Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active.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

GIT Logs

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

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

Package: IdeoViz
Commit: 24136654015bd9132511a64e9d39a735ad76970a
Author: Shraddha Pai <shraddha.pai@utoronto.ca>
Date: 2018-01-20 16:04:51
Commit message:

 Merge remote-tracking branch 'upstream/master'

Conflicts:
	DESCRIPTION
	R/plotChromValuePair.R
	R/plotOnIdeo.R
	man/avgByBin.Rd
	man/getBins.Rd
	man/getIdeo.Rd
	man/plotChromValuePair.Rd
	man/plotOnIdeo.Rd
	vignettes/Vignette.Rnw
 
Package: IdeoViz
Commit: ae2e7bb9d7dcd9792a7c42e2486fef0c4859f85a
Author: Shraddha Pai <shraddha.pai@utoronto.ca>
Date: 2017-12-08 16:53:25
Commit message:

 moving BioC repo to github
 
Package: IdeoViz
Commit: cd168c87a483624af930f8dc1185c6cc02affab1
Author: Shraddha Pai <shraddha.pai@utoronto.ca>
Date: 2017-12-08 16:51:34
Commit message:

 Initial commit 
Package: netReg
Commit: 6b33746c6308116e067c3324b9747fe55ebdb595
Author: dirmeier <simon.dirmeier@bsse.ethz.ch>
Date: 2018-01-20 14:04:28
Commit message:

 Added new version of dlib, replaced deprecated html_document with new version, updated to 1.3.1
 
Package: MLInterfaces
Commit: 208b5827414ad21e08bf1fe2d7e683b4cf1171e9
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-01-20 14:05:50
Commit message:

 removing rgl import and answering BiocCheck; rgl will not load for me, stymieing development
threejs may substitute fully but that has not been done with projectLearner...
 
Package: GenomicFeatures
Commit: 9de41080c9bc2b3d57bcb229a9fc60eeb19c32c2
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 13:12:09
Commit message:

 minor edit
 
Package: GenomicRanges
Commit: 4147f6192940f5d8697f601cf5e4fdb794911067
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 13:07:52
Commit message:

 some leftovers after renaming of Ranges class -> IntegerRanges
 
Package: IRanges
Commit: bcd57928e27fb6332659461a8b55b458c286c037
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 13:01:04
Commit message:

 one more leftover after renaming of Ranges class -> IntegerRanges
 
Package: IRanges
Commit: b83b32d37a643a119d4c0abd4a72ea36d9c4fce0
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:54:12
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/IRanges
 
Package: IRanges
Commit: 00e6b732e98479960e25798d0ba031d677ea1008
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:54:00
Commit message:

 some leftovers after renaming of Ranges class -> IntegerRanges
 
Package: ArrayExpressHTS
Commit: b87eea7435c6bbbad5eada9d50bdd588384b69a7
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:46:22
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: Pbase
Commit: 86817ba4581afab4a26ed0fa31a623311596bcbf
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:41:59
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: rtracklayer
Commit: e6b2880df962fcd73b648d4fc72e7ca962634973
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:37:25
Commit message:

 requires GenomicRanges >= 1.31.7
 
Package: girafe
Commit: e5c5c2bbb535ca365caaeafc2c0b57829a360af0
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:31:36
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: IRanges
Commit: cfb2e963b7938424cac52fea4852941fc12dc462
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:25:02
Commit message:

 requires S4Vectors >= 0.17.24
 
Package: VariantAnnotation
Commit: eaaa54e76d9a3b1ded5abfb6e31b86c6483bee58
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 12:08:42
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: SummarizedExperiment
Commit: 3e35d74fe91e6162341f23cf5d42b897261cb222
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 11:50:44
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: SpidermiR
Commit: ce3274fdc98f6c745bfcf8f7d2a7c81b9230f27e
Author: claudiacava <claud.cava@gmail.com>
Date: 2018-01-20 11:47:11
Commit message:

 update
 
Package: GenomicFeatures
Commit: 45f2da5416f871b883032d9e22e999c96e7560fa
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 11:38:08
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: GenomicAlignments
Commit: acb5da89130f4e1d1873c865132613df95d69e28
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 11:07:19
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: BSgenome
Commit: 59c467e3fe88e1420b063b64d85c3b6771964ae6
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 10:35:31
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: rtracklayer
Commit: ab349d990247d6878155f7c953e8ed5187f74556
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 10:35:14
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: Biostrings
Commit: 88954cbfa7c4eaede805ca44e70928543ec27b50
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 10:34:36
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: XVector
Commit: 897120c1c07c97fbd09631b0b762d7932f81a542
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 10:33:31
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: GenomicRanges
Commit: 1c8943016498691b7da775530a108321bf16fe65
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 10:32:24
Commit message:

 follow renaming of Ranges class -> IntegerRanges in IRanges 2.13.11
 
Package: S4Vectors
Commit: 1b6d23da1dda0a101a62d796bf199f78ce04d815
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 10:31:21
Commit message:

 follow renaming of Ranges class -> IntegerRanges in S4Vectors 2.13.11
 
Package: IRanges
Commit: 6f87c2f362b37466ad18b1dccf861317562e43fb
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-20 10:27:43
Commit message:

 Rename Ranges and RangesORmissing classes -> IntegerRanges and
IntegerRanges_OR_missing classes, respectively.
 
Package: bacon
Commit: 117818895c2bfb5d550801979db3c78b52fc3cf7
Author: mviterson <mviterson@gmail.com>
Date: 2018-01-20 07:19:44
Commit message:

 bug fix: changed html_document2 -> html_document
 
Package: derfinder
Commit: 256d7a772207706faff4ca74e9e061706ce336d3
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-01-20 00:50:27
Commit message:

 v1.13.5 -- fix more links
 
Package: derfinderPlot
Commit: 760e162a53dfac1a11363531d50a8abd3b0b8cd5
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-01-20 00:39:17
Commit message:

 v1.13.2 -- fix more links
 
Package: regionReport
Commit: 311def55c4dbbe1f0f5898ff795e8a001c990056
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-01-20 00:32:50
Commit message:

 v1.13.2 -- fix a link to Ideogram (has a weird name)
 
Package: apeglm
Commit: 5b9b77499ff85cbfdf6e94ad82a5f10d90a1d7d4
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-01-19 23:48:49
Commit message:

 small cleaning up
 
Package: apeglm
Commit: a93197656b04e6bc2e4107ad8ba9edea6b8dee1c
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-01-19 23:48:24
Commit message:

 small cleaning up
 
Package: Pigengene
Commit: 61f99eb72224006f548792f3a92022df2e87a65e
Author: Habil Zare <habil_zare@yahoo.com>
Date: 2018-01-19 23:04:53
Commit message:

 C50:::as.party.C5.0 to comply with version 0.1.1
 
Package: hpar
Commit: 7553ac54645e4fe6fa670dbaa08e1c5a61a89e0a
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-19 22:02:49
Commit message:

 use BiocStyle::html_document (Bioc commit)
 
Package: cosmiq
Commit: 027805244c3ad44c5ad8da861b8934a10674d137
Author: cpanse <cp@fgcz.ethz.ch>
Date: 2018-01-19 20:13:22
Commit message:

 version inc
 
Package: cosmiq
Commit: 19982a267139a726a97705c64c1279f6dd1d11a3
Author: cpanse <cp@fgcz.ethz.ch>
Date: 2018-01-19 20:13:00
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/cosmiq
 
Package: cosmiq
Commit: 382a128608ed183920673380e3505d096ec89c02
Author: cpanse <cp@fgcz.ethz.ch>
Date: 2018-01-19 20:12:40
Commit message:

 fix
 
Package: specL
Commit: 232ef92a81e794d44e09369ef983bdc501e724c3
Author: cpanse <cp@fgcz.ethz.ch>
Date: 2018-01-19 20:11:37
Commit message:

 version inc
 
Package: specL
Commit: cdf1da30fb36a4a8aecbcbcaa9e551781b0e72b8
Author: cpanse <cp@fgcz.ethz.ch>
Date: 2018-01-19 20:11:00
Commit message:

 fix
 
Package: imageHTS
Commit: f5604c76e80d75b8926cca1d09a106a29002162c
Author: Joe Barry <jbarry@Joes-MacBook-Pro.local>
Date: 2018-01-19 20:04:16
Commit message:

 changed from BiocStyle latex2 to latex
 
Package: motifStack
Commit: d07623322ff125edf5cd5728d467d5b813d7c506
Author: Jianhong Ou <jianhongou@dhcp-152-16-223-142.research.duhs.duke.edu>
Date: 2018-01-19 19:57:31
Commit message:

 Fix the warning in windows.
 
Package: apeglm
Commit: 7922388817c0188381da390ca1df6e659f7c2f91
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-01-19 19:45:09
Commit message:

 add nbinomR support for weights
 
Package: DiffBind
Commit: 230c098844e135384fb73e233cac7b1a27d9d74c
Author: Rory Stark <rory.stark@cruk.cam.ac.uk>
Date: 2018-01-19 19:09:07
Commit message:

 bug fixes + precision and dir options -- remove setwd in vignette and man pages
 
Package: flowPloidyData
Commit: 7d598cd1dfb365ebe7e77a5d787f0c8c2b75b53c
Author: Tyler Smith <tyler@plantarum.ca>
Date: 2018-01-19 18:51:33
Commit message:

 Version bump, added NEWS file, removed encoding from vignette

Encoding line is no longer needed in Rmd files.
 
Package: flowPloidyData
Commit: 81c19f56fda371594f2a44f8568736aca6d177f8
Author: Tyler Smith <tyler@plantarum.ca>
Date: 2018-01-19 18:35:34
Commit message:

 Added documentation of fpBad and fpVac
 
Package: GenomicFiles
Commit: eb703f74e9c0fab087c650f5941dc35359e6aac8
Author: lshep <shepherl@gmail.com>
Date: 2018-01-19 18:24:43
Commit message:

 Update vignette to use latex instead of latex2
 
Package: genefilter
Commit: 8feef757de9f15435750e9691748ffe3e4696785
Author: lshep <shepherl@gmail.com>
Date: 2018-01-19 18:23:51
Commit message:

 Update vignette to use latex instead of latex2
 
Package: Rhtslib
Commit: d0876f8e039a43ca647be67241ffbd679644ad22
Author: lshep <shepherl@gmail.com>
Date: 2018-01-19 18:21:51
Commit message:

 Update vignette to use html_document instead of html_document2
 
Package: VariantAnnotation
Commit: de7f434f13d2b5a333ead0ba260b4d953102a53d
Author: lshep <shepherl@gmail.com>
Date: 2018-01-19 18:20:43
Commit message:

 Update vignette to use latex instead of latex2
 
Package: AnnotationFilter
Commit: bc3863a6d6b728a3ecbd9644be9e3089a655491b
Author: lshep <shepherl@gmail.com>
Date: 2018-01-19 18:16:16
Commit message:

 Update BiocStyle from html_document2 to html_document
 
Package: AnnotationFilter
Commit: ad642b83a5e9460425665ad38870251c3a7bdbf2
Author: Daniel Van Twisk <dvantwisk@gmail.com>
Date: 2017-11-09 20:45:29
Commit message:

 Merge pull request #23 from Bioconductor/DoubleFilter

Add virtual DoubleFilter class 
Package: AnnotationFilter
Commit: 543cb176fd73457048b2c18596a3f6ae6de25aab
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2017-11-07 12:09:56
Commit message:

 Add virtual DoubleFilter class

- Add the virtuel DoubleFilter class.
- Add related documentation.
 
Package: annotatr
Commit: 80083985848f29e355785af6d5c84bd62b2d5c11
Author: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Date: 2018-01-18 21:32:08
Commit message:

 Add the ability to facet over two variables in plot_numerical

 
Package: HelloRanges
Commit: 4d88c6f8f236970fa4081cb1febec5c9011a8fa0
Author: Michael Lawrence <michafla@gene.com>
Date: 2018-01-19 18:02:20
Commit message:

 use BiocStyle::latex()
 
Package: hpar
Commit: a363d14b5482bd6feb85568817f95c2711a779fa
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-19 17:47:15
Commit message:

 test for duplicated commits
 
Package: DASC
Commit: 723ffb8e56c521c73114d1bd440cc5a30b72b3eb
Author: lshep <shepherl@gmail.com>
Date: 2018-01-19 17:47:55
Commit message:

 Deprecate package
 
Package: scater
Commit: e080bb7cd07d028e3cb1cd508dadb07bf22b9c95
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-19 13:04:00
Commit message:

 Avoid checking size factor centering when NULL.
 
Package: scater
Commit: 4e87195e051551232a2bfe49eaadbc85e47f1e5e
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-19 10:25:05
Commit message:

 Small bugfix to plotHeatmap.
 
Package: scater
Commit: d7988ac627843cc068c56cf171dd0f4f3c16aad6
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-19 10:24:25
Commit message:

 Added uniquifyFeatureNames for quick uniquification.
 
Package: scater
Commit: c510568d83907ba3de8eba2d845cb92d2f1d774a
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 18:16:14
Commit message:

 Further removal of unnecessary droplet-related files.
 
Package: scater
Commit: 0d07b4c376e97b98c24d2a73add86ebd8df6863f
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 18:00:53
Commit message:

 Removed old SCESet methods.
 
Package: scater
Commit: 34bebdca285019510a1ceb99b5d207c9e51f9512
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 17:52:15
Commit message:

 Purged all 10x functions in the test suite.
 
Package: scater
Commit: baf0e90ea5b0351d32d0d5170a93e81a8c34f3a8
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 17:41:32
Commit message:

 Deprecated droplet functions for DropletUtils equivalents.
 
Package: scater
Commit: d005d970c8a35fe8281051f9c3c0520295692222
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 17:29:47
Commit message:

 Added DelayedArray to Imports list.
 
Package: scater
Commit: 30396e91a66e569083e65ad601f6f70a10f8f5d9
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 17:12:05
Commit message:

 Fixed bug with R^2 calculations for sparse matrix inputs.
 
Package: scater
Commit: b615be78d9052ce97e16d38995ab071baf426b24
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 17:07:01
Commit message:

 Switched from matrixStats to DelayedMatrixStats.
 
Package: scater
Commit: 9a64c8319082d15d1c8d71a99bab73a8a80abd83
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-18 13:45:56
Commit message:

 Restored legacy names for back-compatibility.
Clarified variable names for more sensible code.
Updated documentation for compact, renamed metrics.
Updated tests.
 
Package: scater
Commit: d47b43b6bd35fe6629bf90fed3f3f960515261d1
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 21:54:11
Commit message:

 Renamed qc fields for better safety, sensibility.
 
Package: scater
Commit: 05de5afe63d4d8f0f4853e856b84cf88acc2812c
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 21:25:56
Commit message:

 Updated NEWS.
 
Package: scater
Commit: 8c80cdf56ca7dd1196c65880ef81424b138889ad
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 21:25:22
Commit message:

 Reduced nesting of scater_qc metrics, by removing exprs_vaue layer.
 
Package: scater
Commit: 883d10e534d3282556705afac93b65241d84de9e
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 21:19:54
Commit message:

 Added tests for compactness and overwriting, minor bug fix.
 
Package: scater
Commit: 1ff520b04c86f1d9c6e70279e10c3165f3fd5c3f
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 20:27:32
Commit message:

 Fixes to calculateQCMetrics with new compactness format.
 
Package: scater
Commit: 5bce2f950c46262907ae5cc9996965a7f12d8cf2
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 16:49:49
Commit message:

 Supported compact QC output with nested dataframes.
 
Package: scater
Commit: 2090154d82f5ba82c20655ba54b72abb3a68ccfc
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 11:49:57
Commit message:

 Passed total exprs in qc internal functions to avoid recalculation.
 
Package: scater
Commit: 9b3a73beb7b976193016a5ecefd70cff93a466a0
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-17 11:01:28
Commit message:

 Fleshed out calculateQCMetrics tests for greater rigor.
 
Package: scater
Commit: ddf25e7f3d02868b1f602c0175cbcf1988833a5a
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 19:06:26
Commit message:

 Fixed updated argument naming in tests.
 
Package: scater
Commit: b43c8b9be0b903397a76d06b4a21f2380e1a370b
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 19:02:02
Commit message:

 Merge branch 'master' of https://github.com/davismcc/scater

Conflicts:
	R/qc.R
 
Package: scater
Commit: 2458a217c8689a5f372babd098e09607ea56628d
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 18:45:36
Commit message:

 Switched back to old automatic control set names for now.
 
Package: scater
Commit: abfe83558c2b22d8d28ed94d6d5f78d579b922e5
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 18:45:36
Commit message:

 Switched back to old automatic control set names for now.
 
Package: scater
Commit: 799d1cf142939763cffd42bb55fc15b7eec84e11
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 18:38:16
Commit message:

 Renamed lowerDetectionLimit to detection_limit, avoid camelcase args.
 
Package: scater
Commit: f251ee8604c982cbf8d938f575183ce67c9fa629
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 18:35:33
Commit message:

 Added option to specify the top percentage calculations.
 
Package: scater
Commit: 75aa477c37618fcd323217c77fd2f1deebbf801b
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 18:00:52
Commit message:

 calculateQCMatrix rank output now goes from largest to smallest.
Renamed automatically generated control/non-control sets.
 
Package: scater
Commit: b3db62aa7b7109a9562c45a2935d9519aecfa00c
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 17:58:12
Commit message:

 Removed linearity checks; all metrics are now always computed.
Added lowerDetectionLimit argument to pass to nexprs().
 
Package: scater
Commit: 06b8379bc01ed1eb16aafba0ae963acffcfbe191
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 17:42:05
Commit message:

 Updated documentation for calculateQCMetrics.
 
Package: scater
Commit: 2c567c5f8ab4de934ec41e012a9dbd9cb6349da9
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 16:36:00
Commit message:

 Bumped version number, date.
 
Package: scater
Commit: 71dcaaee0700de459c5c7eac0f373ab355e1f2f8
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 16:35:12
Commit message:

 Stronger tests for normalize() (migrated from scran).
 
Package: scater
Commit: 10e77ea2a893df790dd11787a83fbecd97d23bd2
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 16:28:29
Commit message:

 Merge branch 'master' of https://github.com/davismcc/scater
 
Package: scater
Commit: b2d206552012bc5b868669e0fa827d1fc2095203
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-16 16:27:33
Commit message:

 Patches to nexprs() documentation, testing.
 
Package: scater
Commit: 76716a31765c64dab2001d34329b888db71cf2ae
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-01-16 14:17:59
Commit message:

 Merge pull request #44 from LTLA/master

Merging BioC history with Github history 
Package: scater
Commit: a656f397696321a01cad0b764dc6a8e333733fdc
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-02 15:11:24
Commit message:

 Added plotHeatmap wrapper around pheatmap for SCE objects.
 
Package: scater
Commit: 96de14f8c811e243f23bcc643f483430b030a5c4
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-20 11:45:51
Commit message:

 Minor fix to shut up CHECK.
 
Package: scater
Commit: 20c7cea7bb154b6929470610a950b96496eb933b
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-20 11:43:54
Commit message:

 Merge remote-tracking branch 'bioc/master'

Conflicts:
	R/calculate-expression.R
	R/normalisation.R
	R/plotting.R
	R/qc.R
	tests/testthat/test-classes.R
 
Package: scater
Commit: ba91873eb480345c22db4eec760796cb1141a4a6
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-12-19 11:29:21
Commit message:

 Merge pull request #42 from LTLA/master

Further fixes to plotting 
Package: scater
Commit: 0e1dfd6792af02ac3ef078510e311445a9476223
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-14 16:34:20
Commit message:

 Fixes to C++ matrixStats-code with duplicate subsets.
Generalized subsetting tests in test-cpp.R.
 
Package: scater
Commit: 4c74fa8d88bdc7294085d54bd75c03a3190c8dfd
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-14 16:13:35
Commit message:

 Optimized matrix access by sorting subset vectors.
Modified tests to check behaviour of unsorted subset vectors.
 
Package: scater
Commit: cf2433534a5e2a8e30f510db48dc393003337a5c
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-13 15:03:24
Commit message:

 Bug fix to plotScater with colours/blocks.
Bug fix to calls to nexprs().
 
Package: scater
Commit: ba91fe5f8abea1e89dc6d4dc7422168500a80c96
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-13 14:58:38
Commit message:

 Updated nexprs() docs to reflect subsetting of input.
Updated tests for C++ row/col matrix functions.
 
Package: scater
Commit: e4754697a4d27d32f8cf433dfcb60e231343043e
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-13 14:58:11
Commit message:

 Switched all .Call()s to use new matrixStats-like functions.
 
Package: scater
Commit: 5e87c527184b95cc5d0aab5e71a292e113cdc427
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-13 14:25:38
Commit message:

 Generalized C++ utility functions to their matrixStats equivalents.
 
Package: scater
Commit: 4a1c30e196df575949787c2c61c02963e7daa75d
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-08 13:50:11
Commit message:

 Merge remote-tracking branch 'davis/master'
 
Package: scater
Commit: 77279f1a43433d5ffd1e2885f6906614154dd4b8
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-08 13:49:38
Commit message:

 Streamlined plotScater % top calculations with existing C++ code.
 
Package: scater
Commit: d515e2f67a4d15732f8c88e9660fb60e1c401ed3
Author: davismcc <davismcc@gmail.com>
Date: 2017-12-05 18:28:20
Commit message:

 Tweaking roxygen to fix NAMESPACE
 
Package: scater
Commit: 5e5d3acf8848f0149f83f19d62a08b01a9154ff1
Author: davismcc <davismcc@gmail.com>
Date: 2017-12-03 21:09:48
Commit message:

 Merging PR from Aaron.

Merge branch 'master' of https://github.com/davismcc/scater

# Conflicts:
#	DESCRIPTION
 
Package: scater
Commit: 68d5570db5a8a15c6f00f4c3fa53e8954509cd61
Author: davismcc <davismcc@gmail.com>
Date: 2017-12-03 21:08:23
Commit message:

 Adjustments to 10x import wrapper.
 
Package: scater
Commit: a6a207c07467714716c5be1059cdfa67590af931
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-12-03 21:07:20
Commit message:

 Merge pull request #39 from LTLA/master

Modified plotHighestExprs to support alternative matrices. 
Package: scater
Commit: 597268ae37aecd70ec67be226d4693681347bb59
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 17:32:25
Commit message:

 Documented return value for run* functions.
 
Package: scater
Commit: 6939ca0debd52e18d075e234ef6cf466607fec3b
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 17:27:10
Commit message:

 Minor changes to shut up CHECK.
 
Package: scater
Commit: 8346e4e885106fe54a7a1e05abde374ea2f46796
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 17:26:18
Commit message:

 Fixed tests for updated messages, argument names.
 
Package: scater
Commit: 5a10c1a495bc30e14c81ea03b1f0f581a40b89f0
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 17:05:16
Commit message:

 Renamed use.size.factors arguments in various calls.
 
Package: scater
Commit: 1a00bf58d2257936de34e5b10831a1ca8ee48538
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 17:03:47
Commit message:

 Fixed missing ncomponents documentation in run* functions.
 
Package: scater
Commit: 04b8f7f36e33641d01400ac4acc686910aa0f8fb
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 16:53:59
Commit message:

 Bug fixes in vignettes for new args, function calls.
 
Package: scater
Commit: 8efe366851dfd295ee382490e8f765295f101164
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 15:55:59
Commit message:

 Moved details from plot* to run* documentation.
Mentioned metrics used in PCA for QC.
Mentioned deprecation of arguments in plot* functions.
 
Package: scater
Commit: 9677f60628f814523b13b6600773f97eea001185
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 15:40:52
Commit message:

 Cleaned up warning messages in plotPCA for QC.
 
Package: scater
Commit: 113155e426af2dea0f5fdbf436ba5dccd3e2bfa1
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-03 15:33:49
Commit message:

 Softened transition to new '...' behaviour in plot*.
Minor bug fixes to plot/run calls in MDS, DiffusionMap.
 
Package: scater
Commit: ffed3e9d55275cbdf721e0c922ddc1c54da91c65
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-02 17:07:26
Commit message:

 Added documentation for read10xResults.
 
Package: scater
Commit: aa01f9d215eaede0708b96698acacc432a39f6ef
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-02 17:05:30
Commit message:

 Separated documentation for run* functions for dim. red.
Minor rewording of dim. red. plot* documentation.
Required specification of run_args when re-running dim.red.
Automatic passing of plotting arguments via ... in plot*.
Exported plotMDS, added documentation.
Deprecated return_SCE in favour of explicit run*.
 
Package: scater
Commit: 1aa7a3e110d4602b41b6cc9ef9e2a1b19eeac45a
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-02 16:33:45
Commit message:

 Made axis ticks optional.
 
Package: scater
Commit: 9cee24fc288f862e6617ac78ddd65bda7a9d3536
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-02 14:52:54
Commit message:

 Fixed centering bug in normalizeSCE.
 
Package: scater
Commit: 3a85b7274868078d1bdc86bd7e2d31d435917c8e
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-02 14:41:58
Commit message:

 Fixed bug of not checking centering of default size factors.
 
Package: scater
Commit: 88384feb7f012e984c21ae283ec317109ecbb4b5
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-02 14:19:38
Commit message:

 Updated various documentation on size factor treatment.
 
Package: scater
Commit: 80f984830f450c862c3d506e63449a6d1d5929ef
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-12-02 14:07:40
Commit message:

 Streamlined handling of control-specific size factors, centering.
 
Package: scater
Commit: 9f48e2dadcf7ad59e10e94b447b8ad002b54e079
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-30 17:54:55
Commit message:

 Fixed missing comma.
 
Package: scater
Commit: d68f3a8b1bc3bb40658be01afe87197ab607b015
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-30 17:44:48
Commit message:

 Minor streamlining of code.
 
Package: scater
Commit: cf8a2136b462d7efc24e7bd1e92bfd3e1aaf3d8f
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-29 14:48:10
Commit message:

 Fixed inconsistency between feature_names, rownames.
 
Package: scater
Commit: df8598da8021e3e3401c00c0fb88a4416d269640
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-29 10:10:41
Commit message:

 Modified plotHighestExprs to support alternative matrices.
Streamlined code to remove unnecessary errors, variables.
Added support for plotting raw values, w/o percentages.
 
Package: scater
Commit: 98cf41ea302f69abb94a0c747004531f95f2dc34
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-11-28 18:52:35
Commit message:

 Merge pull request #36 from Shians/master

Changed featureData to rowData in qc.R 
Package: scater
Commit: e963615f95afbd6a3b2ff12696c033e7fac75d5c
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-11-28 18:52:04
Commit message:

 Merge pull request #35 from LTLA/master

Force recompilation after Rcpp updates 
Package: scater
Commit: 671cd8ce6e2514d3ab0311d01331de4cac679459
Author: Shians <registertonysu@gmail.com>
Date: 2017-11-27 01:45:37
Commit message:

 Merge branch 'master' of github.com:Shians/scater
 
Package: scater
Commit: 6db2b391b284cda25b949be967e6ccb50ffed502
Author: Shians <registertonysu@gmail.com>
Date: 2017-11-27 01:45:00
Commit message:

 Recompiled documentation
 
Package: scater
Commit: eec925fd947465517b19e66d3a08d6eb4fd67f29
Author: Shians <registertonysu@gmail.com>
Date: 2017-11-27 01:44:50
Commit message:

 Changed featureData to rowData
 
Package: scater
Commit: 977beec96f1a4d2dfe76b957bae6dce46391786f
Author: Shians <registertonysu@gmail.com>
Date: 2017-11-27 01:41:42
Commit message:

 Changed featureData to rowData
 
Package: scater
Commit: 23196ba299c8694f62ee75bfc140b4e9284cf5a1
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-25 16:29:21
Commit message:

 Merge remote-tracking branch 'davis/master'
 
Package: scater
Commit: 61007b0b014b90848b638f708da7aeff219f341a
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-25 16:27:13
Commit message:

 Bumped version to force recompilation for Rcpp updates.
 
Package: scater
Commit: 7b9e9e63b21d338a4622b919dcb510694fa99141
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-11-21 14:49:19
Commit message:

 Merge pull request #34 from LTLA/master

Various fixes to read10xResults 
Package: scater
Commit: c47ba03731b7e87069a7d049ddc468639fec87b2
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-19 17:45:04
Commit message:

 Clarified log base during normalization.
 
Package: scater
Commit: 736d78b978c2f51efba1d159f17fe1618ade3bf1
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-15 09:20:08
Commit message:

 Cleaned up calc_average C++ code slightly.
 
Package: scater
Commit: c892b9b8a3c7e8ed23f3eb6ab55589f239b00a5f
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-15 09:18:42
Commit message:

 Fixed bugs with read10xResults with duplicate colnames.
Avoid dgTMatrix input prior to C++ code.
Added correct cell barcode subsetting in loop.
 
Package: scater
Commit: 93d43e92e4e8a756251456b292a026173edf7c5d
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-11-14 12:41:13
Commit message:

 Merge pull request #32 from LTLA/master

Minor fixes to calcAverage code 
Package: scater
Commit: af8630810c16ac6d9859384b82cfca224e978d3c
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-04 15:13:04
Commit message:

 Merge remote-tracking branch 'davis/master'

Conflicts:
	DESCRIPTION
 
Package: scater
Commit: 85ebb2681c8b4d248e82a838ec7f08d15e34d957
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-04 15:11:35
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: scater
Commit: f444744021bb2848d2948e3522983ff7e677c784
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-11-04 15:10:00
Commit message:

 Minor fix to variable extraction in plotPCA for QC.
 
Package: scater
Commit: e48f7052849821e16b63efcf5c8674c76ba1c036
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-30 10:22:58
Commit message:

 Merge remote-tracking branch 'upstream/master'

Conflicts:
	DESCRIPTION
	R/normalisation.R
	man/downsampleCounts.Rd
 
Package: scater
Commit: 12fb261cb52fa15d7f38fcc5821989cfef908122
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-30 10:06:53
Commit message:

 Avoid making unnecessary matrix in calc_exprs.
 
Package: scater
Commit: be4975910403d6109618a4aab3806f43bf21ca69
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-30 09:51:54
Commit message:

 Moved margin calculations into if() block.
 
Package: scater
Commit: f2a5db934335a785b27061fce245dc00b67a15a2
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-25 17:27:02
Commit message:

 Updating docs; fixed bug in normaliseExprs
 
Package: scater
Commit: 178b3909fd18f39cd62dee546270603bc050ba2d
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-10-25 10:57:28
Commit message:

 Merge pull request #30 from LTLA/master

Fixes to 10X-related function documentation. 
Package: scater
Commit: 40e4286a5147de9f41af562df0870bb5363fe70a
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-24 11:57:20
Commit message:

 Bug fix to ncomponents= for plotReducedDim.
 
Package: scater
Commit: 5848feb988c63ba47fc6590d1575ece2412817b1
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-22 09:29:26
Commit message:

 Fixes to 10X-related function documentation.
 
Package: scater
Commit: 81ac3c85cb97a0d5de612d7a69638d355612971b
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-20 17:23:32
Commit message:

 Incorporating new downsampleCounts() function
 
Package: scater
Commit: 6bfc2326fd052bb2f3e371a90a63e41531d791c0
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-10-20 08:49:41
Commit message:

 Merge pull request #28 from LTLA/master

Downsampling method 
Package: scater
Commit: 0b712caa36e235bef477d9f4f74f072635c0d910
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-19 11:27:01
Commit message:

 Tested for correct statistical properties in sampler.
 
Package: scater
Commit: 18ba2ad6da5fa4f59c30e83eec52e84dd92119a0
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-19 11:14:53
Commit message:

 Added defense against very unlikely segfault.
 
Package: scater
Commit: ccde05bb64633e1354c639caf5c05984f2a5a0f6
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-19 11:09:16
Commit message:

 Implemented sampling wt. replacement, updated tests.
 
Package: scater
Commit: 251eac69bc5081c70f2b6fd67febae6cc5f537aa
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-18 13:02:30
Commit message:

 Fixed bug in downsampling, added tests.
 
Package: scater
Commit: a3418d713cff5cfb895a12fe710b8eda796b9eee
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-18 12:34:09
Commit message:

 Added function for matrix downsampling.
 
Package: scater
Commit: 968c481ec2330d8b0b2c134d3d6b9d3e5760bfc1
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-18 08:07:05
Commit message:

 Update for release
 
Package: scater
Commit: 87644c7de740c9e645750e9470d0a2c60ff47b85
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-10-10 14:35:04
Commit message:

 Update Appveyor badge 
Package: scater
Commit: e2b19a32072c6c462b0a0f2aff6537cbbec7f57a
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-10-10 14:23:11
Commit message:

 Update Appveyor badge 
Package: scater
Commit: b6af352d833034bc4ebd360471f615bcbddd3ae0
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-10 14:19:01
Commit message:

 Merge branch 'master' of https://github.com/davismcc/scater
 
Package: scater
Commit: a85cc4f8f88b662e2bda4d13768e2927e69672e1
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-10 14:18:48
Commit message:

 Updating appveyor setup
 
Package: scater
Commit: 9b88f6b1380cf27573322fccb9c8ce1b90e21e5e
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-10-10 14:04:52
Commit message:

 Update README with Travis CI badge 
Package: scater
Commit: 5e057e9a005fa5e7402782f6caf3841b08a9b0d9
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-10 13:18:42
Commit message:

 Adding codecoverage back to Travis CI settings
 
Package: scater
Commit: f605cc0f90e752943ab22ab101764d975179bc51
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-10 13:11:30
Commit message:

 Updating to native R support in Travis CI
 
Package: scater
Commit: feef1f010363326e6baa70836a936bbb05095df2
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-10 13:01:04
Commit message:

 Updating dataviz vignette
 
Package: scater
Commit: 9068effcd6052985984336e40103ad120cb0c13b
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-09 21:40:30
Commit message:

 Updating vignettes and calculateCPM code
 
Package: scater
Commit: 608bcfcc3caeb143240cd2858d3746217c457ee3
Author: davismcc <davismcc@gmail.com>
Date: 2017-10-09 14:30:32
Commit message:

 Updating README
 
Package: scater
Commit: 643a2828553dccea517c6eacfe193c457fbec8d4
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-10-09 13:34:41
Commit message:

 Merge pull request #7 from LTLA/master

Compatibility fixes for sparse matrices 
Package: scater
Commit: abe3989476342055f72b7cb0f9a7fc65149cf168
Author: Davis McCarthy <davismcc@gmail.com>
Date: 2017-10-09 13:34:00
Commit message:

 Merge pull request #4 from PeteHaitch/master

Fix potential integer overflow bug in calc_top_features_internal() 
Package: scater
Commit: ec4631587568c9280c759230bee322c5567cd6fe
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-02 17:56:00
Commit message:

 Renamed to .general_*Sums for consistency.
 
Package: scater
Commit: f321da3ff57b7c16d06b738b7818b342b63e318d
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-02 17:33:35
Commit message:

 Propagated .row/colSums to remaining functions.
 
Package: scater
Commit: 9f632848b6600a152505d482ee33d2e0b28a97fd
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-10-02 17:30:38
Commit message:

 Merge remote-tracking branch 'upstream/master'

Conflicts:
	R/10ximport-wrapper.R
	R/qc.R
	R/utils.R
 
Package: scater
Commit: 4aa05f50511c4e9009d7d41ad05965fd5eb794cd
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-09-29 10:37:32
Commit message:

 Updated NAMESPACE.
 
Package: scater
Commit: b788e2feca6597ddba40f0e5c63ba3a7230730c8
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-09-29 10:22:10
Commit message:

 Added Matrix::colSums import.
 
Package: scater
Commit: 2c4e473eb066c28e41f477c22ac90ca3e55e556d
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-09-29 09:55:03
Commit message:

 Coerced read10XResults output to dgCMatrix format.
 
Package: scater
Commit: 5db1b24b0b0332ec109551b3a9ceaa5913a447c9
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-09-29 09:47:49
Commit message:

 Replaced all uses of matrixStats::*Vars with .general_*Vars.
 
Package: scater
Commit: 450be7dc276138dc7270f15745238b7abc8c6e35
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-09-29 09:42:56
Commit message:

 Added tests for correctness of some C++ code.
 
Package: scater
Commit: f44f6a1ed8e033373e3bee2619c27f8830e196fd
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2017-09-29 09:42:36
Commit message:

 Added C++ code to compute row/column variances.
 
Package: scater
Commit: 73e74597041361e14864309f53771ceb4077a1f9
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2017-09-15 19:31:56
Commit message:

 std::accumulate() takes its return type from init
Previously, this line would return an int that was then cast to a double. Now, the result is explicitly a double. This avoids potential integer overflow in the sum
 
Package: VariantToolsData
Commit: 5938a63d5b6a086ad55a9ca6f1badc8fc0d2d124
Author: larman <michafla@gene.com>
Date: 2018-01-19 16:54:41
Commit message:

 use BiocStyle::latex()
 
Package: ideal
Commit: 0baa438133438bda8aa89dd1ca8cf5e6cad04d39
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2018-01-19 16:55:08
Commit message:

 version bump - 1.3.1, with new vignette output format
 
Package: flowCL
Commit: 67cb8e39a7c3c019a3c1a089f207a17ac55ca91a
Author: Justin Meskas <jmeskas@bccrc.ca>
Date: 2018-01-15 19:27:51
Commit message:

 Merge branch 'master' of https://github.com/jmeskas/flowCL
 
Package: flowCL
Commit: 0e1c99eee5310058b9354a614cd000a9fdd635af
Author: Justin Meskas <jmeskas@bccrc.ca>
Date: 2018-01-15 19:15:46
Commit message:

 Bumped to 1.17.2 
Package: flowCL
Commit: 4b3705782a635ab1709f8d65fb8303e2a1065e14
Author: Justin Meskas <jmeskas@bccrc.ca>
Date: 2018-01-15 19:15:06
Commit message:

 1.17.1 did not install. Conflicts in supportingFunction were not resolved. 
Package: flowCL
Commit: 217fede8f501e207f83008b22861eb3ae91021a3
Author: Justin Meskas <jmeskas@bccrc.ca>
Date: 2018-01-15 18:52:54
Commit message:

 NEWS~ deleted 
Package: flowCL
Commit: a4fcb4e005ab295a55a07bfdc00f402d6d06a699
Author: jmeskas <jmeskas@bccrc.ca>
Date: 2018-01-15 18:34:47
Commit message:

 Delete NEWS~ 
Package: ideal
Commit: be09750504079548ae1a87b4c2ea9d158c20fe4d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2018-01-19 16:53:38
Commit message:

 correct output for the vignette, as html_document2 is now deprecated
 
Package: ideal
Commit: e393d69573521bdf7c1025c9862417bcd09c46d2
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-12-18 23:04:23
Commit message:

 edited appveyor config
 
Package: ideal
Commit: f10c8e3f8369928d3c2a644c01882b370ef2d991
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-12-18 19:53:21
Commit message:

 updated travisCI config
 
Package: ideal
Commit: 3b61fd18ddf1892254d2e21b3d79b243cb1718a7
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-12-18 19:51:17
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: ideal
Commit: 09f85d5358def60ed521c7935f309bb875dcb90b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-04-04 14:58:38
Commit message:

 added small note for button, which in the vignette does not trigger any tour
 
Package: ideal
Commit: 51c5ecb8defb7a583082d2c36dd63f8f52f72828
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-04-04 14:36:38
Commit message:

 listing in the vignette now corrected
 
Package: ideal
Commit: 37019fc238e9e8530b7808010c530dd9d083dc43
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-04-04 14:27:20
Commit message:

 pkgs now listed, and with links, in the vignette
 
Package: ideal
Commit: 67689f29ee351179e9f221d288c8d3942661346b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-04-04 14:19:05
Commit message:

 reduced size by removing unessential screenshots, plus removed helper func for installing orgdb and txdb packages - instead of that, there is a small section explaining the same thing in the vignette
 
Package: ideal
Commit: 865bfd7c67b5b6a8d3cbde5c38f27b0287d53a20
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-04-04 12:04:51
Commit message:

 edited vignette to explain fallback solution in case of edger/limma/simple data frames
 
Package: ideal
Commit: 791b9a24dc11ded1dfe3e570b761354205bb0960
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-04-04 08:03:02
Commit message:

 now naming man and r code consistently
 
Package: ideal
Commit: 747992798cb42c35fd9a3ea216e3dc3930731d5d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-04-04 07:59:50
Commit message:

 addressing valerie's comments
 
Package: ideal
Commit: 2ea1bd63d099cc05aa698d7f8c0c9fe251a4626b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-27 08:11:29
Commit message:

 edited some code in the vignette to avoid timeout, plus edited appveyor conf to test also on release
 
Package: ideal
Commit: 9da2fc814888e507bc55b073f2e1e0b28f7ebaed
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-27 06:53:50
Commit message:

 version bump to trigger build
 
Package: ideal
Commit: d87e52429d8c0968aee206684534363e7d98bd55
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-22 20:05:01
Commit message:

 version bump, 0.99.1
 
Package: ideal
Commit: bd5b7179889b97824863dde326cf16d1e4e436df
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-22 20:03:09
Commit message:

 edited appveyor for 64bit
 
Package: ideal
Commit: 4090e2ca0e585572e5fd98eb2f1ced2169ad0275
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-22 13:35:58
Commit message:

 added last edited field to vignette
 
Package: ideal
Commit: 8c907cf329ca3210ed618b10ff9b6ed8bef87a05
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-22 12:28:33
Commit message:

 cutting down the vignette compilation time
 
Package: ideal
Commit: 75f321909ee4b50a1e5249d15bf868622a231505
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-22 11:05:02
Commit message:

 Version 0.99.0 - ready for Bioc submission
 
Package: ideal
Commit: b6ebd22a9b46ebbd997bfcd33369894e135ea1fc
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 22:18:47
Commit message:

 version 0.9.1, version bump after all changes
 
Package: ideal
Commit: 2d2e60fc81fe24345d0c5b8d23db4fe32854d0bf
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 21:52:20
Commit message:

 added practically  all of the downloadable objects, even more ready now :)
 
Package: ideal
Commit: 6a5c613fe4f82dfc3cf832607f0ba6822409ea40
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 17:53:00
Commit message:

 commented out unused code
 
Package: ideal
Commit: 674aa84f5632fce32b974b1babd15c886162e730
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 17:37:30
Commit message:

 added instructions as rendered from the rmd vignette, to md - keeping out the imgs and the html parts
 
Package: ideal
Commit: 3e4948b9d5d5f8772284d62cbaeb31fc596ebdb9
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 17:22:46
Commit message:

 only html vignette as output
 
Package: ideal
Commit: d222190e0965c81a9c7c53c16f8cc3495ce7db24
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 16:45:04
Commit message:

 edited section title after HB feedback
 
Package: ideal
Commit: ab695502bf242dc6a442704656efcf82edfab9ef
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 15:37:53
Commit message:

 version 0.9.0, quite close to submission. added all screenshots, vignette is now finalized. next: downloadable outputs
 
Package: ideal
Commit: e3c536a438342f6d38d4627aa4f9e39d01179776
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 13:17:41
Commit message:

 edited travis for codecov integration
 
Package: ideal
Commit: 04eefc3801b972a658c7e299cfe7993fce1745e6
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 13:14:52
Commit message:

 also added the quick viewer
 
Package: ideal
Commit: dbaf2cd3b95fae3ab09bab38b912656e31c08a36
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-21 10:40:31
Commit message:

 included basically all the text for the intro tours. some are not so fantastically positioned, but i cannot do that much about it..
 
Package: ideal
Commit: c64efe7208bcb7234763aba076195f722a9169d1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-20 22:28:16
Commit message:

 added all intros steps, plus some ids to the elements to make hints more readable since better connected
 
Package: ideal
Commit: 352ee34beace45b617865b0353349a198e6d2ceb
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-20 16:20:49
Commit message:

 v 0.6.2, also added func to setup all annos, plus fixed typo in readme
 
Package: ideal
Commit: aa75a9105ad256130d983b7fe0f90a60a407fc86
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-18 23:07:13
Commit message:

 working towards the tours, making them coded in dfs read from installed data. nice
 
Package: ideal
Commit: bd6651fe99083499f130b2d020ab5f585e0dbf94
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-15 15:43:01
Commit message:

 updated appveyor yaml
 
Package: ideal
Commit: e45d270ba44afbb1abe2ea8270d3b9312619567f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-15 13:28:42
Commit message:

 setting up updated version for travisCI
 
Package: ideal
Commit: 79fc91d132018b646a5fc3580e7eb53d2d95208f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-10 15:00:20
Commit message:

 v 0.6.0 - indeed using introjs. will think of how to make it effective, now not so far from very final version
 
Package: ideal
Commit: c648eb54e4b626401dc1474aed58f8e56541f48f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-06 11:00:04
Commit message:

 added textual help on data setup panel. specifies a little more in detail how the data should look like
 
Package: ideal
Commit: 781d4457557676a687745f0d5ad30419cf53b4c1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-05 23:32:25
Commit message:

 effectively transitioning to adopting rintrojs. need to decide what tours to offer, and how to code them. introbox or coded with ref to elements, need to ponder on both
 
Package: ideal
Commit: b9e2731de5bddff156fdd7cf539d3b60d8446f08
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-05 23:13:28
Commit message:

 added all help texts for bscollapse elements. better text in all other mds for the app
 
Package: ideal
Commit: 386616fcb8349db64cc965b6bc2943ea573b4a28
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-02 16:16:38
Commit message:

 finished first draft of text for vignette - only screenshots are missing. plus, edited a little the code and the docu
 
Package: ideal
Commit: 05e14b1d2ccbc58aaa6dbe2b2143df6d4227d3ed
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-01 22:51:14
Commit message:

 working on both the readme and the vignette, good point to snapshot
 
Package: ideal
Commit: 5dc6fe050796c7d3cb54e412880eda5ae7283f2c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-01 17:09:04
Commit message:

 slight edits to the report template
 
Package: ideal
Commit: 87a6122fae9e5b9b7340bf4d9c68f18d18c4a68d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-01 16:29:26
Commit message:

 edited the vignette, will use pcaExplorer as a basis
 
Package: ideal
Commit: 08090346d0eb892992111f3ee4cc207b3a19102d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-03-01 11:10:46
Commit message:

 added small sec for provided input in the report template
 
Package: ideal
Commit: 13b17b9b8a4aa559a44015c41e0e85341dd77468
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-02-14 11:17:02
Commit message:

 added nice backbone for template report, plus edited tab panel names
 
Package: ideal
Commit: acdf7d8076710f95c7017522ea72f3e9661c1d1b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-25 13:09:02
Commit message:

 added first implementation for heatmaps of go categories
 
Package: ideal
Commit: de9baab1f7ee6dd14baddfd95b17931bfaa68753
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-19 15:37:45
Commit message:

 restore first tests, will build upon this later
 
Package: ideal
Commit: fc15d6e6a05a95e95b33c64830f9690c948a90b2
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-19 14:45:39
Commit message:

 added documentation in roxygen comments for all funcs
 
Package: ideal
Commit: 6609c3233fb27c063f61e324762c3cee3d31f919
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-19 14:45:11
Commit message:

 one only maplot function with support for providing vector of genes to be plotted
 
Package: ideal
Commit: 9781fa460a1333d0b020761791cc39cc7f77549c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-19 14:44:23
Commit message:

 added maplot with custom list, plus commented PoP for bsplus with carousel - for images displaying features
 
Package: ideal
Commit: 7b01eb68b8f502bebd8147a3552cb00cafc5261f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-19 14:43:40
Commit message:

 exports correctly in the namespace
 
Package: ideal
Commit: a1a5df400a816f7cc0fcc3fefe538d1a772ccef8
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-19 14:43:14
Commit message:

 added documentation for exported functions
 
Package: ideal
Commit: d37e73ad2cc3ea2f4b4412f92674d6adbe334d29
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-19 14:41:52
Commit message:

 added example text files for sepguesser examples
 
Package: ideal
Commit: d0f89a73f58d2b0be023b12d89ea51dc628997a4
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-16 12:46:44
Commit message:

 added rug option for the ma plot
 
Package: ideal
Commit: ef9f125cfb6bf5c2a2c70522db610edcfcd2ed0f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-10 16:03:44
Commit message:

 removed footer where not necessary, there is already one at the very bottom
 
Package: ideal
Commit: 4b9054d73619488b378cfbfcdf376f10dd927792
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-10 15:40:46
Commit message:

 removed ideal_ ui and server, not using that structure anymore - for now :)
 
Package: ideal
Commit: a0b226b0eccb74c111905c1dd91f96cd01bede69
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-10 15:38:11
Commit message:

 moved the aux ideal files to the dedicated AUX_ideal folder, also in the devel folder
 
Package: ideal
Commit: 485f737db178b1339b21d883c8e2661c7d8a989e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-10 15:37:39
Commit message:

 topgo now in the depends. it looks kind of ugly but it seems to work just so afaik
 
Package: ideal
Commit: 3d9a7d83ec4f1266b957270c7bde0f012c5f758c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-10 14:55:11
Commit message:

 fixed heatmap brushing, fixed and made robust the goana with functions from AnnotationDbi. also putting now topGO explicitly called, maybe move to depends?
 
Package: ideal
Commit: 402e245e0b98a87ee9e31f7ed23735f3d63f15ec
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-10 13:50:51
Commit message:

 version 0.4.0 - massive moving of code to the one file, to avoid sourceing. coord cartesian instead of limits, gene box info now works correctly and with extra link. also correct display of exp design if dds provided
 
Package: ideal
Commit: 36b71e01c4ec8d9d49c94bed481b09cac4b7680e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-09 13:17:48
Commit message:

 added explicitly helpers.R file, plus using aes_string to avoide NSE notes
 
Package: ideal
Commit: 6f9df90f3e57483886b6044fbfdd25d8a48781b4
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-09 12:47:16
Commit message:

 gene symbols now taken correctly by unnaming the vector, plus on the way to replace ylim with coord_cartesian limits - this will only zoom in
 
Package: ideal
Commit: c7e06d29287c251eaf3925446223019f0c436388
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-09 12:46:11
Commit message:

 volcano plot edited as for plot ma
 
Package: ideal
Commit: 7f95e46d3f8f96d87fbbaf0aec95881c46c88d58
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-09 12:45:44
Commit message:

 backbone for entrez based retrieval of info
 
Package: ideal
Commit: 2da6ab4e0557cbedf6689779c62b1cd5e32303bb
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-09 12:45:00
Commit message:

 using base funcs where possible
 
Package: ideal
Commit: 3d4fd5888fb288cc323c3dc702203b2633311a1f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-09 12:44:32
Commit message:

 ma plots now more robust
 
Package: ideal
Commit: 194e08af11d54b2f14b79e20378f61f2fc6eb50c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-09 12:43:59
Commit message:

 reworked ggplotcounts
 
Package: ideal
Commit: 84bdf81185cb4c7fc8e589a32d259bc7080f2c1e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-06 14:33:03
Commit message:

 added biocparallel in the imports, and better code indenting
 
Package: ideal
Commit: 8aeb7b68608e4e93503557150f1636646769ab67
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-06 14:13:19
Commit message:

 edited NEWS
 
Package: ideal
Commit: 9ab1b95ce2439a0200649aefbe7781dc33ad2be1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-06 14:03:41
Commit message:

 renamed main func to ideal.R
 
Package: ideal
Commit: beb32d59f2042c4449d1f571eaa67c0514803804
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-06 14:01:48
Commit message:

 cleaned up R directory
 
Package: ideal
Commit: 7de1d7131fc40aeda7427de0a4afa8b53558bc60
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-06 13:58:00
Commit message:

 record all .R to proceed then to cleaning
 
Package: ideal
Commit: f9e96675d093428e9edb0a0b56243c079604240e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-06 13:45:24
Commit message:

 version 0.3.0 - quite some massive reorganization of the files, but now way clearer
 
Package: ideal
Commit: 526a804c88d24aa9ddb0a1540391a170183612ba
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-05 17:45:45
Commit message:

 added pkg documentation file
 
Package: ideal
Commit: 45eaa3207dce65d3692c1aab2380a18c1d2a446e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2017-01-05 14:44:45
Commit message:

 restructuring, and also added backbone for heatmap by go cat plot
 
Package: ideal
Commit: 3633f50d4f7d91cee6be3d51a99c504f3a94dea7
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-12-21 16:29:35
Commit message:

 added diagnostic plot of dispersion estimates with collapsible box
 
Package: ideal
Commit: fc6697c44fbc2ae3fbbb0264f19f747ed7e891cf
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-28 12:30:28
Commit message:

 couple of fixes and improvements. added couple of TODOs that i will try to address, and then also things such as writing the report in temp folder
 
Package: ideal
Commit: efaca32563927b97e46a03d6ba4154624a65c080
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-24 15:50:28
Commit message:

 v 0.2.0 - made a draft that can be installed. will anyway need to extend the documentation and so on, but at least I got a source pkg archive
 
Package: ideal
Commit: 604e1fa84a4fd6bb0b2783d12e4a9a768f44fb6f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-24 09:59:27
Commit message:

 cleaning up the code for ui.R. next for server.R
 
Package: ideal
Commit: 1eb0e267e1bf6a97b501aa1875ca3d0f8cdfeb0b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-23 13:12:12
Commit message:

 css trick to have page visualized more correctly - or more nicely
 
Package: ideal
Commit: df70f9cd3d7a7861e94fecc66d2bae43bf14d43e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-21 11:13:46
Commit message:

 added topgo & goseq for GSE, respective tables, structured layout for better column usage, and also changed order of pages for having welcome screen. TODO: separate welcome and instructions to have better content thematic separation. next: work on improvements list
 
Package: ideal
Commit: 4538dc8daa2f4c9ea13e3dd66cde386b904eaaac
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-16 15:22:18
Commit message:

 use sepguesser to guess the separator, seem to be a nicely working heuristics
 
Package: ideal
Commit: 4b6273db687e0255f635669c1eb66d3dd1e4e3be
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-16 14:28:31
Commit message:

 added some formatting via fluid rows, plus change of color for valueboxes, and added some progress indicators for long running operations
 
Package: ideal
Commit: da2d57600db1e83721aaec4a18d6b61373d43b56
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-11 16:48:27
Commit message:

 boxes for main page, and corresponding restructuring to logic server. plus, progress messages now display additional detail. footer expanded for the app
 
Package: ideal
Commit: 027f03199346affd4a2b89e728c3a6669751d7b1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-10 14:41:49
Commit message:

 added progress messages here and there. also, edited layout a little with more well panels. dropdown menu now has no green badge anymore, see what happens for the header if request is accepted
 
Package: ideal
Commit: df6a9a4f66082b44ee0984f19b9d8174061d8f59
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-04 15:32:55
Commit message:

 one step less to have 3 in total, better organization of widgets in tabs. will continue on this
 
Package: ideal
Commit: acc048954a5e300661aadc8277fa5653f606d381
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-04 14:32:39
Commit message:

 edited value boxes to display something in any case. plus, restructuring a little the layout: boxes will be used, collapsible if meaningful, plus will remove some verbatimetextoutputs
 
Package: ideal
Commit: e7cfd132848fda01496ed347443f3bfc9f9ae271
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-03 16:21:12
Commit message:

 added feature filter based on row sums or means, recreating dds object. also, put the brushed table in a box, collapsible
 
Package: ideal
Commit: 30b0862cbc870256ed0d4f9d6aa75aa0fe12f0dc
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-03 12:55:24
Commit message:

 added tab for counts overview: counts table, detected genes, scatter plot sampletosample
 
Package: ideal
Commit: 474f245875a17b1101c601961c100075f49ae327
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-02 17:04:01
Commit message:

 also conditional panel for the gene finder tab
 
Package: ideal
Commit: 0859c3ab149967b5c573156d27f04b84e9d4879d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-11-02 15:09:04
Commit message:

 added info boxes, check to show progress on the quick view in left panel, and also added the conditional panels to display or hide the content of the tabs in the subsequent steps if conditions are not met
 
Package: ideal
Commit: 15c1bcbd564c8a61b25a2192172bd4e80c9b7379
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-10-28 15:30:06
Commit message:

 clean up the results section, also added some widgets for the corresponding parameters. preliminarly inserted also the ihw function for filtering...
 
Package: ideal
Commit: 70bff2751bbb1ccbe0be9c146cb2aef590aa10ec
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-10-28 10:00:08
Commit message:

 better error handling messages, will go on and fix more on this
 
Package: ideal
Commit: 4cba7068fd5449c3d8b13fdae1fcacb71686bba7
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-10-27 15:55:33
Commit message:

 edited a little the startup func
 
Package: ideal
Commit: f6af5765534821425a857cdfdb60a4aa47d5d14e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-10-27 13:40:04
Commit message:

 newly done: infos for the species added for limma and ensembl; also exploring topgo as alternative to limma goana; for limma goana, added the genes that are associated to each; better playing around with progress bars - more will follow on that too
 
Package: ideal
Commit: da0c56b5e7bb479400a406a804fb45d8baea1cd9
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-10-26 15:37:26
Commit message:

 added quick implementation of volcano plot, will proceed with zooming and its annotated version, similar to maplot
 
Package: ideal
Commit: a0692d1ee821ca9a4880935a19fe5848ab343d9c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-10-26 14:29:27
Commit message:

 corrected many errors and converted them to informative messages, plus now things depend properly on reactive values rather than the ones that are passed
 
Package: ideal
Commit: 91e467ba42f9593fd01ae9af764a5a4b327ad745
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-10-26 11:20:34
Commit message:

 good point to take a snapshot: most features are there, will need some polish, but most of the things are there and hey they work :)
 
Package: ideal
Commit: b3dec02708df2296cc482de4e246a97a1c1388fc
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-10-25 14:36:40
Commit message:

 added retrieval of gene infos function, soon to be in the app also
 
Package: ideal
Commit: 6e0e0743241de6cdb8ad501dd309e9e4a12e1485
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-10-20 15:12:14
Commit message:

 added steps to guide the user in the data setup
 
Package: ideal
Commit: a33f578aed6df9a3c73ba1bcc9db5ddf4b3204f3
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-10-20 12:00:11
Commit message:

 quite something happened in between, good place to take a snapshot :)
 
Package: ideal
Commit: 42fcc4f40fcb9783e143ca0b9c72518a974cf8db
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-04-06 16:23:54
Commit message:

 backbone of the code is provided, with pcaExplorer as a template
 
Package: ideal
Commit: af2535d8b8ef13bcc10a417d131fdc0f3d6686e2
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2016-04-06 12:06:41
Commit message:

 initial commit, pkg skeleton created
 
Package: HelloRangesData
Commit: 050d6302321174348f67280be653c2f841a9e7a4
Author: larman <michafla@gene.com>
Date: 2018-01-19 16:32:18
Commit message:

 use BiocStyle::latex()
 
Package: BiocWorkflowTools
Commit: 2e1386c2dd99f697e442fd1245a5e8bb859f2a61
Author: aoles <andrzej.oles@gmail.com>
Date: 2018-01-19 16:16:17
Commit message:

 Update call to BiocStyle format function
 
Package: multiClust
Commit: 5dec139647258765dc2f10fdb9c6478d4d0fa563
Author: nlawlor <nathan.lawlor03@gmail.com>
Date: 2018-01-19 16:08:17
Commit message:

 Update DESCRIPTION

Update version to odd number 
Package: ELMER
Commit: 90ba0685db7f547f39664d697b7943976d5e112e
Author: tiagochst <tiagochst@gmail.com>
Date: 2018-01-19 15:53:24
Commit message:

 update
 
Package: multiClust
Commit: d4d80ec8410683c17b6eea0106815fb1006802f5
Author: nlawlor <nathan.lawlor03@gmail.com>
Date: 2018-01-19 15:44:04
Commit message:

 Update DESCRIPTION 
Package: multiClust
Commit: d0f6748f23f162adf3cb0e1b800da3553e44216e
Author: nlawlor <nathan.lawlor03@gmail.com>
Date: 2018-01-19 15:24:19
Commit message:

 Delete GSE2034_Breast.SD_Rank.ward.D2.Fixed_Probe_Num.Fixed_Clust_Num.png 
Package: multiClust
Commit: 89859af74e20bbfa81fc7418cc831359611e93e1
Author: nlawlor <nathan.lawlor03@gmail.com>
Date: 2018-01-19 15:24:08
Commit message:

 Delete GSE2034_Breast.SD_Rank.ward.D2.Fixed_Probe_Num.Fixed_Clust_Num.pdf 
Package: mtbls2
Commit: 58492363ae01bd560e973509b4804ef7a4c512e8
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2018-01-18 21:26:51
Commit message:

 Sync github and bioc upstraem
 
Package: mtbls2
Commit: 62ae403eca98d085e63e6ce5f237b0b3afe59441
Author: Steffen Neumann <sneumann(at)ipb-halle.de>
Date: 2015-05-25 12:08:31
Commit message:

 remove that brief script for optimising xcms
 
Package: mtbls2
Commit: 22c85d85772119dd5939ecccd4af3c2755079c2e
Author: Steffen Neumann <sneumann(at)ipb-halle.de>
Date: 2015-05-25 12:08:12
Commit message:

 brief script for optimising xcms
 
Package: mtbls2
Commit: 0b6bde8330675b0ba65fcdbe072cbdb07538b12d
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-05-23 22:31:02
Commit message:

 fixed biocViews
 
Package: mtbls2
Commit: f541a1c053519550350e6cd940e143138d1910c9
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-05-23 22:09:29
Commit message:

 Uploading to BioC tracker
 
Package: mtbls2
Commit: 77819c0b45ad7e68c6b7ca1ae5e38c20a7240db1
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-05-23 21:57:32
Commit message:

 ignore generated files
 
Package: mtbls2
Commit: 05b7660be7e11ff45fac1d7ce904ab34e8bd29a5
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-05-23 21:55:43
Commit message:

 merged bioC branch
 
Package: mtbls2
Commit: 1268450502ade1dc69658346374de3cad2acd312
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-05-23 21:42:56
Commit message:

 use dontrun in example, closes #10
 
Package: mtbls2
Commit: 3a3992bb6ce2b079557e2813c4513c6ec13f4d7c
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-05-23 21:42:12
Commit message:

 added rstudio project file to buildignore, closes #12
 
Package: mtbls2
Commit: 1e4373a36971e119dc665600b68e21b132360a5a
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-05-23 21:31:39
Commit message:

 Split lines in DESCRIPTION, closes #9
 
Package: mtbls2
Commit: 8ecfb503816c9c57c28f8ec0eb335f4ac6742c94
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-05-23 21:29:20
Commit message:

 suppress warnings in plotPsSpectrum() coming from CAMERA, closes #8
 
Package: mtbls2
Commit: 4fd76e3e6740f741433e955dce7dddb234050dd9
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-05-23 19:31:32
Commit message:

 Add versioned Risa dependency, closes #6
 
Package: mtbls2
Commit: 1b77a7f97c13c7f029703056450fe65ee60a1996
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-03-18 09:06:07
Commit message:

 passes check at BioC
 
Package: mtbls2
Commit: 538c86d863535b810d743d590b1596d044bd8693
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-03-16 15:41:42
Commit message:

 More attempts to debug BioC SinglePackageBuilder failures
 
Package: mtbls2
Commit: 80dbb727033da6a6aa7ca8a0207205243a18e831
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-03-05 23:14:18
Commit message:

 cleanup leftover files
 
Package: mtbls2
Commit: 427438323e591e1aeeb5bd9fed4ebca43a853d6c
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-03-03 16:31:21
Commit message:

 remove some dependencies
 
Package: mtbls2
Commit: 35686aa7231abbd148cf6f22b334a8041063fa5e
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-02-16 13:55:33
Commit message:

 Fixed versioned depends, reduced number of files (and thus runtime) in vignette
 
Package: mtbls2
Commit: 880cecc01dc6b2b3d9901b55830ded935e02f0d4
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-01-30 09:07:25
Commit message:

 Added QC plots, requires xcms 1.43.1
 
Package: mtbls2
Commit: 7b95497fcd989e2beb32b950adb5f5b24351ea64
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-01-21 10:10:10
Commit message:

 Fix vignette building, now vignette("MTBLS2")
 
Package: mtbls2
Commit: 5f85daf1468dec053f97806c40f5d95a7bef9aa7
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2015-01-20 23:05:02
Commit message:

 First go at package-ifiying mtbls2
 
Package: mtbls2
Commit: 2e5d7768a15ff61152d3766881d4cf56e873aac1
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2014-09-29 08:19:19
Commit message:

 remove hardcoded path to ISA directory, use current working directory instead
 
Package: mