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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: BgeeCall
Commit: e54f8737deeb7e3da46d18e00792146c9d43ccbc
Author: Julien Wollbrett <jwollbrett@bio-51-170.unil.ch>
Date: 2019-07-19 17:44:11 +0200
Commit message:

 update Authors
 
Package: SpectralTAD
Commit: 61a737f03767c43f7a7259caf8cf3cb0e83f6e67
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-19 10:13:49 -0400
Commit message:

 version numbering
 
Package: SpectralTAD
Commit: ee187b76838e35eecebc4225ca6bca54f2af76b9
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-19 10:12:35 -0400
Commit message:

 version numbering
 
Package: SpectralTAD
Commit: 6f2be64691f8e6416995f54683773f5be112d5ce
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-19 10:09:33 -0400
Commit message:

 remove sci notation on file output and update vignette
 
Package: SpectralTAD
Commit: 0c5e39ca2be855f5512a9ce6f279b614e17529aa
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-19 10:07:25 -0400
Commit message:

 remove sci notation on file output and update vignette
 
Package: SpectralTAD
Commit: 778e1b0b36e0a24b680b2c6c5e0a9506a20b4eff
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-18 14:01:17 -0400
Commit message:

 push codecov support
 
Package: SpectralTAD
Commit: a165912443224501081c20394c580a6b381184e9
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-18 09:47:30 -0400
Commit message:

 update readme
 
Package: SpectralTAD
Commit: 7b3fc2b88be21b0b06ad7261ec6cd3fc74c57352
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-18 09:34:13 -0400
Commit message:

 trigger code coverage
 
Package: SpectralTAD
Commit: 922226c8e7e6f5353990e9d679809018db265393
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-18 09:25:45 -0400
Commit message:

 add badges
 
Package: SpectralTAD
Commit: f40a2a70354f932427928794fb200471ee1b97fb
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-17 19:42:24 -0400
Commit message:

 add travis badge
 
Package: SpectralTAD
Commit: a2bfc02738c72e751cc6f45934ced9d003355521
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-17 19:10:03 -0400
Commit message:

 make travis warnings not errors
 
Package: SpectralTAD
Commit: 2a09890c850d83af606374e83d0cc275ce995ec0
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-17 18:36:48 -0400
Commit message:

 make unit tests correspond to new defaults
 
Package: SpectralTAD
Commit: e834a9c5578750f0a4a2e20e6565bd5c041e0cda
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-17 18:24:42 -0400
Commit message:

 add new outputs to vignette
 
Package: SpectralTAD
Commit: 1edc2e0d11849f69f67239b79639303eff4e8e4b
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-17 13:01:33 -0400
Commit message:

 add travis support
 
Package: SpectralTAD
Commit: 68c4e8094876ad948bf6f8afa9fc2ab1d4432fd8
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-17 11:44:31 -0400
Commit message:

 remove unintended ToDo file and revert roxygen version
 
Package: BioMM
Commit: 34ec82172bd79697e32203d43fca216652a14b91
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2019-07-19 15:02:56 +0200
Commit message:

 added vioplot dependency
 
Package: BioMM
Commit: 8257d4f96f45b8327a42d8ffd5b28110abc48724
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2019-07-19 14:27:43 +0200
Commit message:

 updated plotRankedFeature()
 
Package: Ularcirc
Commit: 0e15502c60779bff2119ce1dacbaef3ba762e4e0
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-07-19 07:57:04 -0400
Commit message:

 Remove from daily build report

  - still causing ERRORS
 
Package: BioMM
Commit: 97e59919d224ba0be4db1346568f60e954c18ed6
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2019-07-19 13:55:29 +0200
Commit message:

 fixed bugs in BioMM() and getMetrics()
 
Package: BioMM
Commit: aaf28f0ae8b2de3a15811b657d60bba62f0d6d37
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2019-07-19 11:49:08 +0200
Commit message:

 added dataMode to BioMM()
 
Package: BioMM
Commit: 1ca097babadc5cbad1fd0efb0919efd381f5cba9
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2019-07-19 11:47:04 +0200
Commit message:

 updated pROC::
 
Package: Rhdf5lib
Commit: 9cf354336f775ae059b65a1e07c04ff473d40a98
Author: Mike Smith <grimbough@gmail.com>
Date: 2019-06-11 15:58:26 +0200
Commit message:

 Added entry to vignette for supplying zlib location
 
Package: Rhdf5lib
Commit: 805c3b9435369ad49d6ba74d7a114357ee1f178f
Author: Mike Smith <grimbough@gmail.com>
Date: 2019-06-11 14:22:18 +0200
Commit message:

 Merge changes from zlib branch regarding location of zlib.h

Merge branch 'zlib'

# Conflicts:
#	DESCRIPTION
#	configure
 
Package: Rhdf5lib
Commit: 29a2eb4d4c5f30a1b9f413d79b98de31c5f8104c
Author: Mike Smith <grimbough@gmail.com>
Date: 2019-04-15 11:19:59 +0200
Commit message:

 More experiments with providing zlib location
 
Package: BioMM
Commit: 282c0634c108268a602a2e83f57e969a72800eb5
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2019-07-19 11:33:23 +0200
Commit message:

 use bplapply instead of mclapply
 
Package: IsoformSwitchAnalyzeR
Commit: 32f56fd137440a57730e64db90059b4116207948
Author: kvittingseerup <k.vitting.seerup@gmail.com>
Date: 2019-07-19 10:57:30 +0200
Commit message:

 readme update
 
Package: IsoformSwitchAnalyzeR
Commit: 7481d19d0fcc23b58bfe727ced1b4738618bd655
Author: kvittingseerup <k.vitting.seerup@gmail.com>
Date: 2019-07-19 10:55:30 +0200
Commit message:

 Minor update - see NEWS
 
Package: edgeR
Commit: 8b145abfec6115710781a57d468f352363bae06c
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-07-19 15:06:20 +1000
Commit message:

 edgeR 3.27.9
- Lengthen author list in DESCRIPTION file to include people who contributed particular functions.
- Update Davis McCarthy's email address in maintainer list.
 
Package: edgeR
Commit: aa56bc013ce71a2e7949ea3d44a5e3cca43fa9ae
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-07-18 17:21:27 +1000
Commit message:

 Dependency updates
- edgeR depends on limma 3.41.5 so that plotMD.DGELRT and
  plotMD.ExactText will work as intended on TestResults objects.
- edgeR depends on R 3.6.0 because of changes to `ties` argument
  of approx() in limma 3.39.16 and edgeR 3.27.2.
 
Package: edgeR
Commit: 251d54ca818ec70881f7887fa74a441c4b7570b3
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-07-18 16:59:40 +1000
Commit message:

 Update Aaron's email address. Remove emails for authors.
 
Package: limma
Commit: c078bb46ae6083db784fbcae420793e0e08fa9b3
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-07-19 14:31:49 +1000
Commit message:

 19 July 2019: limma 3.41.11

- Fix bug for the `fast` roast option introduced yesterday.
 
Package: Rsubread
Commit: 344b5ebaee0779f934b4d541258a16b5f5ed9063
Author: Wei Shi <shi@wehi.edu.au>
Date: 2019-07-19 13:12:58 +1000
Commit message:

 update users guide and help pages.
 
Package: Rsubread
Commit: b6d295bf791c7803bd4984800793cc7f2d27520a
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-07-19 12:30:31 +1000
Commit message:

 Toward version 1.35.18
 
Package: macrophage
Commit: 9f5f53a8630bba654de6bf7c5c28dce1087638dc
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-07-18 21:06:24 -0400
Commit message:

 add gencode v29
 
Package: ELMER
Commit: cdb4b2d5c18af22fc50e5bedc988da56b037d187
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-07-18 17:37:45 -0300
Commit message:

 Improving Scatter.plot.R text size
 
Package: genphen
Commit: 740e9cf7f6aebf31bbb602a1009280b55c82663f
Author: simo <simo.kitanovski@uni-due.de>
Date: 2019-07-19 00:00:03 +0200
Commit message:

 X11
 
Package: genphen
Commit: 2e353f36d3409000de7531129645aae37fbe5f18
Author: simo <simo.kitanovski@uni-due.de>
Date: 2019-07-18 23:59:23 +0200
Commit message:

 11x
 
Package: genphen
Commit: 4201b06d77315683d99b9e3a81c5b1c54066d261
Author: simo <simo.kitanovski@uni-due.de>
Date: 2019-07-18 23:59:13 +0200
Commit message:

 11
 
Package: TCGAutils
Commit: 952a84028d59fbf5785eaedf12a9469ca9e7c0ca
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-07-18 17:57:54 -0400
Commit message:

 update doc to reflect new from_type option
 
Package: iSEE
Commit: db3c8935f81fae8171dc27cc18f1c9410e868021
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-07-18 22:38:47 +0100
Commit message:

 Merge pull request #301 from csoneson/quickerboot

Quickerboot 
Package: iSEE
Commit: f9393e0986f42eeaf043b794a4a10ed672a161c6
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-07-18 21:30:01 +0100
Commit message:

 bump version 1.5.4
 
Package: iSEE
Commit: e7a504b6220e10617b5eadb8c58a28bc1eb6ff59
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-07-18 20:52:33 +0100
Commit message:

 Merge branch 'master' into quickerboot 
Package: iSEE
Commit: 1e5957d41d082f07245945e7e3c0d39896e1ecf6
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-07-18 20:47:55 +0100
Commit message:

 place all of observers.R under no coverage status
 
Package: iSEE
Commit: 363846ad6d93fc34adacf7536445a71652ef7405
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2019-07-17 19:34:44 -0700
Commit message:

 Merge pull request #300 from csoneson/reboot

File upload from a running iSEE instance 
Package: iSEE
Commit: 8e66ad007c7179ad3524f9f9a7fb14b7afc578ba
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-07-17 23:00:08 +0100
Commit message:

 prepared NEWS file for next release.
 
Package: iSEE
Commit: ccfa9992786fd40b93e4e6d03e11bd2aa325f352
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-07-17 22:53:54 +0100
Commit message:

 typo
 
Package: iSEE
Commit: 77bf741e51977d986e000985c4d79eae6ea7120a
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-07-17 22:47:37 +0100
Commit message:

 Anticipate FAQ: explain how to raise the maximal size for file upload.
 
Package: iSEE
Commit: b5fa96b9cdd020d8a61c95d1db54ec56a1a1dd0b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-07-17 22:43:21 +0100
Commit message:

 further fix tests
 
Package: iSEE
Commit: 102d70ff6e8d5dad52248d32572dea040081f3b5
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-07-17 22:30:47 +0100
Commit message:

 update unit tests following the reduced number of assays loaded
 
Package: iSEE
Commit: f73b9ef6396d23f0aabafdc97e4ce0ba738cae09
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-07-02 19:21:45 +0100
Commit message:

 rstudio trims whitespaces
 
Package: iSEE
Commit: 7e76c792b0b07470bfa8c9bad6ab85cc92f389de
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-07-02 19:21:15 +0100
Commit message:

 test in the absence of SCE input object
 
Package: iSEE
Commit: ee5f9c2085b942f3750380901cf12296a00c83aa
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2019-07-01 10:42:57 +0200
Commit message:

 Updated whole documentation
 
Package: iSEE
Commit: a8193128e5f2c10a33eec584e783a012b0a88875
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2019-07-01 10:42:39 +0200
Commit message:

 Updated call in the vignette, added note to explain the param behavior
 
Package: iSEE
Commit: f8888d4af5777b87959931f10427c4318bd433f5
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2019-07-01 10:42:19 +0200
Commit message:

 test updated
 
Package: iSEE
Commit: 0945831027b86faecf7c6a75155e68c8551e1192
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2019-07-01 10:42:03 +0200
Commit message:

 Updating calls to ReprocessedAllenData to load only tophat_counts
 
Package: iSEE
Commit: 23cf8a6628f89c82a68de6d72fc082bf3321c5e8
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-06-30 12:48:34 +0100
Commit message:

 disable coverage for functions that require a shiny session
 
Package: iSEE
Commit: fdc96f0e8be7481572d3dce640fb11dd74f376db
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-06-30 12:44:51 +0100
Commit message:

 rename file
 
Package: iSEE
Commit: 018c44991daeaa4d9d7e1865a7ce95608cb9ea1d
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-06-30 12:31:46 +0100
Commit message:

 integer(), character(), and others are given an integer scalar in tests
 
Package: iSEE
Commit: 3fbebb827f2e4a179d16aec05ddd8ca9a2e58aa2
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-06-30 12:21:22 +0100
Commit message:

 cover an edge case of which_numeric
 
Package: iSEE
Commit: b915ad98738b0b37397268bb917c6fb92edf656d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-06-29 19:09:37 -0700
Commit message:

 Added support for file uploads with server re-initialization.
Bugfixes to observers, moved SE setup into server.
 
Package: iSEE
Commit: 637920f00f4d803070abb25df4bb00a088e45bd9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-06-29 17:13:38 -0700
Commit message:

 Lifted all observers out into their own dedicated functions.
 
