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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: scater
Commit: 6bcd6f17e414f945211ed1f3ff41cd59a3861a50
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-20 10:51:18 -0800
Commit message:

 Bypass the data.frame() constructor for speed.
 
Package: scater
Commit: 0fedb34c23608ac23da2e3e410269915a101777c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-20 10:34:39 -0800
Commit message:

 Protect against nested ALTREPs when creating lazy rows/cols.
 
Package: GenomicInteractions
Commit: 284adcb2147079b4fbc602aa015b641957067737
Author: Liz Ing-Simmons <liz.ingsimmons@gmail.com>
Date: 2020-02-20 18:54:43 +0100
Commit message:

 fixed typo in InteractionTrack docs; updated man files
 
Package: scater
Commit: 9cba1b1f7033b3f74c9d50148e7b8e7def9dac4c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-20 09:29:17 -0800
Commit message:

 Reoxygenated.
 
Package: scater
Commit: 0e6a32fcccb6890265a13df2467fc31aff8e8621
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-20 09:28:56 -0800
Commit message:

 Fixed vignette.
 
Package: scater
Commit: ce16aeb4091a27c86770396bd45137ad10ff1be9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-20 08:47:31 -0800
Commit message:

 Allow coercion of DF column names to a safer variant.
Updated tests to check coercion.
 
Package: scater
Commit: 0088059c6987b0fee16e218a342011cfdba51aad
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-19 17:58:54 -0800
Commit message:

 Stop data.frame from trying to fix my names.
 
Package: scater
Commit: 919d395bb94092b5642ea46b14a260f784252436
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-19 16:30:08 -0800
Commit message:

 Updated tests for the DF-maker functions.
 
Package: scater
Commit: f07ca7ff749380ddca329d00fbb439243add45ff
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-19 16:29:22 -0800
Commit message:

 More fine-grained control over the per-cell DF output.
 
Package: scater
Commit: b2c6d81720d0a3293c4ca9f82f01095849569e8a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-19 13:27:58 -0800
Commit message:

 Flipped makePerFeatureDF to use lazy evaluation scheme.
Renamed gg functions to refer to each dimension.
Docfixes, updated vignette for new function names.
 
Package: scater
Commit: b30eb7d968122074568ebd7e8ff5ca7591323c5a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-19 11:25:07 -0800
Commit message:

 Migrate per-cell DF calls to ggsce.
 
Package: scater
Commit: e24ce01932bafbdc87fd16bef82aac679abacaae
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-19 11:10:01 -0800
Commit message:

 Reoxygenated.
 
Package: scater
Commit: f2b547ec7b1080bdf7e83b9e8526875fcc4e1ee8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-19 11:09:30 -0800
Commit message:

 Migrated DF generating code to makePerCellDF.
Added documentation to ggsce.
 
Package: scater
Commit: 15c5b93413588df66ed042229d3d7f697c44cf81
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-18 23:47:58 -0800
Commit message:

 Support data extraction from alternative Experiments.
 
Package: scater
Commit: d91b2738c3dafb4ce8c8057c988855e26fa1303c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-18 22:14:54 -0800
Commit message:

 Reoxygenated and rebuilt attributes.
 
Package: scater
Commit: 9fa897bfaf5843bc6e1c0ef08526c71b3237c9e8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-18 22:13:11 -0800
Commit message:

 Added basic function to create column-based DF from SCE.
 
Package: scater
Commit: 6fd1cbff4987e1a58aa0994ffff7ce1cbf45842f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-18 21:25:27 -0800
Commit message:

 Added draft of altreps for delayed matrix extraction.
 
Package: methylGSA
Commit: 6aceb3b772af27c641438034764ddf3c8188e5f3
Author: Xu Ren <xu.ren@stonybrook.edu>
Date: 2020-02-20 12:40:37 -0500
Commit message:

 updated
 
Package: cicero
Commit: eebfd6fabda17d65ba9c0706bf51fed14a881817
Author: Hannah A Pliner <hpliner@gmail.com>
Date: 2020-02-20 16:57:18 +0000
Commit message:

 Merge branch 'master' of https://github.com/cole-trapnell-lab/cicero-release
 
Package: cicero
Commit: e01d8dfabf9c9bd1c2a8fc59326d28a1da75ac56
Author: Hannah A Pliner <hpliner@gmail.com>
Date: 2020-02-20 16:57:11 +0000
Commit message:

 Fix data.table issue #42
 
Package: cicero
Commit: 513c909b11dc2303a85369f31f7f5b5484a73d5f
Author: Hannah A Pliner <hpliner@gmail.com>
Date: 2020-02-18 14:35:10 +0000
Commit message:

 Update .travis.yml 
Package: cicero
Commit: 0de4133b77484b9fe8f9e7e3d15f3ca79903d7e9
Author: Hannah A Pliner <hpliner@gmail.com>
Date: 2020-02-17 13:46:14 +0000
Commit message:

 Update .travis.yml 
Package: cicero
Commit: aaf12f87a2fa6d7b69951f9d919933989c47e5cf
Author: brgew <bge@uw.edu>
Date: 2020-01-28 10:59:48 -0800
Commit message:

 Add code of conduct document.
 
Package: cicero
Commit: 0a53a50f57553f00fe5f4a3d9579bd5f61792615
Author: Hannah A Pliner <hpliner@gmail.com>
Date: 2019-12-17 13:57:16 +0000
Commit message:

 make default run_cicero not silent
 
Package: fgsea
Commit: d222d77888283a7a002c10438a44cc42fe4ccf94
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-02-20 19:07:08 +0300
Commit message:

 version bump
 
Package: fgsea
Commit: 30296df7853b0ea2a024f0e0f0dbab410bbde4e4
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-02-20 19:06:23 +0300
Commit message:

 Merge pull request #64 from vdsukhov/master

Fix bug in collapsePathways 
Package: fgsea
Commit: 04a229522a52daf60a8c6e24b102c727e01135d9
Author: Vladimir Sukhov <vdsukhov@ya.ru>
Date: 2020-02-20 18:12:43 +0300
Commit message:

 Fix bug in collapsePathways
 
Package: fgsea
Commit: 918fdade1207ad1bc62d262f4278b5181d1aedcd
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-01-29 16:36:51 +0300
Commit message:

 version bump (one tailed tests)
 
Package: fgsea
Commit: 10374447e3f4872d1cddc0d0a31d1e8779f686da
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2020-01-29 13:30:46 +0000
Commit message:

  
Package: trackViewer
Commit: 1ded540b25067f9297733b54ce41628699011f3e
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2020-02-20 10:20:55 -0500
Commit message:

 change the style of error handle.
 
Package: DESeq2
Commit: 9a46d6b98aa974e8d940c62fefa3b4fc53988701
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2020-02-20 08:06:22 -0500
Commit message:

 also fix withDimnames in tests
 
Package: DESeq2
Commit: 456b673e6a1ad990c677e8a91ffc44870b45e8bd
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2020-02-20 07:56:27 -0500
Commit message:

 adding withDimnames=FALSE to assays calls
 
Package: BgeeDB
Commit: 4cdd03366db3ec05cc83f4ad7b3dc304bdc74a9d
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-02-20 13:56:00 +0100
Commit message:

 solve Illegal version bump
 
Package: BgeeDB
Commit: 08cb0d87bf786d4351396e11840d14fa6bf66f97
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-02-20 13:26:27 +0100
Commit message:

 correct bug untar
 
Package: BgeeDB
Commit: d68d30a04c1f8ba6433b892a5d33a0f20c77576d
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-02-20 13:11:24 +0100
Commit message:

 merge bioconductor master upstream
 
Package: BgeeDB
Commit: 124ce1c1fb2e60c764e4de3611edb5999c75494a
Author: Julien Wollbrett <jwollbrett@bio-51-170.unil.ch>
Date: 2018-09-11 11:04:10 +0200
Commit message:

 Merge branch 'develop'
 
Package: BgeeDB
Commit: cd1ca2a2f0883eb237bf9840497ca5abb1ebacce
Author: Julien Wollbrett <jwollbrett@bio-51-170.unil.ch>
Date: 2018-09-11 10:58:08 +0200
Commit message:

 edit title of the package
 
Package: BgeeDB
Commit: 329a8f1e819b87ea3e89e95027f2a2a11892f303
Author: Julien Wollbrett <jwollbrett@bio-51-170.unil.ch>
Date: 2018-06-18 16:57:11 +0200
Commit message:

 Merge branch 'develop'
 
Package: BgeeDB
Commit: 5efd804c81cbcc40bbbe4ce6fe2df17109fb5f03
Author: Julien Wollbrett <jwollbrett@bio-51-170.unil.ch>
Date: 2018-06-18 16:56:41 +0200
Commit message:

 add LICENCE file
 
Package: Gviz
Commit: 4d6b3302595a3d183acb33db292bb8459e95c2cf
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-20 12:21:02 +0100
Commit message:

 Fix issue created by .warn_once in DetailedAnnotationTrack. Changes strand methods. Added some more tests.
 
Package: mCSEA
Commit: dd10e9abcdff124706e3cf4c0c234026a58eb04b
Author: Jordi Martorell Marugán <jmartorellm@gmail.com>
Date: 2020-02-20 03:15:06 -0500
Commit message:

 Fix Bioconductor error
 
Package: SingleR
Commit: 23a3ae768dce96702640204522bae8a40cdb8c62
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-19 14:46:50 -0800
Commit message:

 Bumped version and date, reoxygenated.
 
Package: SingleR
Commit: ca672b465e1b279ba8817d1462f6518c3aca398a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-19 14:32:06 -0800
Commit message:

 Properly support custom genes in multiple reference training.
 
Package: MultiAssayExperiment
Commit: 601d890e03eeeca03752b690d688e75123eaf19f
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-02-19 17:18:14 -0500
Commit message:

 version bump
 
Package: MultiAssayExperiment
Commit: b928c4d4a309e3ae85a4083550d4686eaa0d423a
Author: LiNk-NY <mramos09@gmail.com>
Date: 2020-02-19 17:17:48 -0500
Commit message:

 bug fix: update assay methods to match args in generic
 
Package: trackViewer
Commit: c76eb441b5748589d2bb7cd58f4cd299f10c043a
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2020-02-19 16:59:22 -0500
Commit message:

 fix a issue of vignette when visit ebi proteins api.
 
Package: BASiCS
Commit: 1e7c83a6e88539b838e465b7910cfd9f21563788
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2020-02-19 21:35:13 +0000
Commit message:

 Merge pull request #162 from catavallejos/tailprob_fix

version 1.9.20 (2020-02-16) 
Package: BASiCS
Commit: b6594ef47ac13e7cc261534f9e2ce16057706c19
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2020-02-19 20:24:16 +0000
Commit message:

 No need for ifelse as logicals are essentially 1/0 
Package: BASiCS
Commit: 5b714fac2795e70c6bda96b2640922d7e06b4491
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2020-02-19 18:15:46 +0000
Commit message:

 version 1.9.20 (2020-02-16)

Fix bug in handling of tail probability tests such that
Epsilon*=0 was not handled correctly and all probabilities
were reported as exactly 1.
 
Package: BASiCS
Commit: e0617f5adad6a761b2cf131c4d09ee40e3597e76
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2020-02-17 16:40:25 +0000
Commit message:

 Add while loop in basics_sim for zero colsums (#158)

version 1.9.19 (2020-02-16)

Adds a while loop in BASiCS_Sim to ensure it doesn't fail if some
generated cells have zero counts.  
Package: BASiCS
Commit: bc37ad35217edae97900e5f192f5dc74eaadbd73
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2020-02-17 12:32:13 +0000
Commit message:

 Empirical Bayes (#161)

v 1.9.18 (2020-02-16):

Introduces gene-wise empirical Bayes prior for mu, controlled by `PriorMu`
parameter. The prior is estimated using the moment-matching method,
using scran size factors as estimates for the normalising factor(s)
phi/nu. 
Package: Gviz
Commit: 5c7a25121d7919a093627d1a0125e809aaa107ed
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-19 22:06:56 +0100
Commit message:

 Code cleanup. Replace sapply with vapply
 
Package: Gviz
Commit: 8ba43b15c1f2f18d23d4af66161a8d20b1d039c9
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-19 21:37:38 +0100
Commit message:

 Small changes in the vignette.
 
Package: Gviz
Commit: f9136dd557c3245d33974bbac289036bc0f2bbb3
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-19 21:27:14 +0100
Commit message:

 Clenaup of code (tab to 4spaces)
 
Package: Gviz
Commit: 3be00d194739a218589abe17aa82863f33c3a06d
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-19 11:38:07 +0100
Commit message:

 Test for .buildRange change, bumped version
 
Package: Gviz
Commit: 1e8a32764f1a4f906098760f53df3b2d914b229f
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-19 10:22:21 +0100
Commit message:

 Fix links in rREADME
 
Package: Gviz
Commit: 71a413d41ad4fe16b431d4b65fc32c56421e887d
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-18 15:49:54 +0100
Commit message:

 Cleanup og Gviz-methods
 
Package: Gviz
Commit: 88d3b3104fb02c04b02865825e6931cc3c7439c2
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-18 14:41:52 +0100
Commit message:

 Rewrote values replacement method, clenaup AllClasses
 
Package: Gviz
Commit: a0a5183dd20fb967bcf252d72cac806327c64bcf
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-18 00:31:34 +0100
Commit message:

 additional tests for subsets
 
Package: Gviz
Commit: 1cef5c73b852b3a65cf141050f5840a3eae87ab8
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-17 22:58:51 +0100
Commit message:

 Added tests for subseq and chromosome
 
Package: Gviz
Commit: e7ec41d4a05cdf46a5d597c928fa23066f21e069
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-17 18:33:02 +0100
Commit message:

 [skip travis] added badge for active repo
 
Package: Gviz
Commit: a64ef8ffa09c7ba4c3b6169eaf32337190ee0314
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-17 18:20:44 +0100
Commit message:

 [skip travis] Updaded links in README.
 
