:

 Fix-conflicts
 
Package: scran
Commit: 441280ccf96824fb5965e46d709ed3282435af3c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-03 00:52:35 -0700
Commit message:

 Purged scater from Examples, except in cases requiring PCA.
 
Package: scran
Commit: 81642b862ae0ae949fba30b3247a751b3b566e4b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-02 23:50:35 -0700
Commit message:

 Merge branch 'tscan'
 
Package: scran
Commit: 3e5b5bd7c6862b8b88180b7d1f71821fa030845e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-28 23:52:44 -0700
Commit message:

 Keep reporting 'logFC' column when one coef is supplied.
Test fix for output column names with the coef= option.
 
Package: scran
Commit: 9fb820541e4e0ed507d86a3e91a9af8c30660052
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-28 23:51:26 -0700
Commit message:

 Docfixes, reoxygenated.
 
Package: scran
Commit: 1dbd6613516671c1f390fc155f6c74d7905a1ee8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-28 22:27:50 -0700
Commit message:

 Added tests for testPseudotime.
Clarified meaning of spline coefs for multi-path return value.
Fixed names again, d.f. check, removal of shared cells.
 
Package: scran
Commit: 1f3c3d6db8a8baba11cce79aa10c95bc174f02b7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-28 21:58:26 -0700
Commit message:

 Ensure cells assigned to branch points show up in all paths.
 
Package: scran
Commit: 1c591fefda1475b44e92211f9a79380c985909c3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-28 21:17:21 -0700
Commit message:

 Avoid low-rank problems when pseudotime values are duplicated.
Fixed prefixing in column names for multi-path analyses.
 
Package: scran
Commit: a1dc761ebc0b9790a5614fa33f9c066b93ff7bbf
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-25 23:26:28 -0700
Commit message:

 Initial draft of utility to test for differences in pseudotime.
 
Package: scran
Commit: 82e4555d281e3a4bae5f36a9643fd59e79cdd634
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-25 17:36:27 -0700
Commit message:

 Added coefs= option for easier null specification, docfixes.
 
Package: scran
Commit: b561b74bc4baaa7af35249bbe0cc5f2d5f0120e7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-25 17:21:40 -0700
Commit message:

 Reoxygenated, updated NEWS.
 
Package: scran
Commit: 53f794ee6ad4bf65cd2f33d033683700dc3b1431
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-25 16:57:49 -0700
Commit message:

 Added basic and fast testing for linear models.
 
Package: scran
Commit: 5937a74cb315d8159820fa78d75d140fab3ad0f6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-12 23:12:31 -0700
Commit message:

 Added more test scenarios for clusterMST pseudotime.
 
Package: scran
Commit: 72df67e1ffdbbb71af8893e03102231962e83c29
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-11 23:44:36 -0700
Commit message:

 Docfixes for ClusterMST functions, reoxygenated.
 
Package: scran
Commit: 3d63dc6260bb994c27f652b57181f078cd73fbcc
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-11 23:41:50 -0700
Commit message:

 Added preliminary tests for *ClusterMST functions.
Bugfix to avoid unnecessary randomness.
Extra check for consistent clusters and centroid inputs.
 
Package: scran
Commit: 07f2c575588406fd1969d4d9c18445f871a8ab1f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-11 00:46:45 -0700
Commit message:

 Initial draft of TSCAN-like functions for basic trajectory analysis.
 
Package: Dune
Commit: 51575c98cebc9350f85b55df6e1f09541c8b395f
Author: Hector <hector.rouxdebezieux@berkeley.edu>
Date: 2020-06-03 09:31:52 +0200
Commit message:

 Update test-auxilliary-functions.R
 
Package: Dune
Commit: 0f3839f31cf2e8d140d95cecfed36a2f2447d5c1
Author: Hector <hector.rouxdebezieux@berkeley.edu>
Date: 2020-06-03 09:23:31 +0200
Commit message:

 work following dplyr updates
 
Package: Dune
Commit: d67247df9acfe94e37bda63d909c1143177b2c97
Author: Hector <hector.rouxdebezieux@berkeley.edu>
Date: 2020-04-29 22:50:23 +0200
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/Dune
 
Package: Dune
Commit: 45c6ac6389e28cbab391fa74b55eae03a295f39d
Author: Hector <hector.rouxdebezieux@berkeley.edu>
Date: 2020-04-18 15:16:37 +0200
Commit message:

 Update README.md
 
Package: Dune
Commit: f7c4744929060f5ac2090751d4cf23438bfa97ec
Author: Hector <hector.rouxdebezieux@berkeley.edu>
Date: 2020-04-18 15:14:28 +0200
Commit message:

 Update README.md
 
Package: Dune
Commit: 5de6f94a4dcc0d2b8a5633f88792102b1a7b3c01
Author: Hector <hector.rouxdebezieux@berkeley.edu>
Date: 2020-04-18 15:04:23 +0200
Commit message:

 Update README.md
 
Package: AlphaBeta
Commit: 0a67a4c4bcaa63930af74f859470aec0876b261a
Author: Yadi <shahryary@gmail.com>
Date: 2020-06-03 09:30:22 +0200
Commit message:

 bug fix: fixed buildPedigree function
 
Package: AlphaBeta
Commit: 601fa96449e4c63b2326fb3a60645d88c5a55c04
Author: Yadi <shahryary@gmail.com>
Date: 2020-06-03 09:23:37 +0200
Commit message:

 bug fix: fixed rcMethlvl file and dataread
 
Package: AlphaBeta
Commit: 506ce66438db9d4a614e7452f82a934d8add1f99
Author: Yadi <shahryary@gmail.com>
Date: 2020-06-02 00:29:40 +0200
Commit message:

 Merge remote-tracking branch 'origin/master'

 
Package: AlphaBeta
Commit: 329fb490a6078a51af41231e63677091d93fb6cc
Author: Yadi <shahryary@gmail.com>
Date: 2020-06-02 00:29:33 +0200
Commit message:

 

removed project file 
Package: AlphaBeta
Commit: adbea4f253490a2b01c460d613868a4bfcc639f6
Author: Yadi <shahryary@gmail.com>
Date: 2020-06-02 00:28:13 +0200
Commit message:

 Merge pull request #1 from jlab-code/RELEASE_3_11

Release 3 11 
Package: AlphaBeta
Commit: 975c307b39cbd0a02f2aa606220fe3a7618622c6
Author: Yadi <shahryary@gmail.com>
Date: 2020-06-02 00:25:09 +0200
Commit message:

 Merge branch 'master' into RELEASE_3_11 
Package: AlphaBeta
Commit: 02ee911f7cc16c9179d2f0fadc07ec4443544e37
Author: Yadi <shahryary@gmail.com>
Date: 2020-06-02 00:21:14 +0200
Commit message:

 update RELEASE version number
 
Package: AlphaBeta
Commit: bf50fd1868f2e8eee399e3851ce07b31cd54bd0f
Author: Yadi <shahryary@gmail.com>
Date: 2020-06-02 00:16:44 +0200
Commit message:

 

bug fix: fixed buildPedigree function 
Package: scater
Commit: 9158af348a0e1ebf4409619ca2a91793afef5434
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-03 00:23:58 -0700
Commit message:

 bumped version and date, updated NEWS.
 
Package: scater
Commit: 11abf46eacd8da8b9238d129d1a3d9aeb358c163
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-03 00:08:56 -0700
Commit message:

 Merge branch 'stripped'
 
Package: scater
Commit: b430e9604f8b2a2ffdaffd6aedaafbccb0eb9b87
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-02 23:55:55 -0700
Commit message:

 Massive reoxygenation to account for scuttle migration.
 
Package: scater
Commit: 3c07765e8d95219d17305c7aac70d7e4ecf98953
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-08 01:19:26 -0700
Commit message:

 Stripped out all of the unnecessary stuff in the vignette.
 
Package: scater
Commit: e709d8025f08f709f3694e3ca1e686f1e72a7d3c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-08 01:18:33 -0700
Commit message:

 Fixes to replace imports from migrated functions.
 
Package: scater
Commit: 0f03f01543407446c0e4bb3f35572df815a9ac4c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-07 23:17:41 -0700
Commit message:

 Various updates to use migrated functions in scuttle.
 
Package: scater
Commit: e3e25a6fa6a6828546e030f2863d760d6129450d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-07 23:08:35 -0700
Commit message:

 Removed tests that were migrated to scuttle, updated remainders.
 
Package: scater
Commit: 40faff82a4758674dbebfe4aee63be6880c05254
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-07 21:23:14 -0700
Commit message:

 Restored the scater-pkg documentation page.
 
Package: scater
Commit: ea82d7311ed8b865371987caf360136d194591f3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-07 21:15:16 -0700
Commit message:

 Purged Rcpp as it is no longer necessary.
 
Package: scater
Commit: f19366b71820e7e0ba89dae5993eef90814d7729
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-07 20:59:40 -0700
Commit message:

 Stripped out all functions migrated to scuttle.
 
Package: scater
Commit: 7f5fc9f9dad841d93200073d1f6b418f586ab567
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-03 00:08:29 -0700
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/scater
 
Package: scater
Commit: 8d7eb063fb027ed5671d5d4cf3ca1ede6403c9c5
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-11 23:57:52 -0700
Commit message:

 Added GitHub actions to check compilation.
 
Package: simpleSingleCell
Commit: b8fce07a92e8c77009a796c94c68d324aa432dec
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-02 23:46:06 -0700
Commit message:

 Cleaned up Makefile to use OSCA's master.
 
Package: scran
Commit: a0248f8be1e5e2db5dfb702dc537c8e88544d25b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-02 23:39:04 -0700
Commit message:

 Purged test dependencies on scater.
 
Package: scran
Commit: 90aa77aaa1421372ce072372e6d5ccc3cec5be1a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-02 23:29:20 -0700
Commit message:

 Just compute the Rand index directly if requested.
 
Package: scran
Commit: b5c1a6df0d6daeef514b373b93ab85bcc0ac89e7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-06-02 22:53:51 -0700
Commit message:

 Bumped version and date, updated NEWS.
 
Package: scran
Commit: 30c53acd4d68627e5e500ea4392f57d47a7bede2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-10 15:54:16 -0700
Commit message:

 Reoxygenated.
 
Package: scran
Commit: 107d02e700db3cca09f09d36be1fb07eb0d1cfab
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-10 14:55:33 -0700
Commit message:

 Added tests for coassignProb, extended clusterRand tests.
Hardened coassignProb to NAs during summarization.
 
Package: scran
Commit: 3b92098eeda3ebf667981ec859e7e87e0edc0b7e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-10 12:23:30 -0700
Commit message:

 Generalized bootstrapCluster to work with any comparison function.
 
Package: scran
Commit: 77ee06614109276247618bceda237b9eeda5e4b7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-10 11:56:39 -0700
Commit message:

 Added links from other functions to clusterRand.
 
Package: scran
Commit: fa7a71c6d41ff8350db93d4675fbeeee25e67711
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-10 11:55:59 -0700
Commit message:

 Added tests for clusterRand.
 
Package: scran
Commit: 93c629d598485dcd000e945ad99ac521037cf221
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-10 11:37:14 -0700
Commit message:

 Added clusterRand to do a clusterwise breakdown of the Rand index.
 
Package: scran
Commit: 77ea38ffdb76d03c6c72b615f877c18884ac40a7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-09 23:33:54 -0700
Commit message:

 Updated dependencies.
 
Package: scran
Commit: 594165ffed4db5edcbc801df1f0f41ccc3afb719
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-09 23:00:04 -0700
Commit message:

 Recompiled attributes, reoxygenated.
 
Package: scran
Commit: 78a30da98aa01b7be066142d78c1b8ba1706630c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-09 22:57:52 -0700
Commit message:

 Updated and streamlined vignette.
 
Package: scran
Commit: f98935ad0eabccc2398331ea41aff00c9425ed55
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-09 22:57:02 -0700
Commit message:

 Updated all tests for the scuttle transition.
Removed accidentally committed file.
 
Package: scran
Commit: 107c07198931a36a976ac0512d8281c8c61d380b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-09 20:11:54 -0700
Commit message:

 Bugfixes everywhere for the integrated scuttle code.
 
Package: scran
Commit: 979296261966e5bf35db971e16a23309fb856c25
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-09 18:40:26 -0700
Commit message:

 Purged unnecessary C++ utilities.
 
Package: scran
Commit: feb53ff1aae97c3420eff980de0fe7d6cff3eade
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-09 17:17:29 -0700
Commit message:

 Replace linear model fitting code with scuttle's version.
Streamlined code for correlation internals.
 
Package: scran
Commit: 83d1db1d8d89e2a8a0e01131d16e55e8f65a27b4
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-09 17:15:48 -0700
Commit message:

 Replace all linear model fitting code with scuttle class.
 
Package: scran
Commit: 6e2a9480d1062bcff9b2847735c5174930638180
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-05-09 15:46:14 -0700
Commit message:

 Switched all imports from scater to scuttle.
Updated various calls to scuttle utilities.
 
Package: primirTSS
Commit: 5a5f8cc7be6b313fde108259303b66b55ab8c33e
Author: Pumin Li <ipumin@163.com>
Date: 2020-06-03 14:34:37 +0800
Commit message:

 Fixed conflicts in version change

Merge remote-tracking branch 'upstream/master'

# Conflicts:
#	DESCRIPTION
 
Package: primirTSS
Commit: 66e115ac5e20dabfb76452d4e7abbdd86ba8aad2
Author: Pumin Li <ipumin@163.com>
Date: 2020-06-03 14:05:32 +0800
Commit message:

 data_frame to tibble
 
Package: BEARscc
Commit: 0315da685c58b2e699bed8db7735f57f64f82e44
Author: David Tyler Severson <seversond12@mail.wlu.edu>
Date: 2020-06-02 22:57:00 -0400
Commit message:

 - bumping version change for bioconductor
 
Package: BEARscc
Commit: 2493cb4324b79b23f041b4265fda36b49a44183f
Author: David Tyler Severson <seversond12@mail.wlu.edu>
Date: 2020-06-02 22:53:23 -0400
Commit message:

 - adjusted SingleCellExperiment use to accommodate recent changes that made isSpike defunct
	- specifically switched to altExp as recommended by SingleCellExperiment authors
	- this change was refected in the data objects as well as in the estimate_noise functions and the vignette markdown document
- compressed the data objects to be smaller
 
Package: BUSpaRse
Commit: 3c9922c95a02ebbe569facee9ea8f922a47a5370
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2020-06-02 16:36:58 -0700
Commit message:

 Forgot that this is supposed to be the devel branch
 
Package: BUSpaRse
Commit: 8796fee8e3f217d2d3ec5e8db781c79891a9587e
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2020-06-02 16:35:18 -0700
Commit message:

 Version bump for bug fix
 
Package: BUSpaRse
Commit: ee52bfa4b11a5607e10dcba25a265df633641533
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2020-06-02 16:32:50 -0700
Commit message:

 Make sure that the expected results are tibbles as now all data frame outputs are tibbles
 
Package: BUSpaRse
Commit: d3e61f3e6d7661d5345a3fb9a8184ab999201f4b
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2020-06-02 16:03:16 -0700
Commit message:

 Return tibble instead of base R data frame; this is causing trouble in a newer version of testthat
 
Package: BUSpaRse
Commit: 558eab73c38c2ed368cd44b0b92c7192efa5fb0b
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2020-05-01 18:41:55 -0700
Commit message:

 I don't want to use Travis any more since Bioconductor runs the checks daily anyway and Travis has trouble with FTP, which means the Travis check always breaks at dl_transcriptome.
 
Package: BUSpaRse
Commit: a2fae94f9db579d98d5847e0e92ce9c72df277db
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2020-04-29 11:37:40 -0700
Commit message:

 version bump for release 3.11
 
Package: BUSpaRse
Commit: e61520722e9281f578f095a20f2b32bf8f8bc524
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2020-04-29 11:36:50 -0700
Commit message:

 Get updates to 3.11 release
 
Package: GGBase
Commit: 21615f960b46be69e77aed023b80826b787c3294
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2020-06-02 18:31:48 -0400
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/GGBase
 
Package: GGBase
Commit: 7cb40e85287c7179f96e838b70304c0bcc380346
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2020-02-27 17:08:35 -0800
Commit message:

 improving assays withDimnames situation
 
Package: CSSQ
Commit: 5f7faa411603f8af17f4dfad82a964dcf60d82c1
Author: Ashwath <akumar301@gatech.edu>
Date: 2020-06-02 18:02:11 -0400
Commit message:

 Fixed maintainer
 
Package: CytoML
Commit: c5abe525b51fb279e8d3916ce837d06336205b52
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-06-02 14:31:14 -0700
Commit message:

 Merge branch 'master' into devel
 
Package: CytoML
Commit: 1404a6d51abc58503c24f80568fe56d47cc1bcc5
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-06-02 14:27:24 -0700
Commit message:

 bump
 
Package: CytoML
Commit: 5b7d6d76f98e13c2ab00a071725545b380367469
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-06-02 11:47:17 -0700
Commit message:

 importFrom flowWorkspace cytoset
 
Package: CytoML
Commit: bc8ddcfd48ab23b3d6ffdd8f97d8e83170353b0d
Author: Greg Finak <greg.finak@gmail.com>
Date: 2020-06-01 11:35:01 -0700
Commit message:

 Update LICENSE 
Package: CytoML
Commit: 8e58274a0cc602b861eb8d448cec37ed899277c4
Author: Greg Finak <greg.finak@gmail.com>
Date: 2020-06-01 11:33:33 -0700
Commit message:

 Update LICENSE 
Package: CytoML
Commit: 3e31a2588b119ccc6ef09a47672f3475466d6df2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-30 12:30:43 -0700
Commit message:

 flowjo_to_gatingset alternatively takes cytoset as data input #100
 
Package: CytoML
Commit: dee2b21bc16608b88437b15311fc7ccac2caac01
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-06-02 14:27:24 -0700
Commit message:

 bump
 
Package: CytoML
Commit: 4b216a679a195b7ad434e71137e3a58385dac471
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-06-02 11:47:17 -0700
Commit message:

 importFrom flowWorkspace cytoset
 
Package: CytoML
Commit: 5cf4da88e609c77ffd02e5cd318d3af51bc81ec1
Author: Greg Finak <greg.finak@gmail.com>
Date: 2020-06-01 11:35:01 -0700
Commit message:

 Update LICENSE 
Package: CytoML
Commit: 854b8400ed4483a7741899ce2a6aa61b447611e9
Author: Greg Finak <greg.finak@gmail.com>
Date: 2020-06-01 11:33:33 -0700
Commit message:

 Update LICENSE 
Package: CytoML
Commit: dab85bcd0a814c0ff1c97056e93f79fecbea08c9
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-30 12:30:43 -0700
Commit message:

 flowjo_to_gatingset alternatively takes cytoset as data input #100
 
Package: CytoML
Commit: aa3d71e43efbeb47e02181926ec64636c3a7a48a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-27 16:25:58 -0700
Commit message:

 bump
 
Package: CytoML
Commit: 6a208ee46b86782593b2d08d1871657572a91785
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-27 16:05:57 -0700
Commit message:

 prepend extra meta info to wsp file generated by gs-to-flowjo
 
Package: CytoML
Commit: 93a1d64f43f1cf97c63735df40c94d9f28221dfd
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-26 15:33:11 -0700
Commit message:

 #99: Implement subset by filtering expression in flowjo_to_gatingset
 
Package: CytoML
Commit: 35927af373b656b95442315e505594cff4818386
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-22 18:37:21 -0700
Commit message:

 Handle spaces in paths in gatingset_to_flowjo
 
Package: CytoML
Commit: 2b77c5d148c5369e4dafb23152ca17be98632412
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-22 17:36:33 -0700
Commit message:

 bump
 
Package: CytoML
Commit: d126c7814f775bc83487ec6d135a77b4d31827bc
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-22 17:36:15 -0700
Commit message:

 Add docker image version match to gatingset_to_flowjo
 
Package: CytoML
Commit: b7b45068c825fb924c514e6b14b824a159d3afc4
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-21 18:01:32 -0700
Commit message:

 Update docs
 
Package: CytoML
Commit: 24dd570a480fdfaefb4869f2a9cbba063df88bb4
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-21 14:54:08 -0700
Commit message:

 Merge branch 'master' of https://github.com/RGLab/CytoML
 
Package: CytoML
Commit: 4bb7987a9faf6726baa957c217a004cadf993446
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-21 14:53:53 -0700
Commit message:

 Let gatingset_to_flowjo use binary or docker
 
Package: CytoML
Commit: 6eb3cfef445aaa4a8d6922649516950ccebe16a5
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-20 17:31:53 -0700
Commit message:

 bump
 
Package: CytoML
Commit: 0cb5ff52de4ab3c9a594d036db321f223a270b30
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-20 17:30:51 -0700
Commit message:

 add skip_faulty_gate arugment to flowJo parser. #96
 
Package: CytoML
Commit: f99423c25c76ecafe107329806331eafa6a7b705
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-20 15:58:36 -0700
Commit message:

 add test case for redefined_error xml
 
Package: CytoML
Commit: 887039862f335bd3f3705f2b1b185fdc33be2b22
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-01 09:56:29 -0700
Commit message:

 Make docker availability check work with Windows
 
Package: CytoML
Commit: 7f42b196931a1987f96ff42039d61d69753fb391
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2020-04-27 18:59:01 +0000
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_11 branch
 
Package: CytoML
Commit: a46de31a6b188e2a88939dc844c672337bf271bb
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2020-04-27 18:59:01 +0000
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
 
Package: flowWorkspace
Commit: af891da9b0561e0cb3de5c5cac27f101f4e17069
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-06-02 12:37:06 -0700
Commit message:

 Merge branch 'master' into devel
 
Package: flowWorkspace
Commit: 0ffeecc7254742ea69d2f4ffe4b3d6fe258c0c58
Author: Greg Finak <greg.finak@gmail.com>
Date: 2020-06-01 11:38:37 -0700
Commit message:

 Update LICENSE 
Package: flowWorkspace
Commit: 6d2e6498132641937509a60104089d3fc2a49b0b
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-29 16:18:03 -0700
Commit message:

 Avoid AsIs attribute in .getPopChnlMapping
 
Package: flowWorkspace
Commit: 8d658b4d67a37bf79f9cccd216359d660ad7445c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-20 17:27:55 -0700
Commit message:

 bump
 
Package: flowWorkspace
Commit: dae1c926c7339143046667dd8c5285c8a90a6616
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-20 13:15:09 -0700
Commit message:

 update test due to RGLab/flowCore@654f0c3
 
Package: flowWorkspace
Commit: c4498b1bbc8d7854403320c5b8c0300fbb969df1
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-20 02:14:26 -0700
Commit message:

 #327: Appropriately add flowJo_fasinh transformation
 
Package: flowWorkspace
Commit: 879af942b16b10861b31e7585773820261d719dd
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-18 21:27:48 -0700
Commit message:

 fix gs_get_singlecell_expression_by_gate when gates are defined on the channel that does not have marker #329
 
Package: flowWorkspace
Commit: 76d58909cdf08048c7348030cc8fa7554870c20f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-14 16:34:52 -0700
Commit message:

 Merge branch 'master' of github.com:RGLab/flowWorkspace
 
Package: flowWorkspace
Commit: a362221898a96a5a9e0b5aa529da37b5daa7646f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-05-14 16:15:34 -0700
Commit message:

 faster gs_pop_remove
 
Package: flowWorkspace
Commit: af4661fc94da7ae5512acb8fa341668f06da1f1e
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-05-13 09:45:49 -0700
Commit message:

 Remove residual author tag from cytoframe doc
 
Package: SingleCellMultiModal
Commit: 9401104d7db968db8357ff088a799d0af9f81e2b
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-06-02 14:44:35 -0400
Commit message:

 version bump
 
Package: SingleCellMultiModal
Commit: 0124e2efeec30f862404f03638c57bd986d850ab
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-06-02 13:40:53 -0400
Commit message:

 update csv metadata file
 
Package: SingleCellMultiModal
Commit: 8dcb2074c1b99f99396ff9c81c1963f0e7a00656
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-06-02 13:20:34 -0400
Commit message:

 version bump
 
Package: SingleCellMultiModal
Commit: b5b36ab1413c4639c8f0e24c683683a0c476acfc
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-06-02 13:07:51 -0400
Commit message:

 update metadata helpers
 
Package: S4Vectors
Commit: 72ce5b50e1bbf648658e3c9acf5907fe5445cef7
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-02 09:33:50 -0700
Commit message:

 Small tweak to S4Vectors:::.select_fast_path()

NAs in a numeric list-like subscript ("NL subscript") shouldn't
prevent S4Vectors:::subset_List_by_List() from selecting fast path
S4Vectors:::.fast_subset_List_by_NL().  The use case is to allow
fast subsetting of List derivatives that accept NL subscripts with
NAs (e.g. CompressedSplitDFrameList objects).
Note that S4Vectors:::subset_List_by_List(x, i) will still fail as
usual if 'x' is a List derivative that does NOT accept NL subscripts
with NAs (e.g. CompressedGRangesList objects) but 'i' is such a
subscript.
 
Package: scPCA
Commit: c6e58c59ff29ecc4ed86bbc8244fdaa267fae241
Author: Philippe Boileau <pboileau.swim@gmail.com>
Date: 2020-06-02 09:08:06 -0700
Commit message:

 Updating version number
 
Package: scPCA
Commit: a72a89d480f1aac1b3986e28b20a0adf6b12c34c
Author: Philippe Boileau <pboileau.swim@gmail.com>
Date: 2020-06-02 09:05:34 -0700
Commit message:

 Updating travis ci badge and bumping version
 
Package: scPCA
Commit: 15372d79a7142b83e3b5a385461e97072ec24d73
Author: Philippe Boileau <pboileau.swim@gmail.com>
Date: 2020-06-01 14:18:55 -0700
Commit message:

 updating required packages in .travis.yml
 
Package: scPCA
Commit: 8689e9ffeb96ec83698f3cf4cc61491da7a3bfe3
Author: Philippe Boileau <pboileau.swim@gmail.com>
Date: 2020-06-01 14:12:51 -0700
Commit message:

 attempting travis ci fix
 
Package: scsR
Commit: 5a1ce3eb943ee5c8f69161782694797f6482040a
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-06-02 11:47:56 -0400
Commit message:

 User requested deprecation
 
Package: PAST
Commit: 10105a6b3d4a54c23ee3cd8ac71e90657c9b1f4d
Author: Adam Thrash <cathrash92@gmail.com>
Date: 2020-06-02 11:19:30 -0400
Commit message:

 Update DESCRIPTION

Fix incorrect commit
 
Package: PAST
Commit: 57f7516189c630ec340b8fd2976f6dd4901e1c79
Author: Adam Thrash <cathrash92@gmail.com>
Date: 2020-06-02 11:12:50 -0400
Commit message:

 merge latest
 
Package: PAST
Commit: bfb0143548d865b7c9af01247af953199557ff7d
Author: Adam Thrash <cathrash92@gmail.com>
Date: 2020-06-02 11:07:34 -0400
Commit message:

 Merge pull request #41 from IGBB/issue_40

bug fix 
Package: PAST
Commit: 23fefd85d09d286680442774d79f1d9a4e24d9d4
Author: Adam Thrash <cathrash92@gmail.com>
Date: 2020-06-01 13:42:06 -0400
Commit message:

 bug fix
 
Package: PAST
Commit: 45784045b9e46425d8499d3aa0735e99555a8390
Author: Adam Thrash <cathrash92@gmail.com>
Date: 2020-04-30 09:31:16 -0400
Commit message:

 update RELEASE version number
 
Package: PAST
Commit: 39ca67df0612e28bffa8ecdffd7700bf3565487f
Author: Adam Thrash <cathrash92@gmail.com>
Date: 2020-04-30 09:29:34 -0400
Commit message:

 bug fix: handle no blocks in LD and no genes associated with pathway
 
Package: universalmotif
Commit: b2ce5aa047d85017602d1e33748be4776c2788a7
Author: Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
Date: 2020-06-02 16:36:42 +0200
Commit message:

 use consistent c++ rng
 
Package: universalmotif
Commit: 01b9a6bcd5d997dc9b29e5c2d598816101032207
Author: Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
Date: 2020-06-02 10:07:23 +0200
Commit message:

 todo
 
Package: universalmotif
Commit: 0cd806280beb639e66a2f6268c5945da17179e0a
Author: Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
Date: 2020-05-15 21:46:24 +0200
Commit message:

 fix spelling
 
Package: icetea
Commit: e4153cd3a9116a117e6efafa7dbf5a4ee8a7968d
Author: vivekbhr <bhardwaj@ie-freiburg.mpg.de>
Date: 2020-06-02 14:03:21 +0200
Commit message:

 version back to 1.7
 
Package: icetea
Commit: abfc4d4e8cb6762338574ead08cfb913eb9a9d7e
Author: Vivek Bhardwaj <vivekbhr@users.noreply.github.com>
Date: 2020-06-02 12:39:15 +0200
Commit message:

 Merge pull request #46 from vivekbhr/develop

upstream changes + update 
Package: icetea
Commit: 57d2d6f9fdfcd54e5b33bc4e8aec09f6cb0a7508
Author: vivekbhr <v.bhardwaj@hubrecht.eu>
Date: 2020-06-02 12:38:15 +0200
Commit message:

 updated news
 
Package: icetea
Commit: 9a1593cfdd82f7aa6c76f0b6f709a6cdc5aff112
Author: vivekbhr <v.bhardwaj@hubrecht.eu>
Date: 2020-05-19 16:53:25 +0200
Commit message:

 added citation
 
Package: icetea
Commit: d8699e7c3dc9f0bba974666525e8e828ecd0c5ab
Author: vivekbhr <v.bhardwaj@hubrecht.eu>
Date: 2020-05-19 16:53:12 +0200
Commit message:

 less messages in example
 
Package: icetea
Commit: 4a623d6272e4348288063d4ac4da88a51ad090c4
Author: vivekbhr <v.bhardwaj@hubrecht.eu>
Date: 2020-05-19 12:52:30 +0200
Commit message:

 new function to call peaks by 3 or 5p
 
Package: icetea
Commit: b854dcdf3e9f10bb2ec9f099238572c45bb328f4
Author: vivekbhr <v.bhardwaj@hubrecht.eu>
Date: 2020-05-18 12:33:32 +0200
Commit message:

 update email. update tests
 
Package: icetea
Commit: dd9ec34ea1b23a39aef260d8576b327267f78d51
Author: vivekbhr <bhardwaj@ie-freiburg.mpg.de>
Date: 2020-05-18 12:31:06 +0200
Commit message:

 update
 
Package: icetea
Commit: 6a37139e95ca70517322f99000ee742d6552787e
Author: vivekbhr <bhardwaj@ie-freiburg.mpg.de>
Date: 2020-05-17 12:51:43 +0200
Commit message:

 update to 4.0.0
 
Package: GCSConnection
Commit: 9bfbee4c537acce730db39dd255bd3042609591e
Author: Jiefei-Wang <szwjf08@gmail.com>
Date: 2020-06-02 18:40:21 +0800
Commit message:

 version bump
 
Package: GCSConnection
Commit: 5397810f1fa48dfa1953cf736543c864d5b79994
Author: Jiefei-Wang <szwjf08@gmail.com>
Date: 2020-06-02 18:39:30 +0800
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/GCSConnection
 
Package: GCSConnection
Commit: 0881a08aac3a1a66b20993de6349de15f97209ec
Author: Jiefei-Wang <szwjf08@gmail.com>
Date: 2020-06-02 18:37:19 +0800
Commit message:

 Fix some gramma issues in the vignette
 
Package: CAMERA
Commit: 45384c6aceb8abdb311335e3296695c75b50c651
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2020-06-02 11:43:49 +0200
Commit message:

 Push new devel version to BioC
 
Package: CAMERA
Commit: 21ce8c3fe06ba359c9c9a052c0d3ceef7cb2e6e9
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2020-05-06 21:50:45 +0200
Commit message:

 Merge pull request #46 from jmorim/master

Fix plotPsSpectrum() 
Package: CAMERA
Commit: 27c0b3466948120954f12894844f61c161fc3af4
Author: jmorim <jmorim@github.com>
Date: 2020-05-06 15:12:01 -0400
Commit message:

 Fixed plotEIC legend not labelling m/z's that didn't have assigned adducts
 
Package: CAMERA
Commit: 0ff0ebf7a9de2adb18e51ccf6fc278b391a40906
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2020-03-21 22:26:55 +0100
Commit message:

 Merge pull request #23 from sneumann/sneumann-patch-1

sanity check on groupCorr parameters 
Package: CAMERA
Commit: b1b3b22d6335834d28bcede9b120ae4d9d3a17d0
Author: morimoto <joshua.morimoto@tufts.edu>
Date: 2020-02-27 00:25:43 -0500
Commit message:

 Removed erroneous line for data file
 
Package: CAMERA
Commit: 552d4ecccf311fd664018a64117132c2abcc9d6b
Author: morimoto <joshua.morimoto@tufts.edu>
Date: 2020-02-26 18:58:13 -0500
Commit message:

 Fix plotPsSpectrum()
 
Package: CAMERA
Commit: 65f3e169965f5a5617807a5c2441eafc8f006c4c
Author: sneumann <sneumann@ipb-halle.de>
Date: 2017-11-21 11:03:28 +0100
Commit message:

 Update xsAnnotate.R 
Package: edgeR
Commit: 4f3fd493a04628587ea3214d5b7c71ef517530b4
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2020-06-02 19:19:08 +1000
Commit message:

 edgeR 3.31.3

- Revert incorrect change of `fitted` to `fitted.values` in dispBinTrend.

- Replace instances of rep() with rep_len() or rep.int().

- Reformat processAmplicons().
 
Package: BgeeDB
Commit: 0541e446912cbf0ffe669570a34809ccb9e2d7e6
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-06-02 11:16:26 +0200
Commit message:

 bump version
 
Package: BgeeDB
Commit: 24c688f1668322fc8903a2486d25fdf36e8e6079
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-06-02 11:16:02 +0200
Commit message:

 Merge branch 'common_3_11_and_later' into BIOC_master
 
Package: BgeeDB
Commit: bae76fd0bd9dd59b41550a2037015c57150e2815
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-06-02 11:12:35 +0200
Commit message:

 by default quiet is TRUE when downloading files
 
Package: BgeeDB
Commit: 0de538ecba27135b52396554b6059a15dad6774e
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-06-02 11:11:58 +0200
Commit message:

 update example of makeTable to solve timeout problems
 
Package: GGBase
Commit: f146fe547d376d5e900d4e46f340cd70fed11f02
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-06-01 20:21:14 -0700
Commit message:

 characterORconnection got renamed character_OR_connection in BiocGenerics
 
Package: edgeR
Commit: f5d110d2c4e7d5ba08058dfc70003bf1df779ab1
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2020-06-02 13:04:32 +1000
Commit message:

 Rerun all User's Guide case studies.
 

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