Package: MultiAssayExperiment
Commit: 1285eb9c6770820b9f5a62939dc75d8f121fd120
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-07-18 17:41:55 -0400
Commit message:

 Merge branch 'master' of github.com:waldronlab/MultiAssayExperiment
 
Package: MultiAssayExperiment
Commit: 50944d6fa513cb0f00851f639e97c4b6578c1923
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-07-18 17:41:41 -0400
Commit message:

 update travis file
 
Package: MultiAssayExperiment
Commit: 6a8b680e1979f5cdbe27e2bc9171447115c47a53
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-07-18 17:40:39 -0400
Commit message:

 reformat news from REL
 
Package: MultiAssayExperiment
Commit: c4e9729e3b7cfdd573b3bc782b72f04bd74ab625
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2019-07-06 12:40:57 -0400
Commit message:

 update repo for covr pkg
 
Package: MultiAssayExperiment
Commit: 9e3a1043484595b18dc74ae8ce60e580fc23b5b7
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2019-07-06 12:37:57 -0400
Commit message:

 minor change
 
Package: MultiAssayExperiment
Commit: f014be4a80e4840f7a3bcc33c694ac4d7db1e182
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2019-07-06 12:32:29 -0400
Commit message:

 add encrypted webhook
 
Package: MultiAssayExperiment
Commit: aaeee1d13053c1775f74da20c043812cd2dee8e8
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2019-07-06 11:48:46 -0400
Commit message:

 update yml files
 
Package: MultiAssayExperiment
Commit: 3775faacd84670e53f38fafa538d34431a4a5500
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2019-07-06 11:41:05 -0400
Commit message:

 don't use RTOOLS
 
Package: MultiAssayExperiment
Commit: 6c63565d4bab692e394420cd516a99ffc9fba84b
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2019-07-06 11:29:42 -0400
Commit message:

 minor typo
 
Package: MultiAssayExperiment
Commit: 704c20585f041cefba1f08c32a2106ef06d65094
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2019-07-06 11:26:25 -0400
Commit message:

 update auth token slack notify
 
Package: TCGAutils
Commit: d5add9517f1def7b838c6eca1d16a0793c376155
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-07-18 16:50:52 -0400
Commit message:

 update code chunks
 
Package: TCGAutils
Commit: 25265bf643049300a66e15f71d378c4f96efecb1
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2019-07-18 00:27:19 -0400
Commit message:

 updates to vignette
 
Package: signeR
Commit: 2d93a760c7254e1368c12a58d411aba7b916e3be
Author: Renan Valieris <renan.valieris@accamargo.org.br>
Date: 2019-07-18 17:00:15 -0300
Commit message:

 ignore mutations on edges of chromosomes
fix for #15
 
Package: bcSeq
Commit: 5f5084ae1aa8d1f8a30eb0fb4b7c66c06dc228e5
Author: Your Name <jiaxing.lin@duke.edu>
Date: 2019-07-18 14:39:28 -0400
Commit message:

 edits on the news
 
Package: bcSeq
Commit: 412e62f652fb0d0341ac88f2677d1451c76b3a39
Author: Your Name <jiaxing.lin@duke.edu>
Date: 2019-07-18 14:37:45 -0400
Commit message:

 include Jeremy new library data structure to speed up alignment
 
Package: bcSeq
Commit: 4e86632cc47b3b5ccf5649c96b9e7fc66baa6dd0
Author: Your Name <jiaxing.lin@duke.edu>
Date: 2019-07-18 14:22:03 -0400
Commit message:

 add changes
 
Package: genphen
Commit: d3352a01ca77cc312ac8085f2631cf9388825030
Author: Simo <simo.kitanovski@uni-due.de>
Date: 2019-07-18 20:15:56 +0200
Commit message:

 CXX14
 
Package: omicplotR
Commit: 3d2617f946a0df1d9f912519cc44bcae615b106c
Author: Daniel Giguere <dgiguer@uwo.ca>
Date: 2019-07-18 11:39:05 -0400
Commit message:

 bug fixes, correct namespace and description files

- explicitly calling some functions to prevent conflicts (jsonlite::fromJSON)
- corrected namespace and description
- removed "require(libraries") from ui.
- bug fix for calculating aldex object. sometimes would need to click generate effect plot twice.
- version bump
- changed T to TRUE in rab_script and server.R
 
Package: ToPASeq
Commit: aa7036878895e7f3b9ebaeb024c89ca4da71540a
Author: unknown <ihnatova@iba.muni.cz>
Date: 2019-07-18 16:14:32 +0200
Commit message:

 fixing vig cliper,DEGraph, SPIA
 
Package: AnnotationHub
Commit: 99c8c46477c2af513cdd1456260c61073c926e86
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-07-18 09:47:02 -0400
Commit message:

 Remove debugging message from upload status

  - keep downloading n resource and loading from cache
  - remove id and path from message (AH1: 1)
  - verbose=FALSE can hide additional message
 
Package: ExperimentHub
Commit: 2926063e92b3092705af103ad7814c84e410c25a
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-07-18 08:52:55 -0400
Commit message:

 New global argument for using local cache
 
Package: ExperimentHub
Commit: 5d91b014137a92a495aae9d79feb1eaae9c292cf
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-07-18 08:50:46 -0400
Commit message:

 use scalar || when appropriate
 
Package: ExperimentHub
Commit: e097ab736cdad230b830fb3c510a373cba8ce37f
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-07-18 08:49:26 -0400
Commit message:

 Change LOCALHUB to LOCAL to avoid redundency
 
Package: ExperimentHub
Commit: 4821daa9225f023b774b9bfa8c49b222fd9cedbf
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-07-16 11:00:14 -0400
Commit message:

 Fix LocalHub option

  - add global option, default set to FALSE
  - consistent with AnnotationHub 2.17.4 version
 
Package: AnnotationHub
Commit: e3ce09ab33ec03c378cff0f3f5db03fb59026e62
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-07-18 08:38:57 -0400
Commit message:

 New global argument for using local cache
 
Package: AnnotationHub
Commit: 7c2e90aa190f702bf707bd1f9e09d270259c60de
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-07-17 14:58:17 -0400
Commit message:

 use scalar || when appropriate
 
Package: AnnotationHub
Commit: 5acb7ef09fd392e4218686abf7448276a44b2691
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-07-17 13:28:55 -0400
Commit message:

 rename LOCALHUB as LOCAL

- 'HUB' is redundant
 
Package: AnnotationHub
Commit: 92a70349b015a38861cad459144a3ec003ddf71f
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-07-16 10:38:55 -0400
Commit message:

 Fix LocalHub option

  - add global option, default set to FALSE
  - fix check for isDevel which does not work if there is no internet
 
Package: AnnotationHub
Commit: c7484ae183bed86248d78361011ff05e30bca070
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-05-29 12:32:26 -0400
Commit message:

 Merge pull request #8 from mjsteinbaugh/master

Fix typo in documentation related to CACHE 
Package: AnnotationHub
Commit: bea146b3937bdf8a12d5c0246f458780d65c19ca
Author: Michael Steinbaugh <mike@steinbaugh.com>
Date: 2019-05-29 10:46:58 -0400
Commit message:

 Fix typo in documentation related to CACHE 
Package: BioMM
Commit: 50bc00d4076b7c90ccd0555d058288cf5c5ef625
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2019-07-18 11:05:15 +0200
Commit message:

 updated news and description
 
Package: BioMM
Commit: d68f0f98f3ef74ddc00a33d382ec6b645bdad9ab
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2019-07-18 11:03:25 +0200
Commit message:

 updated omics2pathlist()
 
Package: BioMM
Commit: fc52eb7a24df47e846c18774469a17c246c43866
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2019-07-18 11:01:24 +0200
Commit message:

 removed the example using omics2chrlist()
 
Package: TFEA.ChIP
Commit: 6e2840473792cf4283bc2f1a32608237524e0693
Author: LauraPS1 <lpsantamaria@iib.upm.es>
Date: 2019-07-18 08:39:50 +0200
Commit message:

 error in GeneID2entrez solved
 
Package: dcanr
Commit: 768f0ec7d6c37d75deb2db6dcfd0ae83becaa200
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-07-18 15:29:48 +1000
Commit message:

 fixed bug with dcPipeline where custom pipelines generated binary matrices
 
Package: edgeR
Commit: 4cc6babd83893420d618d13bd47692fb32208a4a
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-07-18 13:06:56 +1000
Commit message:

 edgeR 3.27.8
- Update romer.DGEList.Rd reference with final publication details.
- Change nrot default in roast and mroast to 9999 instead of 1e4 to that two-sided p-value is nicer.
 
Package: edgeR
Commit: 88279e4f257902013a8ec8952e9236496bb8fbad
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-07-18 13:03:29 +1000
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/edgeR
 
Package: edgeR
Commit: b372adc23bddc09a4a2e733c3c418b644701665e
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-07-16 20:15:23 +1000
Commit message:

 roast.DGEList() and mroast.DGEList() now have an nrot argument which is passed roast.default or mroast.default.
Previously the number of rotations could not be set.
 
Package: limma
Commit: 7921863dd458a77377836256b18ae9a3f776e2ad
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-07-18 11:26:01 +1000
Commit message:

 18 July 2019: limma 3.41.10

- roast() and mroast() now have the option via a new argument `fast`
  to user an even fast although less accurate approximation when
  converting t-statistics to z-scores.
 
Package: scAlign
Commit: 973100b61018801b8e07e726a53928dfa0370b81
Author: UCDNJJ <njjohansen@ucdavis.edu>
Date: 2019-07-17 17:13:08 -0700
Commit message:

 Updates to decoder
 
Package: scAlign
Commit: f49804bbca9aa1144a4c470580e0b3ddd05e472a
Author: UCDNJJ <njjohansen@ucdavis.edu>
Date: 2019-07-17 17:09:13 -0700
Commit message:

 Update text for bioconductor webpage
 
Package: BioMM
Commit: 9ebfca5c552b96c4570278e5b443f72d38055aaa
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2019-07-18 00:41:49 +0200
Commit message:

 updated NEWS, DESCRIPTION
 
Package: BioMM
Commit: 0cd6f58365e3c20055481dc1506a39367d033d94
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2019-07-18 00:37:47 +0200
Commit message:

 pROC imported in the required functions, doc
 
Package: CoGAPS
Commit: 2ea9901e296e4cae10ce6e101b1a96a22fbdfdfb
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-07-17 17:53:25 -0400
Commit message:

 Remove ccache usage on Travis for Mac
 
Package: CoGAPS
Commit: d33100ed09d7b48cb631a1694911dae6b1536d9a
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-07-17 17:38:03 -0400
Commit message:

 Use clang for Travis builds on Mac
 
Package: CoGAPS
Commit: 2186a242a1835342f392d219aff9d948afc77015
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-07-02 13:58:43 -0400
Commit message:

 test on osx as well as linux
 
Package: CoGAPS
Commit: cef4119b551883a19859ee4afe590176055ab2f7
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-07-02 13:56:21 -0400
Commit message:

 test on osx as well as linux
 
Package: CoGAPS
Commit: c319a75db00e4565d2492f07692ebb9d73067936
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-07-02 13:53:32 -0400
Commit message:

 don't run Travis on tags
 
Package: CoGAPS
Commit: 7cb8e8cd54bc94583b55b871235e486bf2418de9
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-07-02 13:23:21 -0400
Commit message:

 version bumP
 
Package: CoGAPS
Commit: 4c60d89be742ff994b07f260fef45f2509d41ab2
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-07-02 13:21:34 -0400
Commit message:

 temporarily disable checkpoints to get clean builds
 
Package: CoGAPS
Commit: 84d9714d05424738db6c87b75188384c3596342d
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-07-02 13:17:17 -0400
Commit message:

 version bump
 
Package: CoGAPS
Commit: 05dc309cc82e4c3e761f7ae7c3593da799e61303
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-07-02 13:15:27 -0400
Commit message:

 correct typo in windows Makevars
 
Package: CoGAPS
Commit: bba631935f26ca8fefa4e503576b0f0639c64c27
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-07-02 13:00:59 -0400
Commit message:

 update windows build targets
 
Package: ATACseqQC
Commit: 9621cf855cd405263dafd5c8ec245b24e0dea113
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2019-07-17 18:04:17 -0400
Commit message:

 try to decrease the memory cost for splitGAlignmentsByCut.
 
Package: ATACseqQC
Commit: 68351f7237a1cd65110d40644722dfe3e04cafc9
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2019-07-17 12:32:16 -0400
Commit message:

 try to fix the strand error in splitGAlignmentsByCut
 
Package: TCGAutils
Commit: a6fd1e3b1f16696732718b43e6bcdc1ba53752ee
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-07-17 17:00:40 -0400
Commit message:

 support aliquot_ids input to UUIDtoBarcode function
 
Package: TCGAutils
Commit: cc35a69a042dd79f9023e07bde363312bda65b43
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-06-12 14:02:41 -0400
Commit message:

 update travis.yml
 
Package: genphen
Commit: d28478a445b143d6bcc52a85108a4f81f205ea87
Author: simo <simo.kitanovski@uni-due.de>
Date: 2019-07-17 21:36:09 +0200
Commit message:

 bugix win
 
Package: KnowSeq
Commit: 7d4f6117bf829dfc018ecf982cc6ee023ce56284
Author: Daniel <dacacis@gmail.com>
Date: 2019-07-17 21:29:53 +0200
Commit message:

 Update to V0.99.31
 
Package: Ularcirc
Commit: fe08149e2c0dca14f534f6471340614f6711e4ea
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-07-17 14:09:43 -0400
Commit message:

 Allow to build on daily builder
 
Package: rtracklayer
Commit: e33f892fe2c57194aedf414b91e424b38a61d808
Author: Michael Lawrence <michafla@gene.com>
Date: 2019-07-17 10:35:00 -0700
Commit message:

 fix carrying over the 'which' names to 'NumericList' return value
 
Package: PAST
Commit: 9025dda286480349129fb69fab3b979fd954e957
Author: Adam Thrash <cathrash92@gmail.com>
Date: 2019-07-17 13:25:04 -0400
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/PAST
 
Package: PAST
Commit: 98cf2c7f1393bb90a6673f942494d329df93f256
Author: Adam Thrash <cathrash92@gmail.com>
Date: 2019-07-17 13:23:17 -0400
Commit message:

 proper marker handling
 
Package: PAST
Commit: 4c6c48991bcf5df0d1699af41eb863c6cc70cc10
Author: Adam Thrash <cathrash92@gmail.com>
Date: 2019-05-07 15:13:39 -0400
Commit message:

 Update README.md 
Package: fishpond
Commit: fb1203ce58ff4829580709883f46f138ce6d0613
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-07-17 12:33:11 -0400
Commit message:

 fix vignette headers
 
Package: SpectralTAD
Commit: c72d8c574fd6c75e548a29547d69ce03a1e9be58
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-17 11:35:12 -0400
Commit message:

 version bump 1.1.0 to 1.1.1
 
Package: SpectralTAD
Commit: ea180e9773fe01e171bed0b24539a5e2826a0609
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-17 11:03:15 -0400
Commit message:

 add juicebox and hicexplorer capabilities
 
Package: SpectralTAD
Commit: fa0a18240bdb172764b8ee4b248f5bd1fe0c0dc8
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-07-17 10:55:03 -0400
Commit message:

 Merge remote-tracking branch 'origin/master'
 
Package: SpectralTAD
Commit: 9c01ce135a5d45cf665130284ef1adff0539d287
Author: cresswellkg <cresswellkg@vcu.edu>
Date: 2019-03-28 13:15:28 -0400
Commit message:

 convert default to more robust
 
Package: SpectralTAD
Commit: d9e5c4aaf34c30d3c48fe7b1906013889ed4a102
Author: jstansfield0 <stansfieldjc@vcu.edu>
Date: 2019-03-07 16:17:14 -0500
Commit message:

 fix R version
 
Package: BgeeCall
Commit: bace475875349230c2c986662d1a1b06e90620c9
Author: Julien Wollbrett <jwollbrett@bio-51-170.unil.ch>
Date: 2019-07-17 16:33:11 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: BgeeCall
Commit: 6e6853b99bc84660356722c9c066b3d576b0d71f
Author: Julien Wollbrett <jwollbrett@bio-51-170.unil.ch>
Date: 2019-07-17 16:15:24 +0200
Commit message:

 update author list
 
Package: BgeeCall
Commit: dcbe6e759d1762bb1db57a3cd46a399b9a9e93d5
Author: Julien Wollbrett <jwollbrett@bio-51-170.unil.ch>
Date: 2019-07-17 16:14:50 +0200
Commit message:

 update link to github report
 
Package: BgeeCall
Commit: 24a09409f922a7140496b858a552c534c5192485
Author: Julien Wollbrett <jwollbrett@bio-51-170.unil.ch>
Date: 2019-07-15 18:05:29 +0200
Commit message:

 use simpler arborescence of dir by default. Update news
 
Package: BgeeCall
Commit: 8af8ba129aec72a92cac4ff17a1ac96b15739e17
Author: Julien Wollbrett <jwollbrett@bio-51-170.unil.ch>
Date: 2019-07-15 18:02:13 +0200
Commit message:

 homogenise attribut names
 
Package: BgeeCall
Commit: 1cbadea9757f9ecd1b8467883fd664c20c6a4c11
Author: Julien Wollbrett <jwollbrett@bio-51-170.unil.ch>
Date: 2019-07-15 18:01:02 +0200
Commit message:

 Allows the user to select the output director
 
Package: BgeeCall
Commit: 8163e16a668409918ec53e5de7d6a3c579b77256
Author: Julien Wollbrett <jwollbrett@bio-51-170.unil.ch>
Date: 2019-07-15 17:57:18 +0200
Commit message:

 modify kmer size of kallisto index when read length is < 50bp
 
Package: BgeeCall
Commit: 4922ca12192e5cfd09fb701c31f4e5e2e85f151f
Author: Julien Wollbrett <jwollbrett@bio-51-170.unil.ch>
Date: 2019-07-15 17:49:36 +0200
Commit message:

 remove unused attribut
 
Package: ORFik
Commit: 8fa6893b01e73df580537fc6731ca6fe3b9dcafc
Author: Håkon Tjeldnes <hauken_heyken@hotmail.com>
Date: 2019-07-17 15:13:30 +0200
Commit message:

 Make more logical functions (#85)

* added uORF function and more docs

* small fix

* fixed spaces
 
Package: ORFik
Commit: d28191559789a5632e80deea366d1257f788e721
Author: Håkon Tjeldnes <hauken_heyken@hotmail.com>
Date: 2019-07-08 14:52:06 +0200
Commit message:

 Clarify (#84)

* test new heatmap

* remade vignette, more docs, and better plots

* fixed spaces and vignette
 
Package: Mulcom
Commit: 4ea73607e0834bb0f59488a34c4ec79f874ba6cc
Author: Claudio <claudio.isella@gmail.com>
Date: 2019-07-17 14:00:25 +0200
Commit message:

 prova
 
Package: GOTHiC
Commit: a782e4eb0da5072b65d2db7ee1f1efa564dd0013
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-07-17 07:27:32 -0400
Commit message:

 Undeprecated package
 
Package: limma
Commit: 3fec1c8fbbd325ef8ee93c3e86a0c6349ddb8695
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-07-17 20:36:34 +1000
Commit message:

 17 July 2019: limma 3.41.9

- roast() and mroast() now perform rotations in chunks to conserve
  memory usage.
 
Package: depmap
Commit: a19f1b64ba4a008cc5ef5efd54e4815d985530f9
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-07-15 10:00:43 +0200
Commit message:

 update theo's email
 
Package: depmap
Commit: 8d06f8d458c3d8486dd7a9382cbc50338cad1dea
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-07-15 09:58:01 +0200
Commit message:

 Merge pull request #38 from UCLouvain-CBIO/19_Q2

19Q2 
Package: depmap
Commit: beb844074a5135d8a030cb4cb6c4e0dc190f1b4b
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-06-26 16:31:55 +0200
Commit message:

 merged .R files into one for 19Q1 and 19Q2, new .Rd files
 
Package: depmap
Commit: 46fe28edcb0498d05bea211c0a66e1c71ddd3745
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-06-25 20:11:55 +0200
Commit message:

 zzz.R update for 19Q2 metadata
 
Package: depmap
Commit: 6e5e835691b8604a3def1aa78a4e0942b76b6a97
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-06-17 17:40:53 +0200
Commit message:

 updated .R and .Rd files for data
 
Package: depmap
Commit: 6d3f2f44c573bda0e65f1ef6490f133355195bb3
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-06-17 11:51:53 +0200
Commit message:

 conversion of entrez_id to int
 
Package: depmap
Commit: f2fb91cb10ab1f722800baa0d3eada7b673ad617
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-06-07 15:55:34 +0200
Commit message:

 metadata updates for new dataset
 
Package: depmap
Commit: 80feda7e5a78238b5361139006f5f5681a190998
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-06-07 15:49:37 +0200
Commit message:

 Delete make-metadata.R

Revert to two different make-metadata.R files for each data release 
Package: depmap
Commit: f5f27f84d7e0ef129596eb6f46077cff39327869
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-06-07 15:48:54 +0200
Commit message:

 Delete metadata.csv

Revert to two different metadata files 
Package: depmap
Commit: 8b63ac3020f8aa805541b3d91608e87e22b6a7d0
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-06-04 17:45:46 +0200
Commit message:

 metadata info change
 
Package: depmap
Commit: 6e26dbca18376a6b0c266eafed0a19da6647a16f
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-05-30 13:10:29 +0200
Commit message:

 EH Q2 make-metadata updates
 
Package: depmap
Commit: dcc05c138e178e79cf8d0810003c0dd0e854eb78
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-05-29 13:56:33 +0200
Commit message:

 19_Q2 changes
 
Package: depmap
Commit: 7ae773bbec8a2fe46f1fbd85fba57e99a4d18705
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-05-29 10:33:26 +0200
Commit message:

 Merge branch '19_Q2' of github.com:UCLouvain-CBIO/depmap
 
Package: depmap
Commit: 62aa90e727629dff236969feae19452793967ecd
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-05-24 15:49:08 +0200
Commit message:

 Delete metadata.csv 
Package: depmap
Commit: 2a67768d7c05155358f6340c3259480e6c20944f
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-05-24 15:48:16 +0200
Commit message:

 Delete visualizations.Rmd 
Package: depmap
Commit: a3c77840a7e58a4ff877d44b6dbedde6db12e107
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-05-22 13:48:00 +0200
Commit message:

 Delete make_data.R 
Package: depmap
Commit: 7f347284ab8caa315a7bb574212c258be3222194
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-05-22 13:47:36 +0200
Commit message:

 Delete make-data.R 
Package: depmap
Commit: e327abaa1d119d5d2da45c983f247be660979c4f
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-05-22 13:46:22 +0200
Commit message:

 Merge pull request #34 from tfkillian/master

19Q2 changes 
Package: depmap
Commit: 930a1f969000abe0efc80a8d5eb865cd2cc88424
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-05-22 13:44:55 +0200
Commit message:

 Merge branch 'master' into master 
Package: depmap
Commit: c4bd48053291ed902dc30dfa19f7f899671a7e33
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-05-22 13:05:40 +0200
Commit message:

 metadata.csv
 
Package: depmap
Commit: 79cf9a05d805a058a9cd3a31bc90b84b19a6a5fb
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-05-22 13:01:01 +0200
Commit message:

 make-data and make-metadata 19Q2 updates
 
Package: depmap
Commit: 5b1f2989fe234d1741b6a7dfc7857d0d0d5acf3c
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-16 13:52:28 +0200
Commit message:

 remove metadata section
 
Package: depmap
Commit: 5b7c51787c7f6b6f1d7f626a716eda0e4c64c428
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-16 13:31:57 +0200
Commit message:

 syntax guide
 
Package: depmap
Commit: 8089d106b836c37773d262475bc6412d92c3a1ea
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-16 13:22:58 +0200
Commit message:

 add rd files
 
Package: depmap
Commit: 50a157070e8f72f3906186c81b716abbbcc37f2f
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-16 12:58:55 +0200
Commit message:

 add importfrom
 
Package: depmap
Commit: cf4b451a2cd6eeff4ee566c73a142d22a1fee1fb
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-16 12:57:33 +0200
Commit message:

 fixing checks...
 
Package: depmap
Commit: 431cd59125defeb7aff80f592a3cebfae2a1ef62
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-16 12:47:39 +0200
Commit message:

 message in onAttach
 
Package: depmap
Commit: 47babc47f21f5308eae37a0ac4ae40522f4bcb40
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2019-04-16 12:42:37 +0200
Commit message:

 Merge pull request #30 from tfkillian/master

onLoad function 
Package: depmap
Commit: cff28c324cf99ddc359fb2ac79f869510ece6604
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-16 12:44:09 +0200
Commit message:

 update man pages
 
Package: depmap
Commit: 93820ebe48cca4508c4ec5a9e2f978c3ac2ba9df
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-16 12:40:09 +0200
Commit message:

 onLoad function
 
Package: depmap
Commit: 0e73e75ee5d8ab042ec725ef83e8a6561a37ac75
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-16 12:26:37 +0200
Commit message:

 bump version
 
Package: depmap
Commit: 1d26cf1591d562ed99e0d44950bd742e8e491d72
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-16 12:18:32 +0200
Commit message:

 Merge branch 'master' of github.com:UCLouvain-CBIO/depmap
 
Package: depmap
Commit: f2ff0ab5a82876f9c099c17a5f3e2b7c18c3ec22
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-16 12:18:25 +0200
Commit message:

 delete old vignette, rename new one with old name
 
Package: depmap
Commit: 2cc46801b07d2e7b62560a8f7fbd3c8ce6ce5da0
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2019-04-16 12:14:54 +0200
Commit message:

 Merge pull request #29 from tfkillian/master

changed repository name 
Package: depmap
Commit: a23dd01da0bd6ab178ca5a2e89a74b31b09a8968
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-16 12:13:09 +0200
Commit message:

 changed repository name
 
Package: depmap
Commit: 611ce98c0e16770f3ce3f84b5854f6781cc1662b
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2019-04-16 12:12:20 +0200
Commit message:

 Merge pull request #28 from tfkillian/master

EH changes to visualization vignette 
Package: depmap
Commit: 6f96777d7080d65c16889cadb8800d0e93d0c0e7
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-16 12:13:59 +0200
Commit message:

 replace personal with org repo in readme
 
Package: depmap
Commit: 6098864c976765052301957714a9d10c033c6b43
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-16 12:11:38 +0200
Commit message:

 remove rda data
 
Package: depmap
Commit: 63c0d370a4e6c5f97c77550bf82ee87c2145234a
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-16 12:10:13 +0200
Commit message:

 EH changes to visualization vignette
 
Package: depmap
Commit: f9dc330187b000b551efa5014311ebefda578226
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2019-04-16 12:08:14 +0200
Commit message:

 Merge pull request #27 from tfkillian/master

data import vignette (new EH depmap vignette) 
Package: depmap
Commit: b6775fdb5a0b94eccd777b5b4e7d292b7f09bd8a
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-16 12:06:37 +0200
Commit message:

 data import vignette (new EH depmap vignette)
 
Package: depmap
Commit: 7b427f13916c7e89c08c4829536da232615689f5
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2019-04-16 11:45:24 +0200
Commit message:

 Update README.md 
Package: depmap
Commit: e192434de3792a7352f39170b01de8fa5c89baca
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2019-04-16 11:42:55 +0200
Commit message:

 Merge pull request #26 from tfkillian/master

changes to DESCRIPTION and make-metadata 
Package: depmap
Commit: 011ce8901c4b87f8a421f1b2bbaec9162f830631
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-12 16:59:10 +0200
Commit message:

 changes to DESCRIPTION and make-metadata
 
Package: depmap
Commit: c0bce2cd50f7597f51bd5cc485133bfa1e7a7f1e
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-12 12:59:30 +0200
Commit message:

 Merge pull request #25 from tfkillian/master

ExperimentHub metadata changes 
Package: depmap
Commit: faeb0a0b515991611444886afa3ddc73b54c8577
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-12 12:41:21 +0200
Commit message:

 ExperimentHub metadata changes
 
Package: depmap
Commit: 2698b71789bbfcb2db0106db82118872ac6a68a7
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-12 11:36:44 +0200
Commit message:

 Merge pull request #24 from tfkillian/master

DESCRIPTION update to include biocViews 
Package: depmap
Commit: 3ab10148ead8e9592587c8582c84a7290cc1cf45
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-12 11:35:35 +0200
Commit message:

 DESCRIPTION update to include biocViews
 
Package: depmap
Commit: dd6b72bda94d94bf6ce8d4562b04451b104238f2
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-11 17:34:42 +0200
Commit message:

 Merge pull request #23 from tfkillian/master

ExperimentHub changes 
Package: depmap
Commit: c2cb6c0d399a12da2932515f07c5af455de4aeb3
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-11 17:23:27 +0200
Commit message:

 added biocViews: ExperimentHub
 
Package: depmap
Commit: 660314952743b8ee5cba3baa673d2482bdd9f3ec
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-11 16:39:00 +0200
Commit message:

 changes made for compatibility to ExperimentHub
 
Package: depmap
Commit: 0680b0deb029a6219143afa8dba0ac06b3ee834a
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-10 11:08:26 +0200
Commit message:

 Merge pull request #22 from tfkillian/master

experimenthub changes 
Package: depmap
Commit: 073d156cceca80778b7a78c78f6c20768a65c972
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-10 11:05:52 +0200
Commit message:

 experimenthub changes
 
Package: depmap
Commit: 4829106570c73a5fc40a7a2b9b14948a710742e7
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2019-04-10 06:21:11 +0200
Commit message:

 Merge pull request #21 from tfkillian/master

edits to fix errors on build/check 
Package: depmap
Commit: 7a34986f91d6d638fdfce085ccb039d9cfef67b5
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-09 19:59:34 +0200
Commit message:

 edits to fix errors on build/check
 
Package: depmap
Commit: 329df589ffeb409c180d793afe9a00669a8e9351
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-09 15:53:40 +0200
Commit message:

 Merge pull request #20 from tfkillian/master

removed whitespace .R files and regenerated .Rd files 
Package: depmap
Commit: 0ff54e5b1a9ba9184eec0d447fd3fa08511fb258
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-09 15:49:41 +0200
Commit message:

 removed whitespace .R files and regenerated .Rd files
 
Package: depmap
Commit: a9137f9c27591bea6a5031c5645e73621f3a42c0
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-09 14:27:32 +0200
Commit message:

 Merge pull request #19 from tfkillian/master

Merged changes to .R and .Rmd files. .Rd files were pulled due to conflicts and will be added in the next commit 
Package: depmap
Commit: 35c35eae2d1ff63b65e97a5fc396c33d9290359a
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-09 14:26:49 +0200
Commit message:

 Merge branch 'master' into master 
Package: depmap
Commit: 0865a9fdc027991fc4f262108749a4bb5a6a7d43
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-08 12:16:44 +0200
Commit message:

 merged conflicting changes
 
Package: depmap
Commit: fc08d9e39753d2486d2df3137bf3993a61f6ee21
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-04 17:05:09 +0200
Commit message:

 backup of most changes, including depmap_release.R
 
Package: depmap
Commit: 2641a15fb539dbd099a40a84475fa1525d2118d5
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-03 17:02:55 +0200
Commit message:

 fixed typo in copyNumber.R
 
Package: depmap
Commit: 5d486e5cf0ee8dea9ae31470b145ab6f77af1462
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-03 16:57:54 +0200
Commit message:

 add rd
 
Package: depmap
Commit: 7667c341f8ecc121bdf91236616bcc553f89d565
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-03 16:57:18 +0200
Commit message:

 bump version
 
Package: depmap
Commit: 9f25fb8fa5c3c5960efc2eefdd56ef20b84addeb
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-03 16:54:17 +0200
Commit message:

 compute values in vignette and new release function
 
Package: depmap
Commit: 1b7b5ef94bba34731f5669e23867629ac3d553e4
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-03 16:03:47 +0200
Commit message:

 updated .R, .Rd, visualization vignette and DESCRIPTION
 
Package: depmap
Commit: 4ad6940f6be0f340e7a67a73208eab71380ddda5
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-03 15:50:37 +0200
Commit message:

 depend on and import dplyr
 
Package: depmap
Commit: d820cd45cced6fc378f3f39a870802a0f306a417
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-03 12:56:06 +0200
Commit message:

 Remove hardcoded root.dir (Never hard-code a path! This makes it non-portable)

Also remove superflous spaces.
 
Package: depmap
Commit: ada8777a6682d5717a4dcf15aa6194862521c3ae
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-03 12:55:34 +0200
Commit message:

 no html vignettes in the package
 
Package: depmap
Commit: 2acaec1204755ff6490b4008233683d5fa50c7ad
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-03 12:49:01 +0200
Commit message:

 fix syntax
 
Package: depmap
Commit: 7d057037a88c1a0274271f07811fe4f59a344f17
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-03 12:47:26 +0200
Commit message:

 wrap lines after 80 chars
 
Package: depmap
Commit: d84b0289ce0f47e8b4a142629ae20f271272ef61
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-04-03 12:46:58 +0200
Commit message:

 add author@R and simplify description
 
Package: depmap
Commit: bf4c666f2888b21493ad3f79a73ddb0f015243d3
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2019-04-03 12:37:27 +0200
Commit message:

 Merge pull request #14 from tfkillian/master

grammatical changes in package and data file descriptions 
Package: depmap
Commit: 1811a2e460c49e181926fc1a591ec0fb30d98d86
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-03 11:00:55 +0200
Commit message:

 Merge pull request #13 from tfkillian/master

grammatical changes for PDF manual 
Package: depmap
Commit: c20ba726043745f22cd6ca9e256ee78d74cb728b
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-03 11:00:03 +0200
Commit message:

 grammatical changes in package and data file descriptions
 
Package: depmap
Commit: 8655dd8e171e59ecedf3aedb48004bbf3fd8259b
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-02 23:04:09 +0200
Commit message:

 grammatical changes for PDF manual
 
Package: depmap
Commit: d0ffd30cb56391afd2ae28afa05969dae1c56691
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 13:51:06 +0200
Commit message:

 Merge pull request #12 from tfkillian/master

changes to mutationCalls to remove warning flag 
Package: depmap
Commit: acb578ae3e7b3d5e3b0802c17245152e8e266b21
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-02 13:49:51 +0200
Commit message:

 changes to mutationCalls to remove warning flag
 
Package: depmap
Commit: 587293416dd315d669c9966ffecdc1e2c3662259
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-02 12:38:04 +0200
Commit message:

 final changes
 
Package: depmap
Commit: 2ee85d09a3cff898d54d3b755ada1844d5b1bdbb
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-02 12:35:50 +0200
Commit message:

 merging
 
Package: depmap
Commit: da62bcc9b3296596785b2c6a32ef35c935d54ad2
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 12:26:11 +0200
Commit message:

 Merge pull request #11 from tfkillian/master

Fixing mutationCalls issues 
Package: depmap
Commit: 41720550af4fbbd0460994479e299276e93b5d0e
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-02 12:22:29 +0200
Commit message:

 fixed mutationCall issue that was showing a flag on build/check
 
Package: depmap
Commit: 9107ef4f064d6e0326fdcc13a00f191f9d4eb792
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 11:59:11 +0200
Commit message:

 Delete mutationCalls.rda 
Package: depmap
Commit: e0b7e12bc55959a5495a508dddd9ef83d0b83a96
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-02 11:05:23 +0200
Commit message:

 finished vignettes no issues
 
Package: depmap
Commit: 87335511936aba53234dd00a18739a5b606f9b83
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 10:23:06 +0200
Commit message:

 Merge pull request #10 from tfkillian/master

Pre-ExperimentHub changes 
Package: depmap
Commit: 51786716d3302e0d2cfd9cd13c3e03da6a3b699a
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-02 10:14:55 +0200
Commit message:

 merge to fix conflicts
 
Package: depmap
Commit: c92e2c242233ffb130e581c05ea3d45353b30bfe
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 10:01:17 +0200
Commit message:

 Merge pull request #9 from tfkillian/master

Deleting old data files 
Package: depmap
Commit: cbc6e8f8d88c8a78f6b045c9ef2b5f41e133cd35
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-04-02 09:53:29 +0200
Commit message:

 redone data, .R, .Rd files with correct data headers
 
Package: depmap
Commit: 069371e9ffed4839bbcc1fe2520b39bbeebd4d6c
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:40:23 +0200
Commit message:

 Delete depmap.html 
Package: depmap
Commit: a6125643dcfc392216ab5eb2d714c4f2534fb4d9
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:40:07 +0200
Commit message:

 Delete visualizations.html 
Package: depmap
Commit: 71e12862e13b38596554e4afe2061dc5871d6d74
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:39:50 +0200
Commit message:

 Delete rnai.rda 
Package: depmap
Commit: 9017dabbb44b019683d2d42ef890cd6f4ff53194
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:39:40 +0200
Commit message:

 Delete mutationCalls.rda 
Package: depmap
Commit: b07f10485c601f24b35a36c44c3862f7292d3b3d
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:39:26 +0200
Commit message:

 Delete metadata.rda 
Package: depmap
Commit: 2012c37214266f6cc34e31db066e8a0ef3adb671
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:39:16 +0200
Commit message:

 Delete crispr.rda 
Package: depmap
Commit: 2ba67fb78274370e8cd0949f46bf4043ee39b64d
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:38:53 +0200
Commit message:

 Delete copyNumber.rda 
Package: depmap
Commit: 0748f907bed4e6e6a8fc3fa45f4ee1021ec291e1
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:38:42 +0200
Commit message:

 Delete TPM.rda 
Package: depmap
Commit: 32af15e7ad1409618bbde472ef072afe6e2e5cb0
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:38:31 +0200
Commit message:

 Delete RPPA.rda 
Package: depmap
Commit: 1c7fc6e0835dd21426ac68b170a32cf403007cdb
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:36:38 +0200
Commit message:

 Delete visualizations.html 
Package: depmap
Commit: 2aaca7ad156605727a5deda355917ce0f985e29f
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:36:23 +0200
Commit message:

 Delete depmap.html 
Package: depmap
Commit: 2ed1a398cd7bcc92b1c892eb77d6b1c24abccb39
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:35:46 +0200
Commit message:

 Delete rnai.rda 
Package: depmap
Commit: bd0847e6474cde8e6fa9b0dd9dd667140ee37948
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:35:36 +0200
Commit message:

 Delete mutationCalls.rda 
Package: depmap
Commit: 1bdae1b85b0eb1b6aabfc552bf8c9b3c68f783c3
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:35:25 +0200
Commit message:

 Delete metadata.rda 
Package: depmap
Commit: 6653a26dffbd573424025d18c992b01535b96622
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:35:15 +0200
Commit message:

 Delete crispr.rda 
Package: depmap
Commit: e06d2a9e41dc6f4fc97846440d3cffb7552af9e1
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:35:05 +0200
Commit message:

 Delete copyNumber.rda 
Package: depmap
Commit: ead4343ee802cc01967983e394f0c403dd23f17a
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:34:39 +0200
Commit message:

 Delete TPM.rda 
Package: depmap
Commit: c808554c680d2f6b3fdf0b5109ebb6ec3e9190b1
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-04-02 09:34:29 +0200
Commit message:

 Delete RPPA.rda 
Package: depmap
Commit: 3ceafb6cc292032f01a70bf31c6b3f5b2497f0ae
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2019-04-01 13:19:04 +0200
Commit message:

 Merge pull request #8 from tfkillian/master

pre-ExperimentHub changes 
Package: depmap
Commit: e7bfae73f59c1d700296e5bf0988748fa7621b47
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-29 18:30:17 +0100
Commit message:

 DESCRIPTION line change
 
Package: depmap
Commit: 5a61fed4dc437f9da0f33565872ad75ff4c1b13d
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-29 18:27:26 +0100
Commit message:

 added visualization.html change
 
Package: depmap
Commit: e41440bebe5a7c22a33fee3f363468f8bae110e8
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-29 17:16:03 +0100
Commit message:

 readded correct data files
 
Package: depmap
Commit: 720e4a33a43a1ec956fa46c12bdb1c1dcf3d6ef4
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-29 15:31:56 +0100
Commit message:

 Merge branch 'master' of github.com:tfkillian/depmap

reupload data files with correct header
 
Package: depmap
Commit: 01ec6b7cb4dd4301faf263b06f97c22fabaf4c16
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-29 15:31:38 +0100
Commit message:

 reupload correct data files
 
Package: depmap
Commit: eb893b0ce9507e4ce82e7ba980299a7f6d01e1dd
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-03-29 15:28:03 +0100
Commit message:

 Delete mutationCalls.rda

need to reload data files because they have the wrong header and github won't update them because the files are too large 
Package: depmap
Commit: 77675d418b0387c725ae7cbe25d55287e66f8e72
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-03-29 15:27:54 +0100
Commit message:

 Delete metadata.rda

need to reload data files because they have the wrong header and github won't update them because the files are too large 
Package: depmap
Commit: 0f9a67acddf7a50c94ef1851c8237edd61e9849b
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-03-29 15:27:45 +0100
Commit message:

 Delete crispr.rda

need to reload data files because they have the wrong header and github won't update them because the files are too large 
Package: depmap
Commit: f09393e9628a52a6c6ba358f616127b0e0514e3e
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-03-29 15:27:36 +0100
Commit message:

 Delete copyNumber.rda

need to reload data files because they have the wrong header and github won't update them because the files are too large 
Package: depmap
Commit: 75dc4986b2f83f1272545683ea0b94758a391a2e
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-03-29 15:27:27 +0100
Commit message:

 Delete TPM.rda

need to reload data files because they have the wrong header and github won't update them because the files are too large 
Package: depmap
Commit: 79249ff743802b00b505f9859062d0fb750d7707
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-03-29 15:27:15 +0100
Commit message:

 Delete RPPA.rda

need to reload data files because they have the wrong header and github won't update them because the files are too large 
Package: depmap
Commit: bf0167f7e01714a68eb58ce49086c1b94f6a1dfe
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-03-29 15:27:01 +0100
Commit message:

 Delete rnai.rda

need to reload data files because they have the wrong header and github won't update them because the files are too large 
Package: depmap
Commit: fcba3dfaf8d6c8c39d204de4dfa53bf9e91c79ab
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-29 14:26:19 +0100
Commit message:

 Merge branch 'master' of github.com:tfkillian/depmap

"trying to resolve data header issue"
 
Package: depmap
Commit: 3127192bb461acdfd39ba6b14304ec30a6701535
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-29 14:25:29 +0100
Commit message:

 data files with correct headers
 
Package: depmap
Commit: 289dc8bc405b139f9d819a2f28e5a9bea71f3457
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-03-29 13:30:16 +0100
Commit message:

 Merge branch 'master' into master 
Package: depmap
Commit: 05913fd9d931efb1c23d515460d59095d592acb5
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-28 16:21:49 +0100
Commit message:

 corrected .gitignore deletion
 
Package: depmap
Commit: ab3c59dd4ad5b41b343223d302c73ae3e245e42d
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-28 16:09:18 +0100
Commit message:

 build check changes
 
Package: depmap
Commit: d677c0bb70137e2dd47abacc50736643e21cdfba
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-27 19:49:17 +0100
Commit message:

 DESCRIPTION update
 
Package: depmap
Commit: 45b3dcc9a52c86aea8d991bab944d6fb4e6bca8d
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-27 13:56:59 +0100
Commit message:

 .Rd, DESCRIPTION, README.md and vignette updates
 
Package: depmap
Commit: fabb00096a39d835efccf29d1a73db88cfec2f3f
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-27 12:18:33 +0100
Commit message:

 fixed make_file.R and vignette, data are tibbles
 
Package: depmap
Commit: 4e205cc6848da69840bad6810eea7a2b597e51dd
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-03-26 14:37:48 +0100
Commit message:

 wrap lines
 
Package: depmap
Commit: e5fe4d301e6f421e9a43ef9f05bccca2418d9395
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2019-03-26 14:31:29 +0100
Commit message:

 Update DESCRIPTION 
Package: depmap
Commit: ebacab7b455fdfe3699982cf0cbfadbc30a3be9f
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2019-03-26 14:10:47 +0100
Commit message:

 Merge pull request #6 from tfkillian/master

updated long format data .rda .R and make_file 
Package: depmap
Commit: dc28caf614cf459ea28fd50aa4e50f81a4836c13
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-26 14:01:19 +0100
Commit message:

 updated vignette
 
Package: depmap
Commit: 7811742258db68f6804420b7430433eef5c04b54
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-25 22:29:12 +0100
Commit message:

 vignette update
 
Package: depmap
Commit: 677b0576f0ffc0bc5bdcd96db92dbc5ecaaa7384
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-24 11:41:45 +0100
Commit message:

 revised .R, .rda, make_file and vignette
 
Package: depmap
Commit: aff04b4536d1ec97937a8aaf21e1712d0a0f25d5
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-03-22 00:48:50 +0100
Commit message:

 Merge branch 'master' into master 
Package: depmap
Commit: 4bf9e36126b72a90b900e0235ea6fefa0adc130e
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-22 00:24:55 +0100
Commit message:

 updated long format data .rda .R and make_file
 
Package: depmap
Commit: 6be62d7ef2bd5afbb2c9c56fdf492ce970ebcb0a
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-03-20 10:58:06 +0100
Commit message:

 use long format for rnai
 
Package: depmap
Commit: 93b16910434a5371c8eee58ba8fe0d0405117aaa
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-19 16:20:22 +0100
Commit message:

 added remaining data creation code chunks in inst/scripts/make_data.R and .Rd
 
Package: depmap
Commit: 3a42122415eaa389ac1853a93eb7ae57388e590f
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-19 09:41:11 +0100
Commit message:

 red-added vignette and .Rd files
 
Package: depmap
Commit: a7671e440fd25b51d0b92f622309bf70af62ffdd
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-18 22:33:13 +0100
Commit message:

 removed cleaning vignette
 
Package: depmap
Commit: 982460b1b3059cb15b748fff79802c158239d60f
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-18 22:31:47 +0100
Commit message:

 edited R files
 
Package: depmap
Commit: 1916b118a37da3c70f045ea54a34c4b0feff1c9a
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-03-18 10:55:38 +0100
Commit message:

 Merge branch 'tfkillian-master'
 
Package: depmap
Commit: 3c3869729f31989ff4efdd361c7ccd4e17134111
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-03-18 10:55:05 +0100
Commit message:

 start make_data file to replace data cleaning vignette
 
Package: depmap
Commit: 2be099cbeb57fe54fddfa1ccdad5e7793754d3d8
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-03-18 10:30:45 +0100
Commit message:

 remove superflous gitignore
 
Package: depmap
Commit: b1428fa9d9d4c449ad20f268cb90a4983cf26ee6
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2019-03-18 10:29:16 +0100
Commit message:

 Merge branch 'master' of https://github.com/tfkillian/depmap into tfkillian-master
 
Package: depmap
Commit: 3a28b1ce63ea1962c13e1f02752c285cf6ee9e20
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-18 10:22:09 +0100
Commit message:

 replace R files
 
Package: depmap
Commit: 3ba03d96f32aad41e68d1d42156a7805092b743d
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-11 17:04:57 +0100
Commit message:

 Added clean data vignette with cleaned depmap datasets
 
Package: depmap
Commit: 4017698fce0a6589b78d063b1e157d072101dd75
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-06 17:10:50 +0100
Commit message:

 Additonal vignette diagrams
 
Package: depmap
Commit: 8f2cde966530374e04d7c72900ecc8510a623acf
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-05 19:11:40 +0100
Commit message:

 vignette diagrams
 
Package: depmap
Commit: 43731e8fcb497a7d43c99048d94aabca77f4f1dd
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-03-04 18:43:39 +0100
Commit message:

 additional diagrams
 
Package: depmap
Commit: f112c314ed5048991a95348485ab480f7a136c8e
Author: T F Killian <36329073+tfkillian@users.noreply.github.com>
Date: 2019-02-28 23:47:13 +0100
Commit message:

 Merge pull request #2 from tfkillian/master

depmap_1.0 
Package: depmap
Commit: 4f73b88bcd36750aa347c567c680dbde3c7117d3
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-02-28 22:39:25 +0100
Commit message:

 vignette graphs
 
Package: depmap
Commit: 5b3c5a8954565dd9545c4afe1bb19c167a21aa1d
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-02-27 23:18:13 +0100
Commit message:

 Graphics
 
Package: depmap
Commit: 7d87992c3bf64113e9555133deacbd80e448f926
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-02-27 13:47:51 +0100
Commit message:

 .
 
Package: depmap
Commit: 0de242d8bb000507ba33c4706ed3b2a4f0bb4142
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-02-25 17:24:46 +0100
Commit message:

 Some changes
 
Package: depmap
Commit: 37db825d3fd8bc984efe689aacb819e6847e6cc3
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-02-20 16:49:44 +0100
Commit message:

 updated vignette
 
Package: depmap
Commit: dcf63948a3ad899e83c40f81a6955345c416ef56
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-02-19 17:22:50 +0100
Commit message:

 updated vignette
 
Package: depmap
Commit: 3896abaec0c0182c5be63d4b10f97585ef3bd13b
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-02-19 16:35:32 +0100
Commit message:

 Updated data_utils functions and vignette
 
Package: depmap
Commit: 03eb32dbcc38f5f6f4cd68f76b9d103c631eec80
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-02-18 16:47:10 +0100
Commit message:

 I have updated the DESCRIPTION, NAMESPACE, README.md and data.R files and added a CONDUCT file
 
Package: depmap
Commit: 69a807f112982a5a5254f37840a7151d66b7b6cd
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2019-02-16 00:41:54 +0100
Commit message:

 Merge pull request #1 from tfkillian/master

first version of package 
Package: depmap
Commit: 4e4d20c4945d25e78d39ba8db2876df26e190bc6
Author: tfkillian <theo.killian@gmail.com>
Date: 2019-02-15 16:30:06 +0100
Commit message:

 first version of package
 
Package: FoldGO
Commit: 5c3c9b95a88d242097190a941ae603121b2d48fb
Author: Dan <daniil.wiebe@gmail.com>
Date: 2019-07-17 14:23:31 +0700
Commit message:

 Version bump
 
Package: FoldGO
Commit: b0f386b9e5d31233710f8c20b39f0fcf6ecce7ae
Author: Dan <daniil.wiebe@gmail.com>
Date: 2019-07-16 19:17:51 +0700
Commit message:

 test number issue 2 fixed
 
Package: CAGEr
Commit: 1f2eef25bb11ec0a6fffc02405f77b18da0daffd
Author: Charles Plessy <charles.plessy@oist.jp>
Date: 2019-07-16 06:32:29 +0000
Commit message:

 Depends on MultiAssayExperiemnt instead of previously Importing it.

No need to load it by hand (nor SummaryExperiment) anymore.
 
Package: CAGEr
Commit: 46f95daa9c0a441e619436097ad59d7f018d03ef
Author: Charles Plessy <charles.plessy@oist.jp>
Date: 2019-07-16 06:29:49 +0000
Commit message:

 RStudio editor options.
 
Package: limma
Commit: b1c28d31d66a201d0c2cca96309bb22d5481ac07
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-07-17 17:14:53 +1000
Commit message:

 17 July 2019: limma 3.41.8

- Edits to non-exported function .roastEffects() to reduce the memory
  usage of roast() and mroast().
 
Package: treeio
Commit: 4b25453b943fb072959e728d01fbeb3e8d26cabb
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-07-17 14:37:35 +0800
Commit message:

 store input file
 
Package: Rsubread
Commit: 0a4e73ee03ca15860e7cc2757861145cf1c61497
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-07-17 14:37:31 +1000
Commit message:

 Changed the category number
 
Package: HIREewas
Commit: 85e6bf49393ea8b050f86f5c44d791ae5f91bab8
Author: XiangyuLuo <xyluo1991@gmail.com>
Date: 2019-07-17 11:13:30 +0800
Commit message:

 dfd
 
Package: HIREewas
Commit: 2df3ead913cfc5079376ee7bf1751e755ef58f78
Author: XiangyuLuo <xyluo1991@gmail.com>
Date: 2019-07-17 11:13:05 +0800
Commit message:

 add
 
Package: HIREewas
Commit: 91c2c86aabd2c68f5db722899f48118a4f64d695
Author: XiangyuLuo <xyluo1991@gmail.com>
Date: 2019-07-17 11:07:56 +0800
Commit message:

 add CITATION
 
Package: treeio
Commit: 235aa235b95849bc6f3769c9de671949480392b4
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-07-17 10:46:40 +0800
Commit message:

 mega7 example files
 
Package: ELMER
Commit: 74d6a33bdab9247f81102045c42c5561da4f815a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-07-16 15:11:59 -0700
Commit message:

 Update doc
 
Package: ELMER
Commit: c839b1e98ba4d8a7e570089aabc0bd1ed37e9722
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-07-16 15:09:43 -0700
Commit message:

 Removing doc warning
 
Package: ELMER
Commit: aab2cc562ee38302dd8159f6d4da0c9e2fb585f9
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-07-16 15:07:39 -0700
Commit message:

 Fix doc
 
Package: CNVRanger
Commit: 8e8e0a8c58b4927e9e0a7b6b19fdef5505c376e4
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2019-07-16 17:46:21 -0400
Commit message:

 extend input format description for cnvGWAS
 
Package: CNVRanger
Commit: 0d9af09361cbbecc0903eb8e773b6ad89e486fbf
Author: viniciushdasilva <31412322+viniciushdasilva@users.noreply.github.com>
Date: 2019-07-16 12:57:04 +0200
Commit message:

 Update CNVRanger.Rmd
 
Package: CNVRanger
Commit: 4f3d4402310c37e134cb72d2b177a972ee1a6f9e
Author: viniciushdasilva <31412322+viniciushdasilva@users.noreply.github.com>
Date: 2019-07-16 07:47:24 +0200
Commit message:

 Update CNVsegments.png
 
Package: CNVRanger
Commit: 6b4e934bee8645d2353f3d89d2a8b740ae8dba2a
Author: viniciushdasilva <31412322+viniciushdasilva@users.noreply.github.com>
Date: 2019-07-15 17:01:02 +0200
Commit message:

 vignette_improvement
 
Package: CNVRanger
Commit: 0798f6f08615cb220bdfc5ed1781fad9acf06e0e
Author: viniciushdasilva <31412322+viniciushdasilva@users.noreply.github.com>
Date: 2019-07-15 16:06:25 +0200
Commit message:

 Setup GWAS vignette
 
Package: apeglm
Commit: 5837b8cca67ab8d94aaeef29afe90a09803ed7d9
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-07-16 14:36:04 -0400
Commit message:

 adding in betabin cpp to examples
 
Package: rnaseqDTU
Commit: 45461c9df02e80facb715a244134923dce7b2668
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-07-16 14:31:46 -0400
Commit message:

 cache to false
 
Package: DESeq2
Commit: 35e6016303ff39816ba1c40f5587712e456ed963
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-07-16 14:31:05 -0400
Commit message:

 cache to false
 
Package: DESeq2
Commit: 0c375d0e763ba26fea383d255b942f9c7ec4b262
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-07-16 13:55:36 -0400
Commit message:

 remove print lines
 
Package: DESeq2
Commit: 61600e6095c27e7ed15b068f4afaafa38d189ee9
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-07-16 13:42:28 -0400
Commit message:

 adding Constantine as contrib, fixing docs
 
Package: DESeq2
Commit: c96c1c0ad43280c82403d3e6bc3501332a62e7b8
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2019-07-16 13:22:49 -0400
Commit message:

 Merge pull request #13 from const-ae/sc_performance_opt

Performance optimization from Constantine Ahlmann-Eltze 
Package: DESeq2
Commit: c0620f889cce33aad071567726b7933f3613abb8
Author: const-ae <artjom31415@googlemail.com>
Date: 2019-07-11 15:58:08 +0200
Commit message:

 Avoid unnecessary iterations in nOrMoreInCell()

The original function iterated over each sample and thus repeated a lot
of work if the design matrix is simple (eg. two groups).
This is problematic because for large number of samples, this function
takes up a considerable fraction of the runtime of DESeq().
 