Package: Gviz
Commit: 850d0634dc3f12b2c4d2d406d154a80958c6c9a0
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-17 18:00:36 +0100
Commit message:

 [skip travis] added note regarding the build on windows
 
Package: Gviz
Commit: 3a766e20cd762254ff426d3dd40f6f585d83279a
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-17 17:46:21 +0100
Commit message:

 Edited readme
 
Package: CytoML
Commit: f2c64e86bf4b87568b457f87b0c51eace7cd065d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-19 12:51:14 -0800
Commit message:

 Merge branch 'master' into devel
 
Package: CytoML
Commit: 5df77d3348c2c7298dd0e6a31a9c8ce9a821cc7e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-19 12:50:35 -0800
Commit message:

 bump
 
Package: CytoML
Commit: 873d11a16753e9730f187ec92ca20db7df90303e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-19 12:44:25 -0800
Commit message:

 no longer need to realize_view explicitly since it is now triggered automatically in save_gs for 'cdf=move' option
 
Package: CytoML
Commit: 0834e460fad8b325804f90a54c65437187772eb2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-18 15:10:57 -0800
Commit message:

 fix test case
 
Package: CytoML
Commit: 0657da43ab4def2fc5e74c4cfe3e5fa028ee46de
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-18 14:59:57 -0800
Commit message:

 set M and T to the constant values. #79
 
Package: CytoML
Commit: 628a878aded60a6d38a6a62062d864783df94a20
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-18 13:37:29 -0800
Commit message:

 add 'trans' argument to optionally override the transformations from gatingML file with scales info recorded in yaml #79
 
Package: CytoML
Commit: f6e291144d07a7b6d089cd8b5d073f4fc5113678
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-18 13:36:47 -0800
Commit message:

 comment out some tests
 
Package: CytoML
Commit: 1818171a52f52007c1fce34824821c380d51c40d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-18 12:51:28 -0800
Commit message:

 parse the missing tags from yaml #79
 
Package: CytoML
Commit: 3106a51d32abab26723b2f70fce7769295a665ca
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-02-12 12:16:52 -0800
Commit message:

 Make diva_to_gatingset use save_gs(cdf="move")
 
Package: CytoML
Commit: edc217bbac12f6059d99c298209c6bcad3d47975
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-02-12 09:39:29 -0800
Commit message:

 Realize view in diva_to_gatingset before save_gs
 
Package: flowWorkspace
Commit: 131ae3d730e4b5869bcc6b5e9d0762e705138c94
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-19 12:48:55 -0800
Commit message:

 bump
 
Package: flowWorkspace
Commit: e67a318dc8db12b39ef1d56c523e282b4ec9e533
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-19 12:36:17 -0800
Commit message:

 Merge branch 'master' of github.com:RGLab/flowWorkspace
 
Package: flowWorkspace
Commit: f4bef0ea38c4bb31973b828ad1401c01e22e42d3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-19 12:35:54 -0800
Commit message:

 add test cases for realize_view of subsetted cf
 
Package: flowWorkspace
Commit: 3ae6b994511c62b4faf2b5e095947bde58f0f4b1
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-02-12 12:38:55 -0800
Commit message:

 Handle deprecated "link" option to save_gs
 
Package: flowWorkspace
Commit: 6b01415c2f4dece406d59362e29c8074a0c61496
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2020-02-11 15:24:00 -0800
Commit message:

 Make gh_pop_get_indices_mat take node vector
 
Package: cytolib
Commit: 8aecb31d117f451f8cf7c0092ba6ba28346f7e97
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-19 12:48:19 -0800
Commit message:

 Merge branch 'master' into devel
 
Package: cytolib
Commit: 60379febf12dc79f8cac7ad1a670f33e05bd95f2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-19 12:47:13 -0800
Commit message:

 bump
 
Package: cytolib
Commit: ccd8f34cf57a31c14c5aaf97e21d1673db36c52a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-19 12:37:59 -0800
Commit message:

 add overwrite=false to copy methods and allow 'move' option for subsetted cytoframeview
 
Package: cytolib
Commit: cfb92bdaff53aabe0208f62a9678795593d96f3e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2020-02-14 16:42:37 -0800
Commit message:

 guard against Copying H5CytoFrame to itself
 
Package: Autotuner
Commit: d36a628c5304b88f77901198dbd249df9f3e5dbf
Author: Craig McLean <crmclean@mit.edu>
Date: 2020-02-19 14:13:56 -0500
Commit message:

 Fixed conflicts in version change
 
Package: Autotuner
Commit: 09abec63ca7463ae110fd623c0669021abed142e
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-12-09 14:24:05 -0500
Commit message:

 cleaning dependencies - devtools
 
Package: Autotuner
Commit: 1bdb49693be37b5d3f8ae08d615ed41b407e495b
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-12-09 14:19:53 -0500
Commit message:

 cleaning dependencies - plyr
 
Package: Autotuner
Commit: 98cd2a5e710832918c6146669703aa75f94e61de
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-12-09 13:07:06 -0500
Commit message:

 Cleaing dependencies - rlang
 
Package: Autotuner
Commit: f888f1da4d848d4937f1a0ff0dcd953476a5863b
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-12-09 12:15:33 -0500
Commit message:

 Removing dependencies - dplyr
 
Package: Autotuner
Commit: 486071a5152af2a891c0ebebe9e16b427686f7df
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-27 23:44:22 -0400
Commit message:

 Fixed regex matching of scans and runaway peaks
 
Package: Autotuner
Commit: 2f5a1f25b6abe1f910d2ab444735c3a7f836f987
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-25 13:24:13 -0400
Commit message:

 Added check to confirm files entered are real
 
Package: Autotuner
Commit: 09355f03b2ecc244cbe1bd8fc68a4b2887e66b9b
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-21 09:01:52 -0400
Commit message:

 Fixed notes
 
Package: Autotuner
Commit: f29e8ff852588845973b71591568466d42dc7712
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-20 16:40:46 -0400
Commit message:

 Description syntax error
 
Package: Autotuner
Commit: b5e99ba76160a619c90930c19bbd3a9a5ab57702
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-20 16:33:35 -0400
Commit message:

 Adding files to description
 
Package: Autotuner
Commit: ef4148aca72be481aaae37759243f8e02b540f0f
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-20 16:29:23 -0400
Commit message:

 Revert "updating version for bioc release"

This reverts commit 2b85cf71fbbb07d0ceea9ba22071f9a4beb797d8.
 
Package: Autotuner
Commit: 81e24e84bcfc542a5f59da7888994a4611ea1b1e
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-15 10:22:06 -0400
Commit message:

 travis 9
 
Package: Autotuner
Commit: 4d07e9d2092c589ec6db1f6d9137ce4383847329
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-15 09:52:42 -0400
Commit message:

 Travis 8
 
Package: Autotuner
Commit: 06e7e9ba11599ad63f1a92d6ed937c9ddc5abaa8
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-15 09:24:18 -0400
Commit message:

 Travis 7
 
Package: Autotuner
Commit: c9b11e7222b2ef5f9b214a5425ace5267ecba324
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-15 08:57:52 -0400
Commit message:

 Travis 6
 
Package: Autotuner
Commit: 86bd34990a7db798d142d03c3cccf605245a746b
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-14 18:45:43 -0400
Commit message:

 Travis 5
 
Package: Autotuner
Commit: 15470acc5abb3b702d43a5b5b388e57746cbeb46
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-14 18:12:14 -0400
Commit message:

 travis 3
 
Package: Autotuner
Commit: 651d06375ecaa1a7be5a3f460d1aaa4e19596c5a
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-14 17:29:57 -0400
Commit message:

 Travis test 2
 
Package: Autotuner
Commit: 134ecb9e69d99b2ded0bccbdddbfc3551b376beb
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-14 15:16:25 -0400
Commit message:

 Updating Travis
 
Package: Autotuner
Commit: 4ae5d75ef75208f54e1f759e91b6e30a94beea63
Author: Craig McLean <crmclean@mit.edu>
Date: 2019-10-14 10:40:18 -0400
Commit message:

 Updated regex when finding scans - yufree
 
Package: ToPASeq
Commit: 72a7cd4eacb2e96c0bd741b4479971cd7194633d
Author: unknown <ihnatova@iba.muni.cz>
Date: 2020-02-19 15:00:53 +0100
Commit message:

 PRS pathway names
 
Package: tximeta
Commit: 2b744741ee1643aa05cd0d2858621071b1ec6868
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2020-02-19 07:33:31 -0500
Commit message:

 fix typo
 
Package: treeio
Commit: 76d08ba6731c4be7fa849d4870195e7fa7311350
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2020-02-19 17:12:12 +0800
Commit message:

 update citation
 
Package: treeio
Commit: d4e1f009e3fec01a535e5fa23b849182f513f231
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-12-09 11:06:25 +0800
Commit message:

 update docs
 
Package: treeio
Commit: d18d11e879114e4f95d2e58ae714db2a5b026161
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-12-09 09:40:06 +0800
Commit message:

 Merge pull request #28 from xiangpin/master

support multi phylogeny in phyloxml and extra information 
Package: treeio
Commit: 47172827b935648ea1df8439d9da37b458ca2145
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-12-09 09:15:28 +0800
Commit message:

 Merge pull request #29 from jeroen/patch-1

Add git and docs URL to the description 
Package: treeio
Commit: 7a29b5f62a197d0bd0f8667dc8b64563c0e3bd10
Author: Jeroen Ooms <jeroenooms@gmail.com>
Date: 2019-12-08 16:58:49 +0100
Commit message:

 Add git and docs URL to the description 
Package: treeio
Commit: 6093266f2bc91273e3296520f8f8d3353f7839a8
Author: xiangpin <xshuangbin@163.com>
Date: 2019-12-08 17:47:50 +0800
Commit message:

 add example file of phyloxml
 
Package: treeio
Commit: 8c0b806ebf8c5d1c0deb995b11a048d63e0ea60c
Author: xiangpin <xshuangbin@163.com>
Date: 2019-12-08 17:47:18 +0800
Commit message:

 man of write.beast
 
Package: treeio
Commit: d9a8d9233e61d5768371452ae248192d94da538a
Author: xiangpin <xshuangbin@163.com>
Date: 2019-12-08 17:46:27 +0800
Commit message:

 man of tree_subset
 
Package: treeio
Commit: ad7271169fe954e1457dc883618132381c7b0930
Author: xiangpin <xshuangbin@163.com>
Date: 2019-12-08 17:45:50 +0800
Commit message:

 man of root-method
 
Package: treeio
Commit: afc5c7740c8e64daa66fd262a05b68bb3cb4d7a3
Author: xiangpin <xshuangbin@163.com>
Date: 2019-12-08 17:45:15 +0800
Commit message:

 man of reexports
 
Package: treeio
Commit: 7d05fde097ef0fe61c0ab613ab7340f3b6fd2c33
Author: xiangpin <xshuangbin@163.com>
Date: 2019-12-08 17:42:26 +0800
Commit message:

 add multi phylogeny in examples
 
Package: treeio
Commit: 82bf0773bcf91a0ad2fc46c167145dc7217274b6
Author: xiangpin <xshuangbin@163.com>
Date: 2019-12-08 17:41:32 +0800
Commit message:

 multi phylogeny in phyloxml
 
Package: ggtree
Commit: c9910e6997004e304af57e72db68c2e8b53399a3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2020-02-19 16:27:25 +0800
Commit message:

 update makefile
 
Package: ggtree
Commit: 7f0588e9e591959fbb9a9520c6ae08c300edfe2b
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2020-02-19 16:29:31 +0800
Commit message:

 Merge pull request #279 from brj1/master

if yscale is set do not scale y 
Package: ggtree
Commit: b6872f2e55788e29f6ab7e9631678362fa244cc2
Author: Brad Jones <brj1@users.noreply.github.com>
Date: 2020-02-18 15:55:06 -0800
Commit message:

 if yscale is set do not scale y 
Package: ggtree
Commit: 0c4489dad678cbe051fd16a088a4c8865aa1fb53
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2020-01-28 11:34:39 +0800
Commit message:

 Merge pull request #274 from brj1/master

fixing incorrect links 
Package: ggtree
Commit: 2e66b3dc2e6eff6968d44f69296b9de91c897a49
Author: brj1 <brj1@sfu.ca>
Date: 2020-01-27 14:49:39 -0800
Commit message:

 fixing incorrect links
 
Package: ggtree
Commit: ceb13aecf11f41dcf963136ca28a42ff411281e6
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2020-01-26 23:25:32 +0800
Commit message:

 bug fixed
 
Package: ggtree
Commit: dad7eaae7e9d6ab64adbbbfc6724b2724fdaeb97
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2020-01-25 20:18:06 +0800
Commit message:

 Merge pull request #273 from brj1/master

Unrooted layout fix 
Package: ggtree
Commit: 642f657b0b39bc679c348f9e2927a08e671cfa7d
Author: brj1 <brj1@sfu.ca>
Date: 2020-01-24 11:04:21 -0800
Commit message:

 Replaced ape::unrooted.xy code with function call
 
Package: ggtree
Commit: b82756047f66eaf8d38a5ba4a49c8616bc58900c
Author: brj1 <brj1@sfu.ca>
Date: 2020-01-23 19:03:49 -0800
Commit message:

 added new layout 'ape' which is a copy of the 'unrooted' type in ape::plot.phylo
 
Package: ggtree
Commit: 101a0ad5f2d81f55a77ca623b63fd44faa217f28
Author: brj1 <brj1@sfu.ca>
Date: 2020-01-23 19:00:12 -0800
Commit message:

 unrooted layouts (daylight and equal_angle) now use 1:1 aspect ratio
 
Package: ggtree
Commit: d903c8a1f0ef7460d75316558a3b218b3b6d723a
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2020-01-08 10:55:39 +0800
Commit message:

 geom_highlight
 
Package: ggtree
Commit: cfbe803d05d6812796f94fd48f0bf7a8045cb600
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-12-07 13:22:15 +0800
Commit message:

 Merge pull request #267 from brj1/master

new ggdensitree example 
Package: ggtree
Commit: e201d4b9077c2a073a06035a9b3efc5ee7ba0715
Author: brj1 <brj1@sfu.ca>
Date: 2019-12-06 14:27:49 -0800
Commit message:

 merged; fixed example; changed Brad Jones email
 
Package: ggtree
Commit: 1ba3cd01c0382b5c873bf2e9fc0bba106d649114
Author: brj1 <brj1@sfu.ca>
Date: 2019-12-06 13:48:17 -0800
Commit message:

 added example to ggdensitree andnew example file
 
Package: flowSpy
Commit: 64a8a6588b2e259cd7e38d234d71416a4805a67a
Author: Dai Yuting <809449456@qq.com>
Date: 2020-02-19 15:58:35 +0800
Commit message:

 rename version 1.1.2
 
Package: flowSpy
Commit: ab78e907b21bc42b53314793d134c3150c9a0425
Author: Dai Yuting <809449456@qq.com>
Date: 2020-02-19 15:55:25 +0800
Commit message:

 update version 1.0.2
 
Package: ViSEAGO
Commit: c364eb69457c253892836fb9570d1040b60034f3
Author: abrionne <aurelien.brionne@inra.fr>
Date: 2020-02-19 08:27:17 +0100
Commit message:

 uniprot2go windows debug
 
Package: enrichplot
Commit: 9a10c62ea8b1bb75137ddf2472e19df2fb3274c4
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2020-02-19 13:14:38 +0800
Commit message:

 bump version up
 
Package: sojourner
Commit: e09badb43c0cf4cf597a60b15b543bd6dc177ec0
Author: sheng-liu <shengliumailbox@gmail.com>
Date: 2020-02-18 21:08:02 -0800
Commit message:

 merge bioconductor /upstream changes and version bump
 
Package: sojourner
Commit: daebbd4aba8549911c492597ada7387e30857256
Author: sheng-liu <shengliumailbox@gmail.com>
Date: 2020-02-18 20:33:16 -0800
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: sojourner
Commit: 5aa82ac263bc6c8b3aa995c31129891c3913ed45
Author: Sun Jay Yoo <snjy9182@gmail.com>
Date: 2020-02-17 23:59:43 -0500
Commit message:

 rowr dependency removed.
 
Package: sojourner
Commit: f9bfb0d66df12105dec23d237051f229d6b79ff2
Author: snjy9182 <snjy9182@gmail.com>
Date: 2019-09-05 15:05:01 -0400
Commit message:

 Unit test fixed.
 
Package: sojourner
Commit: 069b94c7c50aa249b5e8d09c8c3c28b8f045419b
Author: snjy9182 <snjy9182@gmail.com>
Date: 2019-09-05 13:07:44 -0400
Commit message:

 More unit tests added.
 
Package: FastqCleaner
Commit: 6b1c8f8a9267fd67d6b3084c676e3dfc449217f9
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-02-18 21:02:07 -0300
Commit message:

 solving warnings and errors
 
Package: infercnv
Commit: a34730724509af0601c5b08d9ea64292339bafb2
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2020-02-18 16:27:33 -0500
Commit message:

 Fix saving file name for preliminary object.
 
Package: iSEE
Commit: 986fa5e85ee52f678f5e947153e553be08ef9a24
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-18 20:41:35 +0000
Commit message:

 Update panel full names in vignette, notably "statistics table" to "data table"
 
Package: iSEE
Commit: c3e8ac0911574563d96fdd936b01ca700b4f5894
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-18 20:25:45 +0000
Commit message:

 update release date
 
Package: iSEE
Commit: fd4d999c048f369a41e77285de33ebd8fc3a52a1
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-18 19:12:45 +0000
Commit message:

 update NEWS; version bump
 
Package: iSEE
Commit: e4f68adea76ab9daffce383cdb9d32b36dc8afbd
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-18 19:12:16 +0000
Commit message:

 Expand SampleRes to DownsampleResolution, downsample.res to downsample.resolution
 
Package: iSEE
Commit: 2176d613b83fdb1eef8eda3408a8420e3e921df2
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-18 19:10:34 +0000
Commit message:

 Rename iSEE-options.R file
 
Package: iSEE
Commit: f0c643e4d6527f252c772225c0fa86bc286b2a09
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-18 19:08:59 +0000
Commit message:

 Rename "statistics" tables to "data" tables
 
Package: iSEE
Commit: 74cf0b91ed65e20ec71861b08428474f1a7b4549
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-17 22:06:20 +0000
Commit message:

 panel.color is a character vector, not a list
 
Package: iSEE
Commit: c579333c80fd759af8aa52e76c5eb33c63563366
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-17 22:02:51 +0000
Commit message:

 panel.color is a character vector, not a list
 
Package: iSEE
Commit: 17be01d78c8c8f71a6543cd3565d9a71914d0278
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-17 21:57:53 +0000
Commit message:

 rename ReducedDimensionPlot source file
 
Package: iSEE
Commit: 71d95992d112e959372c1c671541e0ae2f42a3ef
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-17 21:57:29 +0000
Commit message:

 ignore files produced by unit tests
 
Package: iSEE
Commit: b0644c2a1ca1dd07dff0aebad054d7c8e8a83114
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-17 21:57:00 +0000
Commit message:

 move custom panel colors to iSEEOptions
 
Package: iSEE
Commit: 7dc548cca2878220a333040177128c25f9eddaf7
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-17 19:10:46 +0000
Commit message:

 rename ReducedDimPlot -> ReducedDimensionPlot
 
Package: iSEE
Commit: 3f14ef6b393301a62aa2015c401ba3aaba365383
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-17 19:02:28 +0000
Commit message:

 Rename: MultiSelectHistory -> SelectionHistory, *FeatName -> *FeatureName, *SampName -> *SampleName, SelectCol* -> ColumnSelection*, SelectRow* -> RowSelection*
 
Package: iSEE
Commit: 7c90b0247a92d56bd22f5c6ed2ee36cc9b67af31
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-17 19:01:34 +0000
Commit message:

 fix and restore coverage
 
Package: iSEE
Commit: f21823ed5181b72fa6866390c77ff7aafbf67c0f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-16 19:55:01 -0800
Commit message:

 Reoxygenated.
 
Package: iSEE
Commit: 31bc3c0fdca92aeb6bab1f323d0adaf24d43fecd
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-16 19:54:37 -0800
Commit message:

 Expanded slot names for selection aesthetics.
 
Package: iSEE
Commit: 9076f1d30ecf62aff1200d316d7598cdd92531d6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-16 19:40:51 -0800
Commit message:

 Fixed vignettes, docs and examples for renamed fields.
 
Package: iSEE
Commit: d1cdae4c3b49dd1d16e622a1e20daf1d8c210e0a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-16 19:12:10 -0800
Commit message:

 Remove backquotes.
 
Package: iSEE
Commit: 3d4039a830d88b6ed772dd39bfa463c1946c2fff
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-16 19:11:04 -0800
Commit message:

 Less fragile tests in response to SCE update.
 
Package: iSEE
Commit: ea4ce36e27e2d4dc3457565b215af3098faf498e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-16 19:10:46 -0800
Commit message:

 Reoxygenated.
 
Package: iSEE
Commit: 74895a742dfb0203aaf974320a48df8b1798b92c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-16 18:33:19 -0800
Commit message:

 Expand slot names from Feat to Feature, Samp to Sample.
Reserve Feature/Sample for use in single contexts.
Reserve Row/Column for use in multiple contexts.
 
Package: iSEE
Commit: f3071f2e12616ec08258d1c2f541ddeeb652a4bc
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-16 20:42:42 +0000
Commit message:

 update unit tests
 
Package: iSEE
Commit: 7ea50a61a1eb62261da30d58c7842683b600a550
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-16 20:03:43 +0000
Commit message:

 Revert "Rename: FeatureAssayPlot -> RowAssayPlot, SampleAssayPlot -> ColumnAssayPlot"

This reverts commit 0687f1abb9a01bbb767eb74355eca7911d4ac316.
 
Package: iSEE
Commit: f8997fb659375749c4bcc880b084457465b36806
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-16 20:03:26 +0000
Commit message:

 Revert "Rename: ReducedDimPlot -> ReducedDimensionPlot"

This reverts commit 4256d63c79fccc45a084f1a4c388170b5dd2f33d.
 
Package: iSEE
Commit: d70ec02e30554c8265d143e196e9bb366eaedb81
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-16 18:57:01 +0000
Commit message:

 Rename: ReducedDimPlot -> ReducedDimensionPlot
 
Package: iSEE
Commit: a4c988878dfe93d5be1a7bdbf951f379ade3b35d
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-16 18:31:15 +0000
Commit message:

 fix dimnames in test setup
 
Package: iSEE
Commit: b064238687bee5829ae70b24a5d199e58f63b4e0
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-16 18:28:49 +0000
Commit message:

 Rename: FeatureAssayPlot -> RowAssayPlot, SampleAssayPlot -> ColumnAssayPlot
 
Package: iSEE
Commit: eb115e8d788b7f6d01987249a923a6ab17fd805a
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-16 18:22:22 +0000
Commit message:

 revert a1594ee3
 
Package: iSEE
Commit: 96f81e3d8013580654555b09483fd7a6468f1272
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-15 16:12:34 -0800
Commit message:

 Reoxygenated.
 
Package: iSEE
Commit: 5086be41f8cba12582fefdc4f41c063f50a7ca54
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-15 16:10:20 -0800
Commit message:

 Convert contract descriptions to subclass expectations.
Moved generateTable docs to separate file.
 
Package: iSEE
Commit: c8e98e7040aaac8b9a153ea5fd831afeea90a20c
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-15 20:00:07 +0000
Commit message:

 Document best practice of hex color codes for panel colors
 
Package: iSEE
Commit: 7a26e4a283e4f4246c91f47a7f4f80fe434467c0
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-15 19:42:53 +0000
Commit message:

 update unit test
 
Package: iSEE
Commit: 4289b59c5622303b846c7fd0d5277acdf5c8463e
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-15 19:37:45 +0000
Commit message:

 fix link in man page
 
Package: iSEE
Commit: 6e7db5b57fe91c9376f72107fbb1f3a808c530b7
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-15 19:35:54 +0000
Commit message:

 deparse the individual elements of x[[.heatMapColData]]
 
Package: iSEE
Commit: 7196461433dfb67e303cbfebee639094166e2818
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-15 19:32:05 +0000
Commit message:

 Rename ColumnDataPlot, RowDataPlot, ReducedDimPlot to SampleDataPlot, FeatureDataPlot, ReducedDimensionPlot
 
Package: iSEE
Commit: 6268a9b794bb0270cf1d4deb5008c4f49cab10ce
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-15 14:08:07 +0000
Commit message:

 process syntactically invalid column names safely when ordering heatmap columns
 
Package: iSEE
Commit: 49b0e89f429d92a3c99ff0bcf3463ad087f0ee5e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-15 01:41:29 -0800
Commit message:

 Reoxygenated.
 
Package: iSEE
Commit: 9752314a534c89100adc25be388fee6ba3ea7204
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-15 01:41:01 -0800
Commit message:

 Cleaned up landing page documentation.
 
Package: iSEE
Commit: c50b9ba6c5e3a7f18c0d6a47d2f6a42a497d1024
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-15 01:24:55 -0800
Commit message:

 Docfixes: abandon attempt at slot doc inheritance.
 
Package: iSEE
Commit: 5fc712fc228dfab44c5dfd2ec2fc24e8cfb35136
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-14 15:51:43 -0800
Commit message:

 Upgraded the custom vignette as well.
 
Package: iSEE
Commit: 8611440f9ea75f04346fa37bb42f41dbabb3458b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-14 15:34:53 -0800
Commit message:

 Reoxygenated.
 
Package: iSEE
Commit: 7f8b9cad00aa135559ccef815e47ddeda22ae6a5
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-14 15:31:07 -0800
Commit message:

 Updated configuration vignette.
 
Package: iSEE
Commit: 4ba987953bf5495347e6d20cb1103398fa2a1404
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-14 15:29:50 -0800
Commit message:

 Updated all tests to use the new panel names.
 
Package: iSEE
Commit: d9139936cf6b3ab9b58a66867ce01c7a64dae014
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-14 14:38:55 -0800
Commit message:

 Renamed RowStatTable to RowDataTable.
 
Package: iSEE
Commit: 95d2c60492b2defb99d43b9fd14001924525af47
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-14 14:38:10 -0800
Commit message:

 Renamed ColStatTable to ColumnDataTable.
 
Package: iSEE
Commit: 7ee11fb50ceb1945d26308f6c143f99d762856b5
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-14 14:37:16 -0800
Commit message:

 Renamed ColDataPlot to ColumnDataPlot.
 
Package: iSEE
Commit: a74a222f7f1559a16fec85e72305384f157b0ae3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-14 14:35:57 -0800
Commit message:

 Renamed SampAssayPlot to SampleAssayPlot.
 
Package: iSEE
Commit: 18f821fa64e493f99eda2c46f1691a5e9d7f2410
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-14 13:57:49 -0800
Commit message:

 Renamed FeatAssayPlot to FeatureAssayPlot.
 
Package: iSEE
Commit: 991a07edbc77bb20d92127066865ffeb76470e7f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-14 13:56:49 -0800
Commit message:

 Renamed RedDimPlot to ReducedDimPlot.
 
Package: iSEE
Commit: b65236d174dfc26b72498d405f11287ab1162c9b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-13 22:08:09 +0000
Commit message:

 update basic vignette to be more open about custom panels
 
Package: iSEE
Commit: b57f7046ccd500b3407d0e469d5e703b12b97608
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-13 20:52:44 +0000
Commit message:

 Update link to the book
 
Package: iSEE
Commit: 8087c40884fe4cd60f1f6771747d5e890e623dd1
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-13 20:47:28 +0000
Commit message:

 Describe individual global panel options
 
Package: iSEE
Commit: 75bb962db42ce74cae3e9ef780b7fd84085271e6
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-12 21:47:12 +0000
Commit message:

 Move relevant NEWS entries in 1.99.1 section.
 