Package: DESeq2
Commit: 15cce98f1a17315bbfdb766a29c5ac7ad16073e3
Author: const-ae <artjom31415@googlemail.com>
Date: 2019-07-11 15:26:59 +0200
Commit message:

 Use qr_econ in fitBeta() for further speed up
 
Package: DESeq2
Commit: 2dfa09299b9e6c580a851181f63eb55d463acffb
Author: const-ae <artjom31415@googlemail.com>
Date: 2019-07-10 11:18:02 +0200
Commit message:

 Improve performance of fitDisp()
 
Package: DESeq2
Commit: ac06839e70701251d53d13959358e311343659d8
Author: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
Date: 2019-07-09 11:28:18 +0200
Commit message:

 Add more files to .gitignore
 
Package: DESeq2
Commit: fea940f46d572f68ec7943f1b360cb1e367f6f54
Author: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
Date: 2019-07-09 11:21:15 +0200
Commit message:

 Comment out printing in fitBeta
 
Package: DESeq2
Commit: 30c0151e7f87a5f54339def2618da02e05e4896b
Author: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
Date: 2019-07-09 11:15:36 +0200
Commit message:

 Improve performance of fitBeta.cpp

Avoid creation of m*m diagonal matrices which make the algorithm
slow for large m (=number of samples)
 
Package: celda
Commit: 6a3d54b3fa0976f9e4ffa1c419aedc53ba3237fc
Author: zhewa <314100793@qq.com>
Date: 2019-07-16 13:15:46 -0400
Commit message:

 version bump
 
Package: celda
Commit: f116e7c666153cb36777382af15490702b65f4ed
Author: zhewa <314100793@qq.com>
Date: 2019-07-16 12:38:38 -0400
Commit message:

 fix lints
 
Package: celda
Commit: a5cf80493ca1161d34a55f02e440c61bbdb76a7e
Author: zhewa <314100793@qq.com>
Date: 2019-07-16 11:37:45 -0400
Commit message:

 update findMarkers
 
Package: celda
Commit: f65a8989c6a2ab89f0e21ba43e270568b9410926
Author: zhewa <314100793@qq.com>
Date: 2019-07-10 10:23:43 -0400
Commit message:

 fix example
 
Package: celda
Commit: ced50604b6810dcb8d0a45827cf7ee76f149f1c3
Author: zhewa <zhe@bu.edu>
Date: 2019-07-09 21:33:15 -0400
Commit message:

 Merge branch 'master' of github.com:zhewa/celda
 
Package: celda
Commit: bf8b8863e87bee194fe18983cfa4fee4f61a4ed8
Author: zhewa <zhe@bu.edu>
Date: 2019-07-09 21:32:46 -0400
Commit message:

 add documentation
 
Package: celda
Commit: 4654a94193cc86584c4ad53bfe22220961743581
Author: zhewa <zhe@bu.edu>
Date: 2019-07-09 21:29:19 -0400
Commit message:

 add magrittr import
 
Package: celda
Commit: c2d9e0e6e696df102c5ca7d4a59597c91638a261
Author: zhewa <zhe@bu.edu>
Date: 2019-07-09 21:27:42 -0400
Commit message:

 Merge branch 'MCDT' of github.com:ericreed/celda
 
Package: celda
Commit: de7e28df9ccec445f29ee1572c64e036991da37d
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-07-05 12:37:18 -0400
Commit message:

 Fixed style issues
 
Package: celda
Commit: 0c1325bac954f5b3fa5c351e890444131ebde1fd
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-07-05 12:31:10 -0400
Commit message:

 Fixed leaf and rule labelling discrpency issue
 
Package: celda
Commit: 083717a09973bcec87029e488a3af39d6c8f400c
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-06-20 13:01:31 -0400
Commit message:

 Fixed bug in setting the max features to print
 
Package: celda
Commit: ec3ea4d2473ccd5ebf51d808efb8a55c78ab91b4
Author: Wang <kwdq153@astrazeneca.net>
Date: 2019-06-19 11:02:04 -0400
Commit message:

 Merge branch 'MCDT' of github.com:ericreed/celda
 
Package: celda
Commit: 3830cdbccfe8e4fec2a3df2a75960ae4a300c48b
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-06-14 15:49:51 -0400
Commit message:

 Fixed the tree height issues
 
Package: celda
Commit: 0deb8fdb4ddd3b1de89446764f628bb38be46e44
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-06-11 11:22:35 -0400
Commit message:

 Minor formatting changes for style guide
 
Package: celda
Commit: 87f753b1753274602f9e3a7c3e7c1c8b126d08c7
Author: Zhe Wang <zhe@bu.edu>
Date: 2019-06-07 11:44:08 -0400
Commit message:

 Merge pull request #191 from zhewa/master

fix topRank doc 
Package: celda
Commit: d7993e4cbc8fe4da29976c97477d822764651673
Author: 87875172 <314100793@qq.com>
Date: 2019-06-07 11:42:09 -0400
Commit message:

 fix topRank doc
 
Package: celda
Commit: a7d481910963bb551c068b8f0225f4c3eb254e95
Author: Zhe Wang <zhe@bu.edu>
Date: 2019-06-03 13:55:28 -0400
Commit message:

 Merge pull request #187 from zhewa/master

remove redundant clustSplit 
Package: celda
Commit: 340d49e6d63d67d2c17baaabee87105ff1bab66f
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-05-28 16:27:10 -0400
Commit message:

 Small formatting fix
 
Package: celda
Commit: bd472c2360349c2696bb23d63bfff800bf401d97
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-05-24 15:13:31 -0400
Commit message:

 Style edits
 
Package: celda
Commit: fa60334ead5727f052d7bfa7800b8812b119d2b5
Author: ericreed <erreed@schoolph.umass.edu>
Date: 2019-05-22 10:20:08 -0400
Commit message:

 Replace BuildTreeHybrid with FindMarkers.  This adds functionality to generate decision tree with a priori meta clusters
 
Package: celda
Commit: 3a9d257f817f997317e1308a9f12ffc8694a3825
Author: Eric Reed <erreed@schoolph.umass.edu>
Date: 2019-05-21 15:50:10 -0400
Commit message:

 Merge pull request #1 from campbio/master

pulling updated master branch with my fork 
Package: omicplotR
Commit: d8708aa38f81d4396bc7884fd9ede7c4e2f5d128
Author: Daniel Giguere <dgiguer@uwo.ca>
Date: 2019-07-16 12:58:40 -0400
Commit message:

 updated namespace

- performed bioccheck, added col2rgb import
- version bump
 
Package: omicplotR
Commit: 79ad991cf787105c159b3cf8ac15f6b2de4abfdc
Author: Daniel Giguere <dgiguer@uwo.ca>
Date: 2019-07-16 12:27:52 -0400
Commit message:

 added json import

requires jsonlite import
 
Package: regioneR
Commit: 4420461abb2b9628c645a0f6a0028c4fee7be749
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-16 18:09:32 +0200
Commit message:

 Merge branch 'revamp_toGRanges'

 
Package: regioneR
Commit: 87da96edc25ae6c10775a443225eca25dc12c341
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-16 18:08:15 +0200
Commit message:

 Version bump

 
Package: regioneR
Commit: 9b5297d7b5a4806dd1aa2b2d7de3db0866cd3779
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-16 18:02:23 +0200
Commit message:

 Updated failing tests 

 
Package: regioneR
Commit: d788de937bf695069c96c38e20d0b151eaa099f9
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-16 17:53:46 +0200
Commit message:

 commented out test unused test code

 
Package: regioneR
Commit: 3b81e845cced34c8f394018adfc6c900b3f09ee7
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-16 17:50:30 +0200
Commit message:

 Bug fixing and updated namespace

 
Package: regioneR
Commit: 4d21d394f31996c62fd12b6cdbeb7c676024afc0
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-15 17:36:32 +0200
Commit message:

 Removed dependency from a remote file in vignette

 
Package: regioneR
Commit: 62a0f3126a2a7fc6b99002daa95679b4ca4fa990
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-15 17:31:59 +0200
Commit message:

 Updated vignette to work with better toGRanges

 
Package: regioneR
Commit: d08c07620ec6170f2a20905e30bf5b1ea8deb6fe
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-15 17:27:56 +0200
Commit message:

 Updated docs and namespaces

 
Package: regioneR
Commit: 62d0550dd41220de8486fb3d6ab90020fe8f42ff
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-15 17:27:07 +0200
Commit message:

 Updated toGRanges to work with the new functions and pass the new tests

 
Package: regioneR
Commit: d73072de436f6c7b6a916afd08d891c68cebfd70
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-15 17:26:46 +0200
Commit message:

 updated test suite

 
Package: regioneR
Commit: 74b4bad57102b190271d9490c8abc4d9c10032e5
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-15 17:26:35 +0200
Commit message:

 Added and updated test files

 
Package: regioneR
Commit: 2d26b715331f98a764f59a18e2173c64379d8c97
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-15 17:26:16 +0200
Commit message:

 Added functiopn to get the first non-comment line of a file

 
Package: regioneR
Commit: f4fcdb1406a2ef7dc722194313dadc8cbce5fb83
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-15 16:31:23 +0200
Commit message:

 Added another test case

 
Package: regioneR
Commit: 4901b0763e93e33255462b2c3ccdc23dd8b99667
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-15 15:36:14 +0200
Commit message:

 Updated bed examples

 
Package: regioneR
Commit: c80e5a71749a65f089e18e7162a37ea7420b9779
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-15 15:26:26 +0200
Commit message:

 Create two new functions: hasHeader and getSeparator to help GRanges

Added them to a new utils.R file 
Package: regioneR
Commit: 636190ce9ff3810a087f6afc50b27219083b9ca7
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-07-15 15:25:32 +0200
Commit message:

 

Add new test files for toGRanges tests 
Package: omicplotR
Commit: bc9732f3b837545880d32ca81c7a48b8e4d45d3f
Author: Daniel Giguere <dgiguer@uwo.ca>
Date: 2019-07-16 12:08:16 -0400
Commit message:

 version bump

version bump for omicplotR to propogate update
 
Package: GNET2
Commit: 3fe7f4459b284d0f36b1ee61a0685187754b8a94
Author: Chen Chen <chen.chen@mail.missouri.edu>
Date: 2019-07-16 10:35:50 -0500
Commit message:

 Update plot_utils.R
 
Package: treeio
Commit: b0dd9ded755638e954a343e1923f1782cfb7aa0d
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-07-16 22:48:43 +0800
Commit message:

 mega parser
 
Package: treeio
Commit: 81b8ab23406ce31a7ca28791d2e1bcce84a4620d
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-05-28 19:11:38 +0800
Commit message:

 rename_taxa now use 1st column as key and 2nd column as value
 
Package: treeio
Commit: 770527f3b24ebfd5b1dd1d0096f565bb19cbf92b
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-05-27 18:32:02 +0800
Commit message:

 enable `tree_subset` to specify `group_name` and enable to incorporate `root.edge` by setting `root_edge = TRUE` (2019-05-27, Mon)
 
Package: treeio
Commit: 49d330cb21318901d8922d3e024c6f516309d01c
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-05-22 22:10:49 +0800
Commit message:

 full_join method for phylo object
 
Package: treeio
Commit: 733df715d915ebd729ef22815901bbfe118765a1
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-05-20 17:32:17 +0800
Commit message:

 enable tree subset test
 
Package: treeio
Commit: 98eb5239be9dc61dae09f6b4e3c9c1f769394df9
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-05-20 14:18:14 +0800
Commit message:

 update release version
 
Package: KEGGgraph
Commit: 86a4b31c202b2bd92ecd54d0c2c5dc2937fd7a75
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-07-16 16:56:03 +0200
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/KEGGgraph
 
Package: KEGGgraph
Commit: 92abe437061c0ad70181850990ad61a92f912e71
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-07-16 16:49:08 +0200
Commit message:

 remove warning 'implicit list embedding of S4 objects is deprecated' in the graph merging process
 
Package: mnem
Commit: 4ea8131369f9de151e881eb5a6c08eca19b0f438
Author: MartinFXP <martin.pirkl@bsse.ethz.ch>
Date: 2019-07-16 16:20:32 +0200
Commit message:

 small unit tests bugfix
 
Package: genphen
Commit: 73c328dc1feffe6a952f4972c0c52b51b486ab7e
Author: simo <simo.kitanovski@uni-due.de>
Date: 2019-07-16 16:01:23 +0200
Commit message:

 c++ win
 
Package: ToPASeq
Commit: 61307b51d185990c15c5ea1ca76a931477451b4c
Author: unknown <ihnatova@iba.muni.cz>
Date: 2019-07-16 15:41:25 +0200
Commit message:

 vignette check
 
Package: FoldGO
Commit: ab62e4c1ba6df478c86a62bf5c147371e2917340
Author: Dan <daniil.wiebe@gmail.com>
Date: 2019-07-16 18:21:47 +0700
Commit message:

 Multiple testing procedure corrected
 
Package: edgeR
Commit: fb3f8a2271709ba00f2b6a3e6c30e22eafa500ba
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-07-16 20:15:23 +1000
Commit message:

 roast.DGEList() and mroast.DGEList() now pass the nrot argument to roast.default. Previously the nrot argument was ignored.
 
Package: limma
Commit: 6bba16494e68b7041ebc1455c8308daac0a2544a
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-07-16 18:16:02 +1000
Commit message:

 16 July 2019: limma 3.41.7

- Improvements to zscoreT() so that `approx=TRUE` works for NA `x`
  values and `approx=FALSE` works for very large or very small `df`
  values. A new simple robust approximation from Wallace (1959) was
  added to handle the latter two cases. Previously `approx=FALSE`
  treated any `df` greater than 10000 as infinite; this threshold is
  now raised to 1e300.
 
Package: Mulcom
Commit: f21b1290b3241f5c92ae6f71f0dfb00219d2ec05
Author: Claudio <claudio.isella@gmail.com>
Date: 2019-07-16 10:08:41 +0200
Commit message:

 prova
 
Package: CellMixS
Commit: 079fafa8e852809c75acbc4b57c04efb0be27ad2
Author: almutlue <almut.lue@gmail.com>
Date: 2019-07-16 08:39:33 +0200
Commit message:

 add version bumb to upstream
 
Package: CellMixS
Commit: f716660edbe82c2af7a247a868010e1ee6173e1c
Author: almutlue <almut.lue@gmail.com>
Date: 2019-07-16 08:26:23 +0200
Commit message:

 bug fix: add library ggplot2 to vignette
 
Package: banocc
Commit: d14528737d9af2a810a96f967f66b3f3ff223c9d
Author: George Weingart <george.weingart@gmail.com>
Date: 2019-07-15 17:51:56 -0700
Commit message:

 Removed c++11 references that are making BUILD fail in R3.6.0
 
Package: dcanr
Commit: 883cab8b10f97c8ad87bebd7d16d3ad98cda0b86
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-07-16 10:42:31 +1000
Commit message:

 Fixed bug in parallelisation of permutation tests
 
Package: Ularcirc
Commit: d1b7c37f7f62a8b355f60d2ce6503281d7cc6575
Author: David Humphreys <d.humphreys@victorchang.edu.au>
Date: 2019-07-16 10:10:07 +1000
Commit message:

 changed to bioclite to biocManager in Compatible_Annotation_DBs examples
 
Package: dcanr
Commit: 7a9eb2395813e551b96b54bea31ec7d62c53d8fe
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-07-16 10:26:48 +1000
Commit message:

 Fixed bug with permutation tests
 
Package: dcanr
Commit: 8494e359d229f0247098223a1aead0d4eabf9402
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-05-03 09:42:51 +1000
Commit message:

 updated package site
 
Package: BioMM
Commit: 249a6936ac8acda33b2b0114a55011eeb4c9f9fe
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2019-07-16 00:22:17 +0200
Commit message:

 pROC imported; updated version
 
Package: BioMM
Commit: 9dfbad09f8af5041f8881d6954cf035fa11eb2c0
Author: junfang <junfang.chen@zi-mannheim.de>
Date: 2019-07-16 00:21:17 +0200
Commit message:

 add pROC package for roc() function
 
Package: genoset
Commit: 055534f11d2cd31271ac328d2c8cb6fceab2475d
Author: Peter M. Haverty <phaverty@gene.com>
Date: 2019-07-15 12:58:43 -0700
Commit message:

 roxygenize to fix NAMESPACE
 
Package: vidger
Commit: e74fa838e3496bb37bdd761601a3c2572254698b
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-15 14:58:59 -0400
Commit message:

 bug fix: stat annotation error on matrix functions

 
Package: ELMER
Commit: 8e96cdee18ea91e0bca3db22104031d5f8a786b7
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-07-15 11:58:31 -0700
Commit message:

 update vignette
 
Package: ELMER
Commit: 7e0a722b8f9c71a1b2c2cc9e506bc029fda9721c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-07-15 15:57:06 -0300
Commit message:

 Version bump
 
Package: vidger
Commit: e39e9f9ead6098fa1758bd87e968fe516fdb6358
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-15 14:37:28 -0400
Commit message:

 Version bump

 
Package: vidger
Commit: 8303ed5fa20706f925565ab9a3f45f8567b1056e
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-07 14:51:10 -0400
Commit message:

 bug fix: stat annotation error on matrix functions

 
Package: vidger
Commit: b6e9408426071812531136a0d599a6fb73226d7f
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-07 14:45:32 -0400
Commit message:

 Version bump

 
Package: vidger
Commit: 3ecfc64ce6932762b15dc22ec0d998a26cf21875
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-06 13:13:22 -0400
Commit message:

 Merge pull request #6 from btmonier/devel

Annotation bug fix 
Package: vidger
Commit: 01478afd06af4bdfd800c93437b3f67bb872519d
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-06 12:11:21 -0400
Commit message:

 Fix count annotation bug

 
Package: vidger
Commit: 65d61dbc71f92b3419e48afc1f6d45b89b9f3057
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-06 12:11:11 -0400
Commit message:

 Version bump

 
Package: vidger
Commit: 6f819a463721deb0aa3709f51d0b2545f67d2d6a
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-05 17:01:53 -0400
Commit message:

 Version bump

 
Package: vidger
Commit: 937b9197e2e6fc0897a7271d562559883efc3657
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-05 16:59:48 -0400
Commit message:

 Fix count annotation bug

 
Package: vidger
Commit: 56fe20dfb0683d4b3ce6b68cee905ecf22b2a478
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-05 16:59:10 -0400
Commit message:

 Add .Rproj extensions

 
Package: vidger
Commit: dcfe2c606f1e7afcdbc817e1547fb0509c43c751
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-01-18 10:49:10 -0500
Commit message:

 Version bump

 
Package: vidger
Commit: b12179f34f0a472b213b6bae28dc960b8f8be2e5
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-01-18 10:47:57 -0500
Commit message:

 Add Rproj extension

 
Package: vidger
Commit: 6eec567101905d87ef86984e578e56c51066e7d6
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-01-18 10:28:48 -0500
Commit message:

 Merge branch 'devel'

 
Package: vidger
Commit: ce65aa76c2f7e941efe12843e03a76f4a25173b3
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-01-18 10:23:57 -0500
Commit message:

 Version bump

 
Package: vidger
Commit: 20bfc0cef106bc9912bb08e9c0483dfa7b9ab376
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-01-18 10:23:17 -0500
Commit message:

 Update installation info; add download stats

 
Package: vidger
Commit: 7b169a21c3dd13400d700480cd2f9dab5ee57018
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-01-18 10:10:24 -0500
Commit message:

 Remove appveyor

 
Package: vidger
Commit: 9d1472d6b60b1da97008a5d859b018f883403810
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2018-11-29 10:32:28 -0500
Commit message:

 Merge branch 'devel' 
Package: vidger
Commit: d6f1736618cbc7c68d322b909eee7e772098f1e3
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2018-11-29 10:32:07 -0500
Commit message:

 Version bump

 
Package: vidger
Commit: c0d25f378c14d8625b7cede78dea026796ebf9e3
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2018-11-29 10:29:03 -0500
Commit message:

 Update contact information; add biocView tag

 
Package: vidger
Commit: 87a79f2228fe5ab0e2ac43edc05dba34424db88b
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2018-11-29 10:26:48 -0500
Commit message:

 Initial commit

 
Package: vidger
Commit: fa4e00e15eeb7c0149df84718bf967fab30d36d1
Author: btmonier <brandon.monier@gmail.com>
Date: 2018-06-08 12:49:27 -0500
Commit message:

 Merge branch 'devel'
 
Package: vidger
Commit: 865fb9a3e51ae364ef445c056841e6264488e70a
Author: btmonier <brandon.monier@gmail.com>
Date: 2018-06-08 12:48:15 -0500
Commit message:

 Add SVG logo; change link
 
Package: vidger
Commit: cfa3f065318d6d00266e2487db1d5f824505bdd5
Author: btmonier <brandon.monier@gmail.com>
Date: 2018-06-08 12:47:23 -0500
Commit message:

 Initial commit
 
Package: vidger
Commit: fad201cf74389ad2971625aee687990ff942a170
Author: btmonier <brandon.monier@gmail.com>
Date: 2018-06-08 12:44:31 -0500
Commit message:

 Add SVG logo; change link
 
Package: vidger
Commit: a0469c14e5009dae9be3bf4622c8c2042c0000bf
Author: btmonier <brandon.monier@gmail.com>
Date: 2018-06-08 12:43:34 -0500
Commit message:

 Initial commit
 
Package: ELMER
Commit: 183b2b54aa91a1a878a013a58007b4925de6756e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-07-15 11:34:40 -0700
Commit message:

 bug fix
 
Package: ELMER
Commit: d0f5f6f0510a2dcc5738f94e3173b569e3238b1a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-07-15 11:29:48 -0700
Commit message:

 Merge branch 'master' of github.com:tiagochst/ELMER
 
Package: ELMER
Commit: a4a3058f95733884d4c230b53f9114ab04780156
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-07-15 11:29:38 -0700
Commit message:

 Adding one more verification of the input data
 
Package: ELMER
Commit: dcf1e1c82c21db2df965b9cf4e32ae9d865de70c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-07-15 11:27:17 -0700
Commit message:

 Fixing create mae if sample map has same names
 
Package: Rcwl
Commit: 5f86be5dff1078daedea6394651e73b27f2d616f
Author: Qiang Hu <qiang.hu@roswellpark.org>
Date: 2019-07-15 13:55:34 -0400
Commit message:

 Add list to stepInParam source
 
Package: motifStack
Commit: 244e663ca4252ce93fbefcb8b2443eb70e21fb0d
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2019-07-15 12:50:57 -0400
Commit message:

 remove par from plotMotifStackWithPhylog
 
Package: ELMER
Commit: d6548689a50ac345f066230d474a8ae1fcf00506
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-07-15 13:31:45 -0300
Commit message:

 changing entrezgene to entrezgene_id
 
Package: ELMER
Commit: ecba3b5faee2434a41a2fd4cba904a57be8c97a6
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-07-11 17:43:27 -0300
Commit message:

 Adding correlation argument to get.pair
 
Package: VennDetail
Commit: a9b614061291d2f1c6bbec9bdacf52d4612deba8
Author: bioguo <bioguo@bioguo.local>
Date: 2019-07-15 10:59:55 -0500
Commit message:

 add colors and fix issues
 
Package: Mulcom
Commit: b253f361c310fbe3d9605aa6d7add5d14077cbe7
Author: Claudio <claudio.isella@gmail.com>
Date: 2019-07-15 17:41:30 +0200
Commit message:

 try
 
Package: Mulcom
Commit: c5986280e8251682c2f3765a00215ffeb92a685f
Author: Claudio <claudio.isella@gmail.com>
Date: 2019-07-15 17:03:42 +0200
Commit message:

 first try
 
Package: motifStack
Commit: 1286d0145432dead4c20e3b57fa44cd69f325d01
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2019-07-15 09:09:18 -0400
Commit message:

 fix the issue for grid.eti default units of plotMotifStackWithPhylog
 
Package: motifStack
Commit: 7da5c4c1eb5c6173bb40d28712a4223aa5f28562
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2019-07-15 09:01:55 -0400
Commit message:

 fix a bug that 'grid' and 'graphics' output mixed for plotMotifStackWithPhylog
 
Package: Ularcirc
Commit: cb85546ffec6fdc72310c5563e6c8ed6b36e45ec
Author: David Humphreys <d.humphreys@victorchang.edu.au>
Date: 2019-07-15 22:12:24 +1000
Commit message:

 added \donttest to remove installation error in example
 
Package: onlineFDR
Commit: b4bf9337c1a213fbac83d92a6f7e510a59bbb9a4
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-15 11:04:53 +0100
Commit message:

 Merge pull request #13 from dsrobertson/update_tests

Update tests 
Package: onlineFDR
Commit: 1ab03bb2a99ae0775a9b68bb45a28b110f87f05a
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-15 10:56:26 +0100
Commit message:

 Bump version

1.3.5
 
Package: onlineFDR
Commit: da99f166a14b9aa61047f1986a3495105be544b6
Author: dsrobertson <david.robertson@mrc-bsu.cam.ac.uk>
Date: 2019-07-13 00:55:28 +0100
Commit message:

 Update tests

Improve code coverage further
 
Package: onlineFDR
Commit: 9705b082ba61e6921073d3ba7673d0841f9bcd9c
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-12 17:12:15 +0100
Commit message:

 Update tests

Improve code coverage
 
Package: onlineFDR
Commit: a18ac72b506794073e3bd85717093ffcec5901b4
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-12 12:20:04 +0100
Commit message:

 Update README and index.html
 
Package: onlineFDR
Commit: 71241a0300e6fa37aa47ec499a774bcbfcfbc516
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-12 12:17:40 +0100
Commit message:

 Update README.md 
Package: onlineFDR
Commit: 25005c7d48e11af52c3bbcf1cff33e7503964b65
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-12 12:11:08 +0100
Commit message:

 Update README.md 
Package: onlineFDR
Commit: f9660f5245c313056240d38e13c424857f927731
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-12 12:03:18 +0100
Commit message:

 Update index.html
 
Package: onlineFDR
Commit: c57181caa25d85164e0662aeb69e99c9eaa97229
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-12 11:57:50 +0100
Commit message:

 Update README.md 
Package: onlineFDR
Commit: 8fff25ec8f7cdf5241bc1a0042a474feae80b92f
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-11 16:40:57 +0100
Commit message:

 Update .Rbuildignore 
Package: onlineFDR
Commit: 614c3aa98ec9caefbaaa3514729b6a2bcc7943f5
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-11 15:55:54 +0100
Commit message:

 Update index.html
 
Package: onlineFDR
Commit: 816dfc685c79e3fb0daba84bf6148a5d890e3132
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-11 15:52:37 +0100
Commit message:

 Update README.md

Add codecov badge 
Package: onlineFDR
Commit: 4a6f6ae944dc64ded7d615fc684c4cd784596f91
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-11 15:44:27 +0100
Commit message:

 Update DESCRIPTION 
Package: onlineFDR
Commit: e4215818d4c52988fc7784678f70bbace5402a4f
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-11 15:42:23 +0100
Commit message:

 Update .travis.yml 
Package: onlineFDR
Commit: b8d4681bb3e5edcea4a47ba60f4a10c2a3241b9f
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-11 15:39:58 +0100
Commit message:

 Add nocov to LORDdep

Since LORDdep will be deprecated
 
Package: onlineFDR
Commit: 39e7fd48bbbaefaa357a612ec181c37db530d92c
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-11 15:27:09 +0100
Commit message:

 Update index.html
 
Package: onlineFDR
Commit: 46ac71bc0d699f23134ead909e8b82f1178fbb1a
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-11 15:23:17 +0100
Commit message:

 Update README.md

Add Travis status image 
Package: onlineFDR
Commit: 2671a95320dcb0361e2452209b22b07a6f699aa7
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-11 15:08:57 +0100
Commit message:

 Create .travis.yml 
Package: onlineFDR
Commit: 7686728ecb68e4d239f6602985ef23e3db0ca333
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-10 18:54:21 +0100
Commit message:

 Update homepage
 
Package: onlineFDR
Commit: a411c064a9e02df5d71a52493c6047e77a64e36a
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-10 18:36:16 +0100
Commit message:

 Merge branch 'master' of https://github.com/dsrobertson/onlineFDR
 
Package: onlineFDR
Commit: deb438ed46126614615a872c057ad4a926d51553
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-10 18:36:02 +0100
Commit message:

 Add pkgdown site

Add to README
 
Package: onlineFDR
Commit: 099a38c72b648aa3db9560fe54a5932a68e6c1d0
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-10 18:30:44 +0100
Commit message:

 Merge pull request #12 from dsrobertson/pkgdown

Add pkgdown site 
Package: onlineFDR
Commit: 638a48393d3da93a6e4e91b8c478ae525ce4b88e
Author: dsrobertson <38322298+dsrobertson@users.noreply.github.com>
Date: 2019-07-10 18:28:30 +0100
Commit message:

 Add pkgdown site
 
Package: scTensor
Commit: ef16097acd1f2dc55f0024a320dc945574fa3a69
Author: kokitsuyuzaki <k.t.the-answer@hotmail.co.jp>
Date: 2019-07-15 18:29:05 +0900
Commit message:

 v-1.1.7
 
Package: GOTHiC
Commit: 9ff20f6b68ec314ed574803529286a4c16d2dc8f
Author: Bori Mifsud <b.mifsud@qmul.ac.uk>
Date: 2019-07-15 11:54:33 +0300
Commit message:

 fixed imports and global variables
 
Package: miRLAB
Commit: 793f33f2fb2d99e11ecc4e18074445c1700705b7
Author: Vu Viet Hoang Pham <pvvhoang@gmail.com>
Date: 2019-07-15 10:04:20 +0930
Commit message:

 Add manual
 
Package: geneClassifiers
Commit: 344aa5c83ffa668ff197bdc99a00081d0934bae9
Author: Rowan Kuiper <r.kuiper@skylinedx.com>
Date: 2019-07-14 15:05:31 +0000
Commit message:

 Version bump from 1.9.0 to 1.9.1 due to bugFix in previous commit
 
Package: geneClassifiers
Commit: 97f033206770990f2a7e0b9856afc472d5cdac89
Author: Rowan Kuiper <r.kuiper@skylinedx.com>
Date: 2019-07-14 14:52:25 +0000
Commit message:

 Bugfix and better checking for valid arguments

    o Bugfix: Added signature( "FixedExpressionData", i=ANY, j=missing ) for the "[" and "[[" functions
    o More indepth checking of function arguments
    o Additional unit tests
 
Package: GenoGAM
Commit: 0ac7b967b6926bc6810909bec3c6926a91128c2e
Author: Georg Stricker <georg.stricker@protonmail..com>
Date: 2019-07-14 16:09:57 +0200
Commit message:

 synchronised the new version from Bioconductor
 
Package: GenoGAM
Commit: e63098422a4bc635416e821f24037f012caeb13b
Author: Georg Stricker <georg.stricker@protonmail..com>
Date: 2019-07-14 16:07:23 +0200
Commit message:

 changed the way pvalues are being added to the GenoGAM object due to changes in the underlying object from a dependency
 
Package: GOTHiC
Commit: db539a0fc59c7ea40733d4ec0e5339b3c95b226a
Author: Bori Mifsud <b.mifsud@qmul.ac.uk>
Date: 2019-07-14 15:30:21 +0300
Commit message:

 bumped version
 
Package: GOTHiC
Commit: 69bdfd741dc0fc7cb5fa0724c364f976172dea64
Author: Bori Mifsud <b.mifsud@qmul.ac.uk>
Date: 2019-07-14 15:28:45 +0300
Commit message:

 updated namespace
 
Package: CNVRanger
Commit: 7f689d69a6ea52cd7063f22cb5abea87618b5140
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2019-07-14 08:12:34 -0400
Commit message:

 vignette: extend input format description
 
Package: FELLA
Commit: 197f389250de331bb1f1e900877a5c21bed47559
Author: SergiPicart <elpicart@gmail.com>
Date: 2019-07-14 10:09:39 +0200
Commit message:

 bug fix
 
Package: universalmotif
Commit: 6a1cd13f2aa15a551c97d7f6f2b82de3376d4302
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-07-13 14:26:56 -0400
Commit message:

 fix doc warning
 
Package: scTensor
Commit: 1d55270b2b2a1b529c2324d44995323b04a42844
Author: kokitsuyuzaki <k.t.the-answer@hotmail.co.jp>
Date: 2019-07-13 23:31:27 +0900
Commit message:

 v-1.1.6
 
Package: CNVRanger
Commit: 2b32e0ed13d7fd4a51fb64bf1c2eadc320f68980
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2019-07-13 07:37:59 -0400
Commit message:

 visualization for populationRanges and cnvEQTL
 
Package: geneClassifiers
Commit: d29195191cc7346f4952e64bb43f110cf5ca54dc
Author: Rowan Kuiper <r.kuiper@skylinedx.com>
Date: 2019-07-13 08:03:56 +0000
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/geneClassifiers
 
Package: geneClassifiers
Commit: 680b5094ebd52e5cb238a25ade4991da6c81485d
Author: Rowan Kuiper <r.kuiper@skylinedx.com>
Date: 2017-01-11 20:55:57 +0000
Commit message:

 Version 0.99.9

Removed the startup message 'referring to the Vignette'
Resaved the sysdata files as version 2 to avoid the Depend: R >2.10 in the description file
 
Package: geneClassifiers
Commit: 09acb6c897654fd7ea8ef3926ceb7cfac30a8912
Author: Rowan Kuiper <r.kuiper@skylinedx.com>
Date: 2016-12-28 10:37:41 +0000
Commit message:

 Version 0.99.8

Instead of single classifier definition files, the .classifierHook containing all standard classifiers is now merged in the sysdata.rda file.
 
Package: geneClassifiers
Commit: 72d6e160133ee02bf255ff99af4267045d368467
Author: Rowan Kuiper <r.kuiper@skylinedx.com>
Date: 2016-12-21 14:31:55 +0000
Commit message:

 Version 0.99.7

Previous commit (v0.99.6) could not build the missingCovariate vignette under Windows while the version before (0.99.4) had the same vignette source and passed without errors. Therefore increased the version to try another build.
 
Package: geneClassifiers
Commit: 05f1c3152dcb5d1661b297a327464f241cbe2a3b
Author: Rowan Kuiper <r.kuiper@skylinedx.com>
Date: 2016-12-21 14:11:05 +0000
Commit message:

 Version 0.99.6

-the only places where the @ to access slots are used are in getter/setter functions.
-rewrote the class 'initialize' functions as constructors.
-shortened the dataset names
-replaced the datasets by a systemdata.rda file for internal namespace use only
-replaced the checks during package loading by unit tests.
 
Package: geneClassifiers
Commit: ac523a6f11f74f5f82c5140651ee2f2358f4b352
Author: Rowan Kuiper <r.kuiper@skylinedx.com>
Date: 2016-11-18 14:05:54 +0000
Commit message:

 Version 0.99.4

Bug repair (in the initializing method of the FixedExpressionData class): Moved 'isLog2Transformed' check into the MAS5.0 'Normalization method specific code' section.
 
Package: geneClassifiers
Commit: 21e2be99db88461a4bc461812466b74efa403a65
Author: Rowan Kuiper <r.kuiper@skylinedx.com>
Date: 2016-11-14 13:07:52 +0000
Commit message:

 Version 0.99.4

Vignette update
 
Package: geneClassifiers
Commit: 00fcdf7e223cea06b6e179802d125c1df9b08cb4
Author: Rowan Kuiper <r.kuiper@skylinedx.com>
Date: 2016-10-27 17:22:33 +0000
Commit message:

 Version 0.99.3

Version bump
 
Package: geneClassifiers
Commit: 22c6ef73bc6f2bd9afb4e9fd7bb5a70ef1115531
Author: Rowan Kuiper <r.kuiper@skylinedx.com>
Date: 2016-10-27 14:03:42 +0000
Commit message:

 Version 0.99.2

In response to the Bioconductor review many changes were made.

In general:
1) S3 classes were replace by S4 classes. Therefore a complete restructuring was performed resuling in a more modular structure and better maintainable code.
2) More selective importing and exporting in the NAMESPACE file. (Using roxygen2)
3) Adjusted the grammar according to suggest in the review
 
Package: geneClassifiers
Commit: 2b43d2ea91b1f47c160bd5d1aac0ce5cf922a0fb
Author: Rowan Kuiper <r.kuiper@skylinedx.com>
Date: 2016-10-04 18:26:26 +0000
Commit message:

 Vesion 0.99.1

Version bumb
 
Package: geneClassifiers
Commit: 3bb964cdef8896337581224202ae9d5bf7b17f47
Author: Rowan Kuiper <r.kuiper@skylinedx.com>
Date: 2016-10-03 18:33:10 +0000
Commit message:

 Version 0.99.0

First commit
 
Package: MoonlightR
Commit: 31757b6de63eb6b1164522d8f2081f95885354e1
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-07-12 15:51:33 -0400
Commit message:

 update 2019 july 2
 
Package: MoonlightR
Commit: 7cded2fa377bb6ce8d5de2aa466205f0cdc9722c
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-07-12 15:48:31 -0400
Commit message:

 update 2019 july
 
Package: MoonlightR
Commit: 10f011ba1e775f2d53ac95a0bdbba509d54999ab
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-20 15:38:39 -0400
Commit message:

 fix in DPA

fix in DPA
 
Package: MoonlightR
Commit: b882da52b80e5e237973285beb69439fda1d8138
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-06 10:18:32 -0400
Commit message:

 update version  1.10.1

update version 1.10.1
 
Package: MoonlightR
Commit: e226ae9bf6f25fc54d2ab6a7fd1694223afd334c
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-02 10:54:57 -0400
Commit message:

 Remove set.seed usage in R code part2

Remove set.seed usage in R code part2
 
Package: MoonlightR
Commit: 5e1ea7b12ebbec9b89c84fe6f08db5f62ecffe53
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-02 10:50:16 -0400
Commit message:

 Remove set.seed usage in R code

Remove set.seed usage in R code
 
Package: MoonlightR
Commit: c5ee52ebdd2c181003f9670d5861211bacadc680
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-02 10:38:36 -0400
Commit message:

 fix part2

fix part2
 
Package: MoonlightR
Commit: 5e5cfe85c5d79d0a05251a9fc966075c2d0ffb03
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-02 09:49:04 -0400
Commit message:

 fixing errors warning notes

fixing errors warning notes
 
Package: MoonlightR
Commit: 453e007079e2b05fcc0f013981d281c033f20f34
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-02 09:33:02 -0400
Commit message:

 Removing LPA from vignette

Removing LPA from vignette
 
Package: MoonlightR
Commit: e761de1f57c3cfa3006638276bca1d4d5fdc7516
Author: Antonio Colaprico <antonio.colaprico@gmail.com>
Date: 2019-05-02 09:10:54 -0400
Commit message:

 Merge pull request #2 from lwaldron/patch-1

Correct GitHub links in DESCRIPTION 

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