Package: iSEE
Commit: 68ed8c5443d4038a2cdff705c1254abdbe5493f2
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-12 21:30:10 +0000
Commit message:

 update NEWS
 
Package: iSEE
Commit: c047d458749bfaf3b2abcd4ee2f83484df6f9053
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-12 21:23:20 +0000
Commit message:

 restore test coverage; fix .execute_custom_function to avoid trailing ","; roxygenisze
 
Package: iSEE
Commit: 66aa73497a58ad73ff56beda6222b2c0a2eda344
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-12 21:12:10 +0000
Commit message:

 typo and fix check of assay row centering
 
Package: iSEE
Commit: 1b5ffcd8ce82cb3879269e8e1a4609532e8dbd46
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-11 22:57:17 +0000
Commit message:

 rename default global options
 
Package: iSEE
Commit: 4e06fae65d700bfbd49646bcbdb10e0a031f5cc0
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-10 23:00:17 +0000
Commit message:

 set panel global options following the knitr::opts_chunk framework
 
Package: iSEE
Commit: 07f6216ef4b4d1ba67db6c667dd2b36bcb21e15b
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2020-02-10 23:52:40 -0800
Commit message:

 Merge pull request #362 from iSEE/custom

On-ramp for customized panels 
Package: iSEE
Commit: 8df8407138fad080f72a6143a71f0f925556fa5b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-10 23:25:14 -0800
Commit message:

 Reoxygenated.
 
Package: iSEE
Commit: 1ab8187afcb97e29d07d7dc1811bd8077a954770
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-10 23:25:01 -0800
Commit message:

 Upgraded custom vignette for new functionality.
 
Package: iSEE
Commit: 637f6be0575289da1a003049db8b7bcb7337d52c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-10 23:20:32 -0800
Commit message:

 Bugfixes to custom panels, further methods to clean up UI.
 
Package: iSEE
Commit: 64a7fb1d41725ca70734e9a56e525db12a35237d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-10 21:58:16 -0800
Commit message:

 Updated tests for auto-discovery of arguments.
 
Package: iSEE
Commit: 49c19fcc04fe6076ae929d2068e2d90181e77458
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-10 21:42:02 -0800
Commit message:

 Auto-detect arguments from the custom function definition.
 
Package: iSEE
Commit: c6b3ebc1d6a448bb556d964928b8bee3ee246414
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-10 19:39:56 -0800
Commit message:

 Revert "Cleaned out old bits in customization vignette."

This reverts commit d6f3e8e3acbfc39e10a285311df84d8d6ecdb7c2.
 
Package: iSEE
Commit: 21734e1e3c16392f0f8682923fe6368c7795f71b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-10 13:29:36 -0800
Commit message:

 Merge remote-tracking branch 'upstream/master' into custom
 
Package: iSEE
Commit: 35d374bf9b202e5e0cba360ea99b2b034a810a7f
Author: Your Name <you@example.com>
Date: 2020-02-10 19:41:04 +0000
Commit message:

 restore 100% coverage
 
Package: iSEE
Commit: a3acbc300a06560550b06ef0ae2ffe8d47468bb2
Author: Your Name <you@example.com>
Date: 2020-02-10 19:27:07 +0000
Commit message:

 update heatmap tests; prefix ComplexHeatmap and circlize commands; safe acccess to syntactically invalid column names
 
Package: iSEE
Commit: a990d2827de79fb3d66228add165621e26c27728
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 18:54:25 -0800
Commit message:

 Cleaned out unneccessary functions.
 
Package: iSEE
Commit: 90be0cafedd947c5c720f37dcb0434c30d248ea6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 18:34:17 -0800
Commit message:

 Simplified heatmap code for clearer responsibilities.
 
Package: iSEE
Commit: 3eb979fc2db486766fcb5b39d20ef7d1cf1d41b6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 17:18:44 -0800
Commit message:

 Documented all newly created internal functions.
 
Package: iSEE
Commit: 1362de9a94689a819b13df22a9943241e2625804
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 12:20:23 -0800
Commit message:

 Broke up heatmap-generating code for easier reading.
 
Package: iSEE
Commit: 0c89d6cf50f5bd0d8021f192c7eb6ad97dfc54a9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 02:28:47 -0800
Commit message:

 Purged the command store utilities, use more functions instead.
 
Package: iSEE
Commit: ff01579dc2d2af45522ddc1c5853b59e73f650eb
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 02:03:29 -0800
Commit message:

 Fixed heatmap code to work with sparse assays.
 
Package: iSEE
Commit: 414e7a4414239ee9fbd99f84824d4eb7cdd7efcc
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-10 12:55:53 -0800
Commit message:

 Added 'where' argument for user control of class/method location.
 
Package: iSEE
Commit: 3d34933b5321413c8a8c9943c8062817012fddd1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-10 12:38:44 -0800
Commit message:

 Added preliminary tests for new custom-class creators.
 
Package: iSEE
Commit: 5c114d333f36846b5f2c362cb8e89e4eabfb60b0
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 23:43:17 -0800
Commit message:

 Reoxygenated.
 
Package: iSEE
Commit: 60c74d2cb154253259e5667d8341f9af3ab636f1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 23:41:06 -0800
Commit message:

 Added observers to respond to custom UI elements.
 
Package: iSEE
Commit: f3e1a13a11cc7c263a9fad9cfa99d98b589d0d5d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 23:32:44 -0800
Commit message:

 Bugfixes to custom panel creator and example.
 
Package: iSEE
Commit: 44259a5e20be24fcebd842031791c490cd6cb55f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 22:39:56 -0800
Commit message:

 Initial attempt at a class-generating function.
 
Package: iSEE
Commit: 982b5c2888e31dc2c6f01c8f2fdef03afda35ee9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 18:54:25 -0800
Commit message:

 Cleaned out unneccessary functions.
 
Package: iSEE
Commit: 6b2cfe864ede7cd8aabd85726e98b369f19be23d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 18:34:17 -0800
Commit message:

 Simplified heatmap code for clearer responsibilities.
 
Package: iSEE
Commit: 71519a4340a5c532593f8f17c6e70fd3a86e83a6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 17:18:44 -0800
Commit message:

 Documented all newly created internal functions.
 
Package: iSEE
Commit: 7367e65548a262a90cf0fc63b1f0d587b977cca6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 12:20:23 -0800
Commit message:

 Broke up heatmap-generating code for easier reading.
 
Package: iSEE
Commit: a0d23e3a11dc94a2bfb3775579a490ba6d3f4fec
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 02:28:47 -0800
Commit message:

 Purged the command store utilities, use more functions instead.
 
Package: iSEE
Commit: 5bf6bf697e54aaa58172dea8bec0031ba4a30e89
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-09 02:03:29 -0800
Commit message:

 Fixed heatmap code to work with sparse assays.
 
Package: iSEE
Commit: 368aa9039786250cbc844680e97c39b61400349d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 16:04:00 -0800
Commit message:

 Reoxygenated.
 
Package: iSEE
Commit: d7a6b03e461eb723d46c3fa7ec560ae0e0b0dced
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 16:03:48 -0800
Commit message:

 Standardized doc file name for Table classes.
 
Package: iSEE
Commit: 4de3bcb0c047631460ff5f7abbd0881bf2ab8fc1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 15:57:24 -0800
Commit message:

 Added an actual example of creating your own landing page.
 
Package: iSEE
Commit: 38f698a1bc94065dea1f290580e7e3e6a8ee7e75
Author: Your Name <you@example.com>
Date: 2020-02-08 19:34:12 +0000
Commit message:

 exclude render from coverage
 
Package: iSEE
Commit: 4b5afed5b730dbbe156bd85ef4839b46ea7254ac
Author: Your Name <you@example.com>
Date: 2020-02-08 19:20:32 +0000
Commit message:

 cover .exportOutput for Panel
 
Package: iSEE
Commit: 4a20bb7e7956bde748588adc60c8b4e8ff3b4ba2
Author: Your Name <you@example.com>
Date: 2020-02-08 19:19:04 +0000
Commit message:

 cover .exportOutput for Table
 
Package: iSEE
Commit: 1ffa8ee54d77a947addd76a21d1c900d14b0876a
Author: Your Name <you@example.com>
Date: 2020-02-08 19:17:42 +0000
Commit message:

 cover .exportOutput for DotPlot
 
Package: iSEE
Commit: a6b345295e2e30ab7a78a82b062253e9889daf4a
Author: Your Name <you@example.com>
Date: 2020-02-08 19:08:45 +0000
Commit message:

 cover outputs_general.R
 
Package: iSEE
Commit: ce99625d9028ebc654f4c1ac42db1d425583aedb
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2020-02-08 17:09:04 +0100
Commit message:

 One more doc fix, and adding Rd files
 
Package: iSEE
Commit: 5503fb50014caf729d02243e993a09e35cc03ad0
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2020-02-08 11:53:55 +0100
Commit message:

 Doc fixes
 
Package: iSEE
Commit: cbb613ffeafc14bd5684942d56f9fdb88ff9da94
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2020-02-07 16:41:48 +0100
Commit message:

 Consistent placement of .fullName documentation
 
Package: iSEE
Commit: 0a703454da5d53b64a82bd3efbd0f9897f9e596a
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2020-02-07 16:40:42 +0100
Commit message:

 Documentation syntax
 
Package: iSEE
Commit: 783bca00835ee776fd4f279009d1383ee8e7d9e5
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2020-02-07 15:21:23 +0100
Commit message:

 Update address to GitHub repo
 
Package: iSEE
Commit: 0dc06bb5e54e00643f37620b8bb4bb5a120ae42d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 11:23:11 -0800
Commit message:

 Protect against case of missing 'se' in iSEE().
 
Package: iSEE
Commit: 25ad45d441feca498f942ecdc82c9ec2b34754ef
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 11:20:37 -0800
Commit message:

 Added tests to cover new SE-filling code.
 
Package: iSEE
Commit: 25f671f4b1ff909520b315ea5919a7d5de5b671a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 10:39:21 -0800
Commit message:

 Bugfix for missing dimnames in underlying assay matrix.
 
Package: iSEE
Commit: 683f95ad870af6b9ef72d038dc780f5684dc4e8f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 10:35:06 -0800
Commit message:

 Name dimensions of input SEs if necessary, fixes #356.
 
Package: iSEE
Commit: 5ee7ad7424cc899a128716e4a0d9f7adcfd3bfbe
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2020-02-08 02:26:38 -0800
Commit message:

 Merge pull request #353 from iSEE/outputs

Saving outputs as PDF/CSV 
Package: iSEE
Commit: fead16648e79b1a2747be489bfb77d337edaa526
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 02:03:53 -0800
Commit message:

 Fixed ancient bug with square plot's handling of NA's.
 
Package: iSEE
Commit: 5d754cd58eb5585d684e0818c758fee0b4928bdf
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 01:35:35 -0800
Commit message:

 Merge branch 'outputs' of https://github.com/csoneson/iSEE into outputs
 
Package: iSEE
Commit: f2c6944b4d1cae19577e81310dd9a81d228017a8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 01:35:27 -0800
Commit message:

 Eliminated test for deleted internal utility.
 
Package: iSEE
Commit: 7790dc76897f0b20b46804a7666a5221d26c7752
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2020-02-08 01:16:54 -0800
Commit message:

 Merge branch 'master' into outputs 
Package: iSEE
Commit: 519b60fd47cc9ec48150f52fd986970841a0fc3b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-08 08:52:01 +0000
Commit message:

 Ignore .github folder 
Package: iSEE
Commit: cbac3524da64eabae511b24809cce7c92e260f27
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 01:02:34 -0800
Commit message:

 Reoxygenated.
 
Package: iSEE
Commit: 97d391f73aa06b90fccfaa4e2ba9bca6e62d971c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 01:02:22 -0800
Commit message:

 Restored force() to defend against future bugs.
 
Package: iSEE
Commit: 98d5b4e50573860378071e916c99c3b323f0c807
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 00:57:45 -0800
Commit message:

 Fixes to docs and imports to pass CHECK.
 
Package: iSEE
Commit: eb84b44bad96570eec3273191f356db398b41182
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 00:49:53 -0800
Commit message:

 Added option to download state as an RDS file.
 
Package: iSEE
Commit: 3e79de5c253e2e3f43766a57b07e80c6bda11561
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-08 08:48:22 +0000
Commit message:

 Merge pull request #354 from iSEE/kevinrue-patch-1

Update issue templates 
Package: iSEE
Commit: ac7a847629bb61381015637f686f06dfc00858fe
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 00:37:02 -0800
Commit message:

 Added missing internal documentation.
Robustified to non-memory case.
Updated NAMESPACE.
 
Package: iSEE
Commit: 20660839fab4c1ed35d5fdd9184cbd0a792e08d2
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-08 08:35:11 +0000
Commit message:

 Update issue templates 
Package: iSEE
Commit: 16fd0196f035cf37028e4965f0fbbcd131a42fa4
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 00:26:04 -0800
Commit message:

 Removed unnecessary create_plot_output utility.
Centralize responsibility to the renderOutput functions.
 
Package: iSEE
Commit: dd19e6743da8d90fc5014005a3f778268e8a7461
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 00:20:32 -0800
Commit message:

 More balanced distribution of options in dropdowns.
 
Package: iSEE
Commit: 4463d090d128ffcb49fae9190d93aaf85cfb9e58
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 00:14:39 -0800
Commit message:

 More options on which panels to download.
 
Package: iSEE
Commit: 7724e573ad9bfb27e0cc27dcde990a262c921952
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-06 23:30:19 -0800
Commit message:

 Removed the rendering from the modal set-up.
 
Package: iSEE
Commit: 850d95c6a575786e4970f1299b67f863ae0b0eda
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-06 22:48:18 -0800
Commit message:

 Reoxygenated.
 
Package: iSEE
Commit: 0a709ae33d6452578a312d25384dde87f3396c09
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-06 22:47:59 -0800
Commit message:

 Fix to ensure only relative file is zipped.
 
Package: iSEE
Commit: d281989e556a8a29c4034a4f66644bcfbbbb061f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-06 22:37:33 -0800
Commit message:

 Initial draft of saving output functionality.
 
Package: iSEE
Commit: 7e8c014c1b249289970b81f691e16ba92f34277e
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-06 22:58:09 +0000
Commit message:

 Merge pull request #352 from iSEE/com

badge links to travis-ci.com 
Package: iSEE
Commit: c97a4dcc552ef486f44d39b1d8655c8a2f200fae
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-06 22:45:47 +0000
Commit message:

 badge links to travis-ci.com
 
Package: iSEE
Commit: 4ad998a7de35d7b3e48c498edd3c24493a1c8ff3
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-06 22:28:12 +0000
Commit message:

 Merge pull request #351 from iSEE/pkgdown

use workaround at https://github.com/r-lib/pkgdown/issues/1206 
Package: iSEE
Commit: 494840ca6c32ffe2373fca139daf0fff2e7573dc
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-06 22:06:59 +0000
Commit message:

 use workaround at https://github.com/r-lib/pkgdown/issues/1206
 
Package: iSEE
Commit: e84c094ffa5bf6ae871e06731fd35827c97135ce
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-06 08:27:50 +0000
Commit message:

 Merge pull request #349 from iSEE/cleanup

restore dpl v1 travis option 
Package: iSEE
Commit: a48f20cbb0f11e6ca4f3ec93b0bfb0aa757dcb5b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-06 08:16:59 +0000
Commit message:

 restore dplv1 travis option
 
Package: iSEE
Commit: ae79e37711a336e8b70b905b42243ad658cc79fe
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-06 07:59:42 +0000
Commit message:

 Merge pull request #348 from iSEE/deploy

fix new travis defaults 
Package: iSEE
Commit: c3a99312e54c17995e629b3c1b387108c7c29e25
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2020-02-06 07:46:09 +0000
Commit message:

 fix new travis defaults
 
Package: TCGAbiolinks
Commit: 57d6b71c755d36493027b58237abb5d1df460b5c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2020-02-18 15:34:25 -0500
Commit message:

 Removing data download from vignette
 
Package: NBAMSeq
Commit: 74e5d5b73df05fbce97a70039d45ea7277bfd635
Author: Xu Ren <xu.ren@stonybrook.edu>
Date: 2020-02-18 15:03:02 -0500
Commit message:

 updated
 
Package: NBAMSeq
Commit: ede3f7f68842334eb8cbb7942856384d793ea7df
Author: Xu Ren <xu.ren@stonybrook.edu>
Date: 2020-02-18 14:59:29 -0500
Commit message:

 updated
 
Package: infercnv
Commit: 9dd50e2bc93edf2eb9a14a8a6ef70024046e4732
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2020-02-18 14:51:23 -0500
Commit message:

 Version bump to 1.3.4 .
 
Package: infercnv
Commit: 17d8d1985c87cd8ff96d521633c65d900e8706bf
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2020-02-18 14:50:31 -0500
Commit message:

 Updated NEWS file for version 1.3.4 .
 
Package: infercnv
Commit: 864f6c596672455a04a854da9e0fde4eee522f0d
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2020-02-12 12:31:23 -0500
Commit message:

 Added options to save rds results after each step (save_rds) or final results (save_final_rds), with default TRUE.
Updated generated doc.
Removed old commented out code.
 
Package: infercnv
Commit: 8de24bc91c9ddfa5997d395aa536b61fd4678053
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2020-02-12 11:58:04 -0500
Commit message:

 Fix size of pdf output settings to use the given width and height values instead of the "USr" format.
Fixes in plot_cnv() when using observation groups with 1 or 2 cells.
Fix checks in plot_cnv() of references for when subclusters are not defined in the object.
Fix (sub)cluster definition when an annotation only has 1 cell (although this should probably be avoided).
 
Package: infercnv
Commit: 350cb854dbf8b8a61b5fc05b37c15c0b8925218a
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2020-02-07 13:41:51 -0500
Commit message:

 Updated dockerfile.
 
Package: RITAN
Commit: 2881e4e1c6a7471b973398c9e9dc0ab736a57ebb
Author: Zimmermann, Michael <mtzimmermann@mcw.edu>
Date: 2020-02-18 12:07:20 -0600
Commit message:

 syntax fixes for BioC
 
Package: RITAN
Commit: 7a0173dfd63d13f0de80370145b8c6da07210632
Author: Zimmermann, Michael <mtzimmermann@mcw.edu>
Date: 2020-02-05 13:56:23 -0600
Commit message:

 general check() cleanup
 
Package: scfind
Commit: c5b017a3f072102da67a84e735335f501202f0e6
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2020-02-18 12:09:01 -0500
Commit message:

 User requested deprecation
 
Package: mCSEA
Commit: 6d07550ff7087d070eed5fc3e82204fa65d509a6
Author: Jordi Martorell Marugán <jmartorellm@gmail.com>
Date: 2020-02-18 08:51:31 -0500
Commit message:

 Repair vignette
 
Package: enrichplot
Commit: 17dd93f05167ebfadf7f50bab9ba88a8f6b398ef
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-12-07 13:35:46 +0800
Commit message:

 Merge pull request #36 from huerqiang/master

change Category labels from ID to Description 
Package: enrichplot
Commit: ed9d000a8f38db46118d8cc4824532431b39023a
Author: huerqiang <13766876214@163.com>
Date: 2019-12-07 01:10:17 +0800
Commit message:

 change `ID` to `Description`
 
Package: enrichplot
Commit: 0c253fb7e255bc8582f8da246b8d1c4c258f4b52
Author: huerqiang <13766876214@163.com>
Date: 2019-12-06 23:24:31 +0800
Commit message:

 change `ID` to `Description`
 
Package: enrichplot
Commit: 63591f129277d60ce0d63beae930c44e47234ebd
Author: huerqiang <13766876214@163.com>
Date: 2019-12-06 20:09:15 +0800
Commit message:

 change `ID` to `Description`
 
Package: enrichplot
Commit: 9cae9176f48e593b8cfcf8a75b0d474259e4d697
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-12-06 18:40:04 +0800
Commit message:

 Merge pull request #35 from huerqiang/master

fix function `prepare_pie_data` 
Package: enrichplot
Commit: 67de511c7d49202e4ea367a10e5682fa591bfdb9
Author: huerqiang <13766876214@163.com>
Date: 2019-12-05 23:58:44 +0800
Commit message:

 fix prepare_pie_data()
 
Package: enrichplot
Commit: f3c4aeade4aac2e87b2b0e1df90f56cbcfceab34
Author: huerqiang <13766876214@163.com>
Date: 2019-12-05 20:50:12 +0800
Commit message:

 fix function prepare_pie_data
 
Package: enrichplot
Commit: c62f85d576cd66023f60f0886c4e1db4a0018451
Author: Erqiang Hu <13766876214@163.com>
Date: 2019-12-05 00:58:22 +0800
Commit message:

 Merge pull request #3 from YuLab-SMU/master

merge from YuLab 
Package: enrichplot
Commit: db7a02ac78a49639a1690a769aac24b03faa3e16
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-12-02 14:13:35 +0800
Commit message:

 update readme
 
Package: enrichplot
Commit: 17a1e365abc98fbe35e12605c6b0fd105eaa5d78
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-12-02 14:11:39 +0800
Commit message:

 update readme
 
Package: enrichplot
Commit: 8a07e041bbcfb7aba2dad2e0ac60cd8d9ab72aa1
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-12-02 14:08:44 +0800
Commit message:

 clean up code
 
Package: enrichplot
Commit: dbac7df7f09bc432a0ded9ab285df5d710b59de1
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-12-02 13:48:04 +0800
Commit message:

 optimize deal_gene_pie
 
Package: enrichplot
Commit: cde415bb4b3a61747b0fe004ee9651affb0f46c4
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-12-02 13:33:09 +0800
Commit message:

 Merge pull request #34 from huerqiang/master

add cnetplot.compareClusterResult() 
Package: enrichplot
Commit: c03af2ccffd4f6a54ebc399aba6fa050c967bd46
Author: huerqiang <13766876214@163.com>
Date: 2019-12-01 04:54:02 +0800
Commit message:

 add author
 
Package: enrichplot
Commit: 2fe434d6732a8bdcfd7f3b4f19cbf5b9cfcf258e
Author: huerqiang <13766876214@163.com>
Date: 2019-11-29 18:13:40 +0800
Commit message:

 add geom_node_text
 
Package: enrichplot
Commit: 7c62b67c4c5b685f86b61df3a82d68a1f6bddac1
Author: huerqiang <13766876214@163.com>
Date: 2019-11-29 15:42:45 +0800
Commit message:

 add labs
 
Package: enrichplot
Commit: 68324e4d2ed960c1a295da483edd68b74bd3e0ed
Author: huerqiang <13766876214@163.com>
Date: 2019-11-29 15:28:54 +0800
Commit message:

 add theme(legend.position="none")
 
Package: enrichplot
Commit: bff8c00c822cb2b1c746dc9e523d25da8341ebff
Author: huerqiang <13766876214@163.com>
Date: 2019-11-29 15:16:03 +0800
Commit message:

 add scale_size
 
Package: enrichplot
Commit: 49ead14c6b1b09e0b712dc028b95aa1cb26f4274
Author: huerqiang <13766876214@163.com>
Date: 2019-11-29 14:29:14 +0800
Commit message:

 add if(is.null(dim(y)) | nrow(y) == 1), if(ncol(ID_Cluster_mat2) > 4)
 
Package: enrichplot
Commit: 70e215e880b345ebcf8cb82c9946045153b89ca5
Author: huerqiang <13766876214@163.com>
Date: 2019-11-29 00:54:55 +0800
Commit message:

 add node_label
 
Package: enrichplot
Commit: ba72c48cc728f3277a7aa637f0bd84ef02840fe7
Author: huerqiang <13766876214@163.com>
Date: 2019-11-29 00:12:07 +0800
Commit message:

 delete "p <-"
 
Package: enrichplot
Commit: 53292ed4b3edf221a49f2431a73e0725579df5be
Author: huerqiang <13766876214@163.com>
Date: 2019-11-28 23:57:45 +0800
Commit message:

 add cnetplot.compareClusterResult() and deal_gene_pie()
 
Package: enrichplot
Commit: 2ed062e100dbe979f2e7af50006128a0f1b2c477
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-11 20:30:20 +0800
Commit message:

 Merge pull request #29 from huerqiang/master

add pie_scale, legend_n 
Package: enrichplot
Commit: e8ca12e562fc90e5de68df34fa0e32a4b6c1f42e
Author: huerqiang <793345316@qq.com>
Date: 2019-11-11 19:25:42 +0800
Commit message:

 change the default layout
 
Package: enrichplot
Commit: 3e1b0b0ee9766ac5c89c810ea20131196d8d1db8
Author: huerqiang <793345316@qq.com>
Date: 2019-11-11 17:10:16 +0800
Commit message:

 change the default layout
 
Package: enrichplot
Commit: 88917bfeb24acef8b2f4cdfaedd8423a87392ee7
Author: huerqiang <793345316@qq.com>
Date: 2019-11-11 16:51:10 +0800
Commit message:

 change default layout
 
Package: enrichplot
Commit: 16fb8525240c6be306abd9223a4f5891a8b81d20
Author: huerqiang <793345316@qq.com>
Date: 2019-11-11 12:06:06 +0800
Commit message:

 add pie_scale param in emapplot.enrichResult
 
Package: enrichplot
Commit: f74f10e092eb9f4253f72594498a2b12ebcee30f
Author: huerqiang <793345316@qq.com>
Date: 2019-11-11 11:08:52 +0800
Commit message:

 add annotation
 
Package: enrichplot
Commit: 14df7be47c7001bbe16214dc8f39deb68a4ae903
Author: huerqiang <793345316@qq.com>
Date: 2019-11-11 10:11:23 +0800
Commit message:

 delete n param in emap_graph_build()
 
Package: enrichplot
Commit: 8bb0a11404eafc3a4cf64bbd77aab826c1a7dfe7
Author: huerqiang <793345316@qq.com>
Date: 2019-11-10 16:25:27 +0800
Commit message:

 add pie_scale param
 
Package: enrichplot
Commit: 65e395a3231ed4b30e1d95c7c9d9186738a85960
Author: huerqiang <793345316@qq.com>
Date: 2019-11-10 15:29:35 +0800
Commit message:

 add legend_n param
 
Package: enrichplot
Commit: 62f8947a8c0d04e5612206e9c5de8d887333090d
Author: Erqiang Hu <13766876214@163.com>
Date: 2019-11-08 19:52:38 +0800
Commit message:

 Merge pull request #2 from YuLab-SMU/master

merge 
Package: enrichplot
Commit: b2aea4aee5f895a66919b49aa5bfdbaa00c13582
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-08 17:08:58 +0800
Commit message:

 import scatterpie
 
Package: enrichplot
Commit: 15f70114e3a441b4d21ac9248248a8ea63789df9
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-08 16:59:21 +0800
Commit message:

 change parameter
 
Package: enrichplot
Commit: eb5b1ec4210b6ad10015b7bd2bb3d084ed50a34b
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-08 16:30:08 +0800
Commit message:

 Merge pull request #27 from huerqiang/master

add node label 
Package: enrichplot
Commit: 3e2d694d3d427a6a76e5d9eb74b9650ae6a77988
Author: huerqiang <793345316@qq.com>
Date: 2019-11-08 14:00:22 +0800
Commit message:

 add theme_void()
 
Package: enrichplot
Commit: 94cbbf17eb09a38625c417391cc27e55f150159d
Author: huerqiang <793345316@qq.com>
Date: 2019-11-08 13:37:20 +0800
Commit message:

 add return
 
Package: enrichplot
Commit: adb1ab102c05a228275fb66c6e0df0d76b640883
Author: huerqiang <793345316@qq.com>
Date: 2019-11-08 13:11:32 +0800
Commit message:

 convert ID_Cluster_mat to data.frame
 
Package: enrichplot
Commit: fd36093ae0ec84741e892650a6866af2a5ed8fee
Author: huerqiang <793345316@qq.com>
Date: 2019-11-08 13:01:17 +0800
Commit message:

 add pie param
 
Package: enrichplot
Commit: f127827ca5457d1a99810b6396056fc2ac3b5946
Author: huerqiang <793345316@qq.com>
Date: 2019-11-06 20:25:36 +0800
Commit message:

 add labs()
 
Package: enrichplot
Commit: 40aa2795d9db3b0fe8d8e542a81c1b036694a3d4
Author: huerqiang <793345316@qq.com>
Date: 2019-11-06 20:13:45 +0800
Commit message:

 delete "else"
 
Package: enrichplot
Commit: d1118754b41542ca5b41f41311f46cef9022471d
Author: huerqiang <793345316@qq.com>
Date: 2019-11-06 13:06:56 +0800
Commit message:

 when y just have one line
 
Package: enrichplot
Commit: 7f2e36e60aa5a2e3c76814bcc19d21d4ee2671f7
Author: huerqiang <793345316@qq.com>
Date: 2019-11-05 19:54:00 +0800
Commit message:

 delete group param in scatterpie::geom_scatterpie
 
Package: enrichplot
Commit: fd0ad730dbb0957a7b277deddb6b200405a952f4
Author: huerqiang <793345316@qq.com>
Date: 2019-11-05 19:38:23 +0800
Commit message:

 delete group param in scatterpie::geom_scatterpie
 
Package: enrichplot
Commit: 0c4b954d0c65f72b755dd2f0bb3c2be9e993d26e
Author: huerqiang <793345316@qq.com>
Date: 2019-11-05 16:50:36 +0800
Commit message:

 deleate group param
 
Package: enrichplot
Commit: a70e84b41c29cf4fa302702f7f4ae874c2441900
Author: huerqiang <793345316@qq.com>
Date: 2019-11-05 16:33:15 +0800
Commit message:

 fix a bug for one_cluster
 
Package: enrichplot
Commit: 42d6117cb4ddc4ddbc6405e0eeb350c99d00622d
Author: huerqiang <793345316@qq.com>
Date: 2019-11-05 15:54:02 +0800
Commit message:

 fix a bug for one_line_y_union
 
Package: enrichplot
Commit: 3705bb5df01246718330c6a9cc34a09be7952d20
Author: huerqiang <793345316@qq.com>
Date: 2019-11-05 15:31:53 +0800
Commit message:

 add deal_data_pie() function
 
Package: enrichplot
Commit: 75b7270d1c698fe5fef54a449b7f0dfe88bf514f
Author: huerqiang <793345316@qq.com>
Date: 2019-11-03 20:18:58 +0800
Commit message:

 fix function emapplot.compareClusterResult for nrow(y_union) == 1
 
Package: enrichplot
Commit: e02c266324ed9be0e740f504f07180a39d78df8c
Author: huerqiang <793345316@qq.com>
Date: 2019-11-03 15:51:20 +0800
Commit message:

 add node_label
 
Package: enrichplot
Commit: a33c6d8a88218ee5f55414eb01c94d6ae44f014f
Author: Erqiang Hu <13766876214@163.com>
Date: 2019-11-03 13:23:41 +0800
Commit message:

 Merge pull request #1 from YuLab-SMU/master

合并 
Package: enrichplot
Commit: 6e77ca8ea7ad7a64daa411049ea4fac9e0f221ee
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-02 16:53:36 +0800
Commit message:

 add barplot, dotplot and fortify methods for compareClusterResult
 
Package: enrichplot
Commit: f0e767d6242ca0fa6cc9f465a9a5bd2ab54612f3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-01 23:37:34 +0800
Commit message:

 fixed some bugs
 
Package: enrichplot
Commit: 172231c9d79a2ef774a6256cce64dd11370f4c9c
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-11-01 23:03:46 +0800
Commit message:

 Merge pull request #26 from huerqiang/master

add emapplot.compareClusterResult function 
Package: enrichplot
Commit: 2885efe62682e16d99fee18bfc7f28ad2a55c2cc
Author: huerqiang <793345316@qq.com>
Date: 2019-11-01 15:01:18 +0800
Commit message:

 fix function graph_build
 
Package: enrichplot
Commit: 3e26719415ee21b5940c9c9603f3584f54432316
Author: huerqiang <793345316@qq.com>
Date: 2019-11-01 14:17:25 +0800
Commit message:

 fix function graph_build
 
Package: enrichplot
Commit: 5779af3d99bf7997ed5eb11a55ff3dc2c01591e9
Author: huerqiang <793345316@qq.com>
Date: 2019-11-01 14:09:33 +0800
Commit message:

 add graph_build function
 
Package: enrichplot
Commit: 222ca30c00c85a9b35b7b2e828c074c6369229f9
Author: huerqiang <793345316@qq.com>
Date: 2019-10-31 19:00:22 +0800
Commit message:

 change labeller value
 
Package: enrichplot
Commit: be0a0a8679ae8280abd15ee555844052600c7b3f
Author: huerqiang <793345316@qq.com>
Date: 2019-10-31 18:47:39 +0800
Commit message:

 change the value of "ID_Cluster_mat$radius"
 
Package: enrichplot
Commit: b1b6eda53a76004d02dabde9bb83c9687ee1d54e
Author: huerqiang <793345316@qq.com>
Date: 2019-10-31 18:37:40 +0800
Commit message:

 change"label_size" to  "labeller=function(x)"
 
Package: enrichplot
Commit: f1268f646d90c00d45824c4741064bf9f5eb0fc0
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-10-30 12:11:37 +0800
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: enrichplot
Commit: 04f7db3db4c05216629026dfd7a6756f18e2ff7b
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-10-30 10:36:44 +0800
Commit message:

 bioc3.10
 
Package: enrichplot
Commit: 01a80eac61f8340444c7366243842df731bd9a08
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-10-30 10:02:10 +0800
Commit message:

 fixed warning msg
 
Package: enrichplot
Commit: 5b34faf5f162e73405ce3927e102b4ed66c1887e
Author: huerqiang <793345316@qq.com>
Date: 2019-10-29 14:10:06 +0800
Commit message:

 test params
 
Package: enrichplot
Commit: f393ba9cde07c211a5a404353549e542bae154b6
Author: huerqiang <793345316@qq.com>
Date: 2019-10-29 13:38:56 +0800
Commit message:

 nothing
 
Package: enrichplot
Commit: a28466fb816fa8c06cc50794320b276dff0a2534
Author: huerqiang <793345316@qq.com>
Date: 2019-10-29 13:18:19 +0800
Commit message:

 change "size" to "size_label"
 
Package: enrichplot
Commit: 61aa22d01288f28baa927eaffb0391f42af38a4f
Author: huerqiang <793345316@qq.com>
Date: 2019-10-29 13:05:10 +0800
Commit message:

 add "import clusterProfiler"
 
Package: enrichplot
Commit: 9dd5c422da6debf40ab295f054ef753cdbb8811c
Author: huerqiang <793345316@qq.com>
Date: 2019-10-29 12:34:06 +0800
Commit message:

 change function merge_compareClusterResult
change the pretreatment of x using
clusterProfiler:::fortify.compareClusterResult
 
Package: enrichplot
Commit: 7bb1a315abb1ae780cf54e1aed964314b4090102
Author: huerqiang <793345316@qq.com>
Date: 2019-10-25 18:00:00 +0800
Commit message:

 add emapplot.compareClusterResult function
 
Package: SeqArray
Commit: 9a2782ae547a3d4dc50b23cca655cde7d7dbccd7
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2020-02-18 01:11:52 -0600
Commit message:

 tweak
 
Package: SAIGEgds
Commit: 2ddce2fac5214c723f774b584abd877a18cf5cfa
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2020-02-18 01:05:48 -0600
Commit message:

 update retry
 
Package: Rsubread
Commit: aa7d0ba61247bf9ecabfa082fb6c121d5c731414
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2020-02-18 14:35:15 +1100
Commit message:

 The 2.1.2 version
 
Package: GmicR
Commit: 1fba0b0b947f425e543c675e4afbffea1be1de97
Author: Richard Virgen-Slane <richardvirgen-slane@WARE3736.local>
Date: 2020-02-17 15:56:58 -0800
Commit message:

 Bug fixes. Bump to version 1.1.6.
 
Package: BiocPkgTools
Commit: 626a31f7b359c43d7cebdbfdc85644680a6bf833
Author: Sean Davis <seandavi@gmail.com>
Date: 2020-02-17 18:33:57 -0500
Commit message:

 version bump
 
Package: BiocPkgTools
Commit: ad64dce07c025a62d81d8c7daadb28da1f0d2b05
Author: Sean Davis <seandavi@gmail.com>
Date: 2020-02-17 18:33:10 -0500
Commit message:

 Merge branch 'master' of github.com:seandavi/BiocPkgTools
 
Package: BiocPkgTools
Commit: caac2bae489f16d2e0f5c27ce51ee93ee4912e78
Author: Sean Davis <seandavi@gmail.com>
Date: 2020-02-17 18:31:30 -0500
Commit message:

 Merge pull request #40 from FelixErnst/master

fixed regression for input check of getPackageInfo() 
Package: BiocPkgTools
Commit: 49bbd5db2c0b01edaeb6f593937fbea5e9624037
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2020-02-14 20:35:56 +0100
Commit message:

 fixed mislabeled context() in getPackageInfo unit test
 
Package: BiocPkgTools
Commit: b7c9ef02afbb76dc166a20fcf47530768256de0c
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2020-02-14 20:21:29 +0100
Commit message:

 fixed regression for input check of getPackageInfo()
 
Package: SMITE
Commit: ccef7093eaf04b6b0a9b40416c667924cbd30955
Author: Andrew <andrew@Andrews-MBP.fios-router.home>
Date: 2020-02-17 18:30:18 -0500
Commit message:

 fix generic error
 
Package: PADOG
Commit: e3eb9caf609449d2de44173e57cf7deb3a4ed868
Author: Adi L Tarca <atarca@med.wayne.edu>
Date: 2020-02-17 18:04:31 -0500
Commit message:

 fixed multiple class for matrix
 
Package: atSNP
Commit: 58176b50fae1ebf232693612229860091efef59e
Author: Sunyoung Shin <sunyoung.shin@utdallas.edu>
Date: 2020-02-17 13:09:59 -0600
Commit message:

 debugging vignette issue 2
 
Package: atSNP
Commit: 7ecd1bb453864b0f03232f1042b22d6e1890112e
Author: Sunyoung Shin <sunyoung.shin@utdallas.edu>
Date: 2020-02-17 11:33:39 -0600
Commit message:

 debugging vignette issue
 
Package: tximeta
Commit: 52f7244cdb145f5c9e2cbc9d50c6e93cb0d9f6f4
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2020-02-17 10:39:45 -0500
Commit message:

 add note on errors connecting to db
 
Package: ToPASeq
Commit: 5867c0aee2532344c4ce76291c595225b0229285
Author: unknown <ihnatova@iba.muni.cz>
Date: 2020-02-17 14:24:36 +0100
Commit message:

 nodes in pathways without ID type
 
Package: Gviz
Commit: a6b1ab463a1bc222a7dc8bd3e482352e7ee07042
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-14 17:38:05 +0100
Commit message:

 Bumbed version after adding bunch of tests.
 
Package: Gviz
Commit: 3501807f9d9e8797327115df27cf62a6567ee982
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-14 15:12:45 +0100
Commit message:

 Tests for internal fucntions.
 
Package: Gviz
Commit: c169fe9133c47030c925681a925ca1778ae8e671
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-14 01:33:38 +0100
Commit message:

 fixed test for .import.bam.alignments
 
Package: Gviz
Commit: d1052e17ca8652998cc46b2b147eca581acc79c1
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-14 01:18:11 +0100
Commit message:

 .import.bam.alignment always returns GRanges with same mcols
 
Package: Gviz
Commit: 5501c19da0af0808e2461cbc14392ec3cc862e76
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-14 00:23:43 +0100
Commit message:

 test .import.bam.alignments
 
Package: Gviz
Commit: eedbe92fa81eaea171e48bf29a557c513c6c13d6
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-13 23:46:11 +0100
Commit message:

 test for start, end, width
 
Package: Gviz
Commit: 15eeedcdbe9b4a55ec6a40a8d91c93877645c718
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-13 23:19:43 +0100
Commit message:

 Added small bam file for testing only.
 
Package: Gviz
Commit: 0809cc502403e6bf3771ff596baf2ce4ed2d3896
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-13 21:52:45 +0100
Commit message:

 added test for RNASequenceTrack
 
Package: Gviz
Commit: 8b944217ee54e372329a79c3d2c7da9c24f0518d
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-13 21:38:16 +0100
Commit message:

 fixed issues in man pages
 
Package: Gviz
Commit: 6ec8f9279453ccf498a7dd4693538b2a472cc14e
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-13 20:27:52 +0100
Commit message:

 Replaced BSgenome.Celegans.UCSC.ce2 with BSgenome.Hsapiens.UCSC.hg19
 
Package: Gviz
Commit: 2085cae4fcb835b3a5e28e6d4716d32fa4232ae7
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-13 20:14:49 +0100
Commit message:

 Added missing entries in man and NAMESPACE
 
Package: Gviz
Commit: fb2909f0cb8565abae12de3073338fc0c51ac545
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-02-13 18:43:21 +0100
Commit message:

 Test for general accessors
 
Package: rhdf5
Commit: a279ef0ce5e95f638549d4d82eadc83e69ba2df1
Author: Mike Smith <grimbough@gmail.com>
Date: 2020-02-17 09:33:31 +0100
Commit message:

 Remove C++11 requirement
 
Package: rhdf5
Commit: 8ebc015744439170344896e498164d0bd2ae8216
Author: Mike Smith <grimbough@gmail.com>
Date: 2020-02-11 13:50:51 +0100
Commit message:

 Merge pull request #54 from grimbough/Rtools40-1

Incorporating changes require for rtools 4.0 
Package: rhdf5
Commit: c6e00c27e4ca20dd51e51cca7705716fa7f11972
Author: Mike Smith <grimbough@gmail.com>
Date: 2020-02-11 13:10:57 +0100
Commit message:

 Tweaks for coping with UTF-8 file paths
 
Package: rhdf5
Commit: a6f566845eb922fb81bf6e7feb7cbce6a652127f
Author: Mike Smith <grimbough@gmail.com>
Date: 2020-02-11 13:10:13 +0100
Commit message:

 Remove linking to C++ library
 
Package: FastqCleaner
Commit: 9e6fdab2393e5cd4e5ceb7857d132f035b5a1bf7
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-02-17 05:05:35 -0300
Commit message:

 fix conflicts
 
Package: tRanslatome
Commit: 40396dde820e4b19f74c9a7a5581954cbb58d166
Author: erik.dassi@gmail.com <erikdassi@users.noreply.github.com>
Date: 2020-02-17 08:41:57 +0100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/tRanslatome
 
Package: tRanslatome
Commit: d29b781687217a8f03076e70d6de6e73035adb06
Author: erik.dassi@gmail.com <erikdassi@users.noreply.github.com>
Date: 2020-02-17 08:41:27 +0100
Commit message:

 bugfix in converting FCs to log2FCs in TranslatomeDataset
 
Package: plyranges
Commit: 88d5434a41308147c9c5ef03ace533b4264dcb02
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2020-02-17 18:27:19 +1100
Commit message:

 add news
 
Package: plyranges
Commit: 33b3a5d4db04f07dcfbb6f4ac565ad6d97ea6363
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2020-02-17 18:10:25 +1100
Commit message:

 cleaning up reduce/disjoin internals - cleans up disjoin cases when an expansion occurs.
 
Package: batchelor
Commit: 7fc813fbb1afa5bff99cff8bafed305dea6ec21f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-16 21:59:41 -0800
Commit message:

 Bugfixes for parsing tree-based weights in PCA.
 
Package: scran
Commit: e0c21fce76423a52ec74f4fb693526d705218882
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-16 19:52:16 -0800
Commit message:

 Reoxygenated, bumped version and date.
 
Package: scran
Commit: 726c31f8e1cbd6ad4f5508932921c77427c83089
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-16 19:28:17 -0800
Commit message:

 Fixed calculation in getClusteredPCs.
 
Package: scater
Commit: 567c3163fc40b5fd0491ee4d3741202ab99785bf
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-16 19:15:46 -0800
Commit message:

 Unname vectors in merged colData after aggregation.
 
Package: plyranges
Commit: a58b8c0505f05fc1b748b321eaabdd91d805ef8e
Author: Stuart Lee <lee.s@wehi.edu.au>
Date: 2020-02-17 13:03:18 +1100
Commit message:

 set tidyselect version, update coverage method for delegating ranges, fix docs for bam reading
 
Package: DAMEfinder
Commit: e90f6e78625b66887e491472bc935dcbadd58e17
Author: Stephany Orjuela <sorjuelal@gmail.com>
Date: 2020-02-16 22:26:49 +0100
Commit message:

 Merge pull request #31 from markrobinsonuzh/cleanup_branch

Cleanup branch 
Package: DAMEfinder
Commit: 9d2e96aef5de69fdd7f7936877fb023c0933e645
Author: sorjuela <sorjuela@gmail.com>
Date: 2020-02-16 22:25:30 +0100
Commit message:

 bump version
 
Package: DAMEfinder
Commit: 2331b1b367e52cbfdde3a178d35ba8e23028c23c
Author: sorjuela <sorjuela@gmail.com>
Date: 2020-02-16 22:23:20 +0100
Commit message:

 fix horizontal lines
 
Package: DAMEfinder
Commit: 660a8a963bd1861d3b0070027e5c50a7fa105703
Author: sorjuela <sorjuela@gmail.com>
Date: 2020-02-16 22:19:35 +0100
Commit message:

 update readme, remove old news versions
 
Package: scater
Commit: 04a9c014d03c7f2f183297ca7adca15281cc7cd9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-16 11:56:30 -0800
Commit message:

 Updates for more stringent SE assignment.
 
Package: synergyfinder
Commit: 337cd18a5789fb249239025663b85045a33ece1c
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2020-02-16 19:10:15 +0200
Commit message:

 Merge branch 'RELEASE_3_10'
 
Package: synergyfinder
Commit: 21e65b7b22094c0deca3c5ecdc16ee432b6f92c4
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2020-02-16 19:09:40 +0200
Commit message:

 Make ZIP to be compatible to 2 X 2 combination matrix
 
Package: BASiCS
Commit: 5e189b6552cb81e95f8dcc7d478f4192152abd97
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2020-02-16 15:15:50 +0000
Commit message:

 version 1.9.16 (2020-02-16)
- Adds extra line in `test_sim.R` to avoid warning in BiocCheck
 
Package: BASiCS
Commit: bce6c4899076e73f6c6bd9ee9ad4ca6172b82ba4
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2020-02-16 15:11:22 +0000
Commit message:

 version 1.9.15 (2020-02-16)
- Use expect_equal in scran test (now all suitable tests)
- Minor change in `test_differential_test_reg.R` to use 3 instead of 2 decimal
points. This hopefully avoids issues associated to a bug in `round`. For details
see: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17668
 
Package: BASiCS
Commit: fb863278cc91f4dcc9ec5e7b3ad97eec82aba967
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2020-02-14 09:15:09 +0000
Commit message:

 Minor patch: use expect_equal in scran test (now all suitable tests)
 
Package: synergyfinder
Commit: 3e337a84068da34f089016c2d969b0b818b8ef09
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2020-02-16 12:16:52 +0200
Commit message:

 update version number to 2.1.8
 
Package: synergyfinder
Commit: 0b4f21f36feaac3fbd52f732c9f354017097cb69
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2020-02-16 11:49:54 +0200
Commit message:

 update version number to 2.0.8
 
Package: synergyfinder
Commit: b5c1f401d4f024e8bc6d5806194531357a99495b
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2020-02-16 11:49:07 +0200
Commit message:

 untrack .so and .o files
 
Package: synergyfinder
Commit: 478c5ac322de6d41ce91c931fe78a444ff627e01
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2020-02-13 16:24:15 +0200
Commit message:

 fix compile problems on Windows and Linux OS.
 
Package: limma
Commit: fb2ce173d94fee80707ba421876c85530f2ad112
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2020-02-16 21:16:40 +1100
Commit message:

 16 Feb 2020: limma 3.43.4

- voom now checks explicitly for NA or negative counts and gives an
  informative error message.

- Cleaning up of internal code to avoid partial matching of function
  arguments, attributes or list component names. The automatic package
  tests are now run with the warnPartialMatchArgs,
  warnPartialMatchAttr and warnPartialMatchDollar options all set to
  TRUE.
 
Package: SingleCellExperiment
Commit: c86fadb77af1777650aace6ca9cfe8c9cb8463cd
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-16 00:45:11 -0800
Commit message:

 Updated tests for stricter SE assays assignment.
 
Package: ChIC
Commit: e77e6d22aaccf4ad070d8f44209f4264e44f85b2
Author: carmencita <carmen.livi@ifom.eu>
Date: 2020-02-16 09:31:49 +0100
Commit message:

 version bump
 
Package: ChIC
Commit: 6623a24e237013ac23055e49a87c23cd5c165a11
Author: carmencita <carmen.livi@ifom.eu>
Date: 2020-02-15 12:06:51 +0100
Commit message:

 adjusting vignette
 
Package: ChIC
Commit: 84eedc636fae4acc6293c2325627ad592245a602
Author: carmencita <carmen.livi@ifom.eu>
Date: 2020-02-15 10:12:58 +0000
Commit message:

 Merge pull request #6 from Itagliaf/master

Fix in wrapper 
Package: ChIC
Commit: fc2cf8ab2bcfb5dd480e4ee1acee1b24a4b0bd6f
Author: Ilario Tagliaferri <ilario.tagliaferri@gmail.com>
Date: 2020-02-11 10:20:54 +0100
Commit message:

 chicWrapper: Path to create graph set to NULL in specific function argument so all
the graphs are printed into the opened pdf device.
 
Package: ChIC
Commit: d8ae9445119b3705e104129e26c947cc30fcf577
Author: Ilario Tagliaferri <ilario.tagliaferri@gmail.com>
Date: 2020-02-10 19:06:03 +0100
Commit message:

 Fixed wrapper to write all the graphs on a single pdf
 
Package: ChIC
Commit: 14381549b86b9baae15ec1d54bd90daceadd8954
Author: Ilario Tagliaferri <ilario.tagliaferri@gmail.com>
Date: 2020-02-10 18:33:44 +0100
Commit message:

 Changed check to calculate the rf score for a target in the wrapper.
 
Package: ChIC
Commit: fb7b065f84f1256e073ec97b0bff31a5b2c5e583
Author: Ilario Tagliaferri <ilario.tagliaferri@gmail.com>
Date: 2020-02-10 13:38:25 +0100
Commit message:

 Added if-else to avoid creation of graphs that need the values from
the compendium
 
Package: scater
Commit: b7f289eb8c3e017bc43788be1c87306c5ac27450
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-15 20:55:44 -0800
Commit message:

 Update tests for new sizeFactors behavior.
 
Package: SingleCellExperiment
Commit: 092c5c7c536d8a36fcc8f3c6b95e059c3291af13
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 15:04:40 -0800
Commit message:

 Minor docfixes, reoxgyenated.
 
Package: SingleCellExperiment
Commit: a8561a88aaa3da75a2713db4672e4a0724b2892d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 15:04:16 -0800
Commit message:

 Fleshed out intro vignette.
 
Package: SingleCellExperiment
Commit: 8932a72063b182b45bdc0ef22cd35fa81dc33b0a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 14:30:20 -0800
Commit message:

 Added the colLabels concept for storing column labels.
 
Package: SingleCellExperiment
Commit: d108add3be9c7a8272f569fcce8379f1a04ae79e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 14:06:31 -0800
Commit message:

 Allow extra actions from sizeFactors when missing.
 
Package: SingleCellExperiment
Commit: 375ea87ed13c489c9972766c4c1efbe8aef28245
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-08 00:10:22 -0800
Commit message:

 Removed unnecessary setting of SF names.
 
Package: SingleCellExperiment
Commit: 1c58ebccb1b888f887276f3a6a27c72b31854754
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-07 22:12:39 -0800
Commit message:

 Another minor docfix.
 
Package: SingleCellExperiment
Commit: 295e0baaaa7c5476feff843ffcae0c922227faf3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-07 22:02:05 -0800
Commit message:

 Docfixes.
 
Package: SingleCellExperiment
Commit: 4db63f937edff3e17dc858f793cbe620dc149099
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-07 21:59:05 -0800
Commit message:

 Reoxygenated, bumped version and date.
 
Package: SingleCellExperiment
Commit: e9fe4cfb034bcbb0cb84ab4fe8336adb358f65b1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-07 21:58:25 -0800
Commit message:

 Stripped out tests for defunct methods.
 
Package: SingleCellExperiment
Commit: ddf64502ad3232cf55db022906305113bf05ce95
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-07 21:42:18 -0800
Commit message:

 Cleaned out unnecessary validity checks.
 
Package: SingleCellExperiment
Commit: e97dd315c3cc32b1daa4cdde0b0d9ae0e40948e4
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-07 21:40:13 -0800
Commit message:

 Updated updateObject to shift size factors.
 
Package: SingleCellExperiment
Commit: 7c2c437f3b9ca38d5a446c622ebcb62ab5f5036f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-07 21:27:20 -0800
Commit message:

 Removed defunct sizeFactors functions, added auto-updaters.
 
Package: SingleCellExperiment
Commit: bd01c5c474b9858d39fe8727af75573aa5b0d6a0
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-07 21:04:34 -0800
Commit message:

 Began deprecating the spike-in methods.
 
Package: DeMixT
Commit: f86f09d65bd58b257844dcd4074e0edadbc878d2
Author: pengyang0411 <pengyang0411@gmail.com>
Date: 2020-02-15 21:02:06 -0600
Commit message:

 update to v1.3.5
 
Package: DeMixT
Commit: a30e229598a144cb17a2e8c272e469f7828b0369
Author: pengyang0411 <pengyang0411@gmail.com>
Date: 2020-02-04 22:54:44 -0600
Commit message:

 update to v1.2.4
 
Package: PCAtools
Commit: bbda0281dd398d99ea1825e86fdfffadfa68152d
Author: Kevin Blighe <kblighe@CLINICALBIO.dlink.com>
Date: 2020-02-15 11:34:13 -0300
Commit message:

 Update library.bib
 
Package: RegParallel
Commit: 42dd0257ebb12a316538fd6fbf595eec63e79543
Author: Kevin Blighe <kblighe@CLINICALBIO.dlink.com>
Date: 2020-02-15 11:27:59 -0300
Commit message:

 Update library.bib
 
Package: EnhancedVolcano
Commit: 3bf702f2e5790bc0af2f51d5e88d82a87469ff7e
Author: Kevin Blighe <kblighe@CLINICALBIO.dlink.com>
Date: 2020-02-15 10:21:45 -0300
Commit message:

 Update library entry
 
Package: PCAtools
Commit: dd336785b04955e8ec1a8cff7bffdeeda4f80ca3
Author: Kevin Blighe <kblighe@CLINICALBIO.dlink.com>
Date: 2020-02-15 09:21:29 -0300
Commit message:

 Update version for pre-release v2
 
Package: PCAtools
Commit: a871c7658a7bca5cdd5c0000ba08319f42c9b1dd
Author: Kevin Blighe <kblighe@CLINICALBIO.dlink.com>
Date: 2020-02-15 09:17:56 -0300
Commit message:

 Update version to v2, and update vignette text
 
Package: GNET2
Commit: 4c7080eadd0c65858602d705a704f90454c599d7
Author: Chris Chen <chen08900@gmail.com>
Date: 2020-01-16 13:43:07 -0600
Commit message:

 Merge branch 'master' of https://github.com/chrischen1/GNET2
 
Package: GNET2
Commit: 1274f0d967a98a6b3ede2a298de9152db5a9eea1
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2020-01-16 11:34:02 -0600
Commit message:

 Merge branch 'master' into master 
Package: GNET2
Commit: 861b8dff770f72de91ca4a243b35a8cf5f9b93b1
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-11-15 15:48:14 -0600
Commit message:

 Merge pull request #15 from chrischen1/master

add force_split option 
Package: GNET2
Commit: 4f9bc7fac5944c2afb97752ca3abddb10f365167
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-11-06 08:35:04 -0600
Commit message:

 Merge pull request #14 from chrischen1/master

update 1.3.4 
Package: GNET2
Commit: 0480f5aa175d66047934469a767a522da169a5ce
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-11-05 22:32:07 -0600
Commit message:

 Merge pull request #13 from chrischen1/master

update 1.3.2 
Package: GNET2
Commit: 1f82eb9c49f2d93be8c0df2a694cb02103ed6e73
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-11-04 14:43:00 -0600
Commit message:

 Merge pull request #12 from chrischen1/master

fix conflicts 
Package: GNET2
Commit: 82a321ac707c3a83e42bb5eddc3ab459fad9e0ae
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-09-18 12:08:13 -0500
Commit message:

 Update README.md 
Package: GNET2
Commit: 886f4edb7143a0d6aaa51f9a957c523c4fc10507
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-07-01 21:22:22 -0500
Commit message:

 Merge pull request #11 from chrischen1/master

fix crash 
Package: GNET2
Commit: ca21e8b06302e2b99b794a59f5eaf261612e4c57
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-07-01 16:24:37 -0500
Commit message:

 Merge pull request #10 from chrischen1/master

update docs 
Package: GNET2
Commit: 7399c5967d7b342cb3e262cc9de13e587a2af19f
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-07-01 16:23:52 -0500
Commit message:

 Update README.md 
Package: GNET2
Commit: 51ca4f627f9f29c107461091570635d018235197
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-07-01 14:46:59 -0500
Commit message:

 Merge pull request #9 from chrischen1/master

merge bioC version 
Package: GNET2
Commit: 6296d81d991cc5e079b8314e6840b0bf19c377a9
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-07-01 14:46:50 -0500
Commit message:

 Merge branch 'master' into master 
Package: GNET2
Commit: a19b20bbf7e21a86d98b541313322392f3b09f1d
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-06-27 10:55:42 -0500
Commit message:

 Merge pull request #8 from chrischen1/master

Fix several conditions that may cause error in tree construction. 
Package: GNET2
Commit: 1f32ffcb44eb8751c81095ffc912f81e5852f21c
Author: Chen Chen <chen.chen@mail.missouri.edu>
Date: 2019-06-27 10:54:59 -0500
Commit message:

 Fix several conditions that may cause error in tree construction.
 
Package: GNET2
Commit: 9df65e3d9e1f423e1631ffae71a95c2e81b10a29
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-04-03 16:17:19 -0500
Commit message:

 Merge pull request #7 from chrischen1/master

Package accepted by bioC-devel. 
Package: GNET2
Commit: a00ab284073d360f461205cb342913008321711d
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-03-29 14:39:05 -0500
Commit message:

 Merge pull request #6 from chrischen1/master

Passed all BioC server checks 
Package: GNET2
Commit: cab64e250a2c3d35e5c102f92a142795e070ee6a
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-03-28 23:23:00 -0500
Commit message:

 Merge pull request #5 from chrischen1/master

first version submitted to bioC 
Package: GNET2
Commit: c02870496da1e8924cb74124b391019c39dba54e
Author: Chris <chrischen1@users.noreply.github.com>
Date: 2019-03-28 00:23:15 -0500
Commit message:

 Merge pull request #4 from chrischen1/master

pass all cmd checks 
Package: scran
Commit: 88e8ea9e0d2d95832cfca34ac37cada8e2663786
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-15 02:15:32 -0800
Commit message:

 Reoxygenated, bumped version and date.
 
Package: scran
Commit: 4ded56905ef3bfef63d7bc2ce531c9478a93f9e0
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-15 02:14:59 -0800
Commit message:

 Easier removal of NAs from the marker effect matrix.
 
Package: scRNAseq
Commit: a3304a6b94967a220110df4dfdef2acba79a17dd
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-15 01:43:51 -0800
Commit message:

 Forgot to add rownames for Bach.
 
Package: scRNAseq
Commit: 8fbf4e8ceb79bb89ae8d455cd3bb6a4b934a9d4e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-15 01:15:44 -0800
Commit message:

 Docfixes, added missing imports. Bumped version and date.
 
Package: scRNAseq
Commit: aa6b172797162a1f745a81235658dd96963074e3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-15 01:15:13 -0800
Commit message:

 Reoxygenated.
 
Package: scRNAseq
Commit: d92e5d2feb83f40d51933efea7c263fada0dec88
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-15 00:45:11 -0800
Commit message:

 Extended test coverage.
 
Package: scRNAseq
Commit: 2b205c96fd67049a734376ba021e10c7062ebaf8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-15 00:32:02 -0800
Commit message:

 Pull down genomic coordinates.
 
Package: GenomicFeatures
Commit: 551f5688805b9c40e5a204c540220f21bdf3d3d4
Author: Michael Lawrence <michafla@gene.com>
Date: 2020-02-14 17:41:41 -0800
Commit message:

 version bump
 
Package: GenomicFeatures
Commit: 72b487caf3125708076f3412daf08995ba9a71ff
Author: Michael Lawrence <michafla@gene.com>
Date: 2020-02-14 17:40:47 -0800
Commit message:

 keep seqlevels in mapToTranscripts()
 
Package: GenomicFeatures
Commit: 3c9fd5395b26d4fb9a8361744c2cffed711b1827
Author: Michael Lawrence <michafla@gene.com>
Date: 2020-02-14 17:39:55 -0800
Commit message:

 asGFF,TxDb is robust to absence of CDS ranges
 
Package: GSEABenchmarkeR
Commit: b60ceb15a91f8dbcd4db129ff7bac6ffebf28af0
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2020-02-14 18:00:25 -0500
Commit message:

 vignette: add purpose of the package
 
Package: FastqCleaner
Commit: b815c5de17f601d5d0d5e7bb6fc7e2441bb44f1a
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-02-14 17:48:49 -0300
Commit message:

 fix conflicts
 
Package: FastqCleaner
Commit: cd6ff17977aac96821f5a3f2ac529845544ebaeb
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-02-14 17:44:36 -0300
Commit message:

 fix conflicts
 
Package: FastqCleaner
Commit: 318bccbb5e2162c44ee3b25af1e20ec1f594d5d9
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-02-14 17:36:20 -0300
Commit message:

 fix conflicts
 
Package: FastqCleaner
Commit: da50aecbb5e05b0fb40dbd652974031c2932d1aa
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-02-14 17:34:34 -0300
Commit message:

 fix conflicts
 
Package: FastqCleaner
Commit: 361c81600e2d514d13e5b57d5ad9c977bb94d9c6
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-02-14 17:32:49 -0300
Commit message:

 fix conflicts
 
Package: FastqCleaner
Commit: 996e6e3d60d056fee23637edf19a0c1e693d00c1
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-02-14 17:29:26 -0300
Commit message:

 fix conflicts
 
Package: FastqCleaner
Commit: b6a0ce52e8ec294fc5cf3eb3a856ad2ca2735533
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-02-14 17:28:06 -0300
Commit message:

 fix conflicts
 
Package: Modstrings
Commit: 1d1bcb8c5fa4d88ed02132132a683b6ce45f593c
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2020-02-14 17:15:28 +0100
Commit message:

 fixed regression in combineIntoModstrings()
 
Package: FastqCleaner
Commit: 748b108f7ae6024d9140ef7d7a2121905676843c
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-02-14 17:19:11 -0300
Commit message:

 fix conflicts
 
Package: FastqCleaner
Commit: 608ed0447ba01afce7309d8dee4da1b56bf2c41f
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-02-14 17:15:49 -0300
Commit message:

 fix conflicts
 
Package: FastqCleaner
Commit: f604e8435c97fea4d25f08c9fc63611b5a33e02c
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-02-14 17:13:01 -0300
Commit message:

 fix conflicts
 
Package: FastqCleaner
Commit: f8a31e960541186e84c4e2c59aeecd90f2abbc86
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-02-14 17:08:29 -0300
Commit message:

 fix conflicts
 
Package: FastqCleaner
Commit: 1170a6abb8fc3fccd783b4ac94fcc68c9564a59f
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-02-14 17:02:53 -0300
Commit message:

 fix conflicts
 
Package: FastqCleaner
Commit: 895a43a1b0a62f98390c4a822f8a44972475a57d
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-01-12 22:16:10 -0300
Commit message:

 add previous commits
 
Package: FastqCleaner
Commit: 0f1d08121328ef0ef8206c11fdc762b05d870715
Author: Leandro Roser <learoser@gmail.com>
Date: 2020-01-12 21:55:12 -0300
Commit message:

 test
 
Package: PADOG
Commit: 703956735c69f520a63925f7909274feff9e16b3
Author: Adi L Tarca <atarca@med.wayne.edu>
Date: 2020-02-14 14:38:14 -0500
Commit message:

 changed from KEGG to KEGGREST
 
Package: PADOG
Commit: 5f682b0c191b354608710632d846706415191099
Author: Adi L Tarca <atarca@med.wayne.edu>
Date: 2020-02-14 14:37:10 -0500
Commit message:

 changed from KEGG to KEGGREST
 
Package: PADOG
Commit: 02a0d95b93f856a71907672cc05ea2b9e7179892
Author: Adi L Tarca <atarca@med.wayne.edu>
Date: 2020-02-14 14:35:41 -0500
Commit message:

 changed from KEGG to KEGGREST
 
Package: PADOG
Commit: c4081a2cadc2419e8a6906acf8461a89adf93064
Author: Adi L Tarca <atarca@med.wayne.edu>
Date: 2020-02-14 14:34:52 -0500
Commit message:

 changed from KEGG to KEGGREST
 
Package: PADOG
Commit: 4ed064fba3f72540fb69b70f85ea9955b5e07d27
Author: Adi L Tarca <atarca@med.wayne.edu>
Date: 2020-02-14 14:33:49 -0500
Commit message:

 changed from KEGG to KEGGREST
 
Package: SeqSQC
Commit: 3527554184d8747d898057fc7af883ea6b502d0d
Author: qian <qliu7@buffalo.edu>
Date: 2020-02-14 14:23:18 -0500
Commit message:

 fixed a bug in SampleQC() when X variants not present, will force close gds file if happening.
 
Package: GenomeInfoDb
Commit: 2e1c2dc5cebdf39cf6b57b3eafbc5c4ff00a61ae
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-02-14 10:45:49 -0800
Commit message:

 Link Sscrofa11.1/susScr11 to GCA_000003025.6 instead of GCF_000003025.6
 
Package: batchelor
Commit: a54aa96e37f898e7638f83a1ee3ef2056c35de28
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-14 09:35:01 -0800
Commit message:

 Reoxygenated, bumped version and date.
 
Package: batchelor
Commit: badd9753778e70f65f6e0c023ca4edda4ee50e0e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-14 09:34:41 -0800
Commit message:

 Yet more doc clarification about list inputs.
 
Package: batchelor
Commit: aa652005237bb72b9815786280eb6bbe92ad0e44
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-14 09:29:31 -0800
Commit message:

 Fleshed out docs for PCA weighting.
 
Package: batchelor
Commit: bc9a31b7d3a3598e79635b5107d09d02f1461daf
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-14 09:13:46 -0800
Commit message:

 Added tests for multiBatchPCA's new weighting mode.
Plus bugfix for errors.
 
Package: batchelor
Commit: f5a865e737577784d5a90fa0257b2178fe1fca73
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-13 23:08:54 -0800
Commit message:

 Preliminary support for tree-based weights in PCA.
 
Package: batchelor
Commit: 46f30228d01b505e7fd969b48899a52fbf792779
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-12 21:52:25 -0800
Commit message:

 Updated tests for more thorough single-input checks.
Testfixes to address inequality of median inverse/inverse median.
 
Package: batchelor
Commit: 98acfaa84c8531996c33e2cf4522a0dfef4cfe90
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-12 21:44:42 -0800
Commit message:

 Avoid unnecessary fragmentation of a single batch for multinorm.
Explicitly calculate median of inverses instead of inverse median.
 
Package: batchelor
Commit: 013278ba4e7b74bce291b81c8fed11364f6e914f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-02-12 19:42:16 -0800
Commit message:

 Pass BPPARAM to calcAverage for rescaling factors.
 
Package: BridgeDbR
Commit: 9c79ac53bd2bede11af65abe98ddcfbfd00f48aa
Author: Egon Willighagen <egon.willighagen@gmail.com>
Date: 2020-02-14 17:42:27 +0100
Commit message:

 Two more update to use Bs instead of Mx
 
Package: BridgeDbR
Commit: fbb16d212de9a96419ab95852e06128fc4eeb880
Author: Egon Willighagen <egon.willighagen@gmail.com>
Date: 2020-02-14 17:25:22 +0100
Commit message:

 updated the code for getDatabase() to allow downloading data from any location provided by /data/gene_database/
 
Package: BridgeDbR
Commit: c5d049afe6e5a19a4189989ceef9b7616cde3e60
Author: Egon Willighagen <egon.willighagen@gmail.com>
Date: 2020-02-14 16:30:06 +0100
Commit message:

 updated URL of the /data/gene_database/ location to point directly to bridgedb.github.io
 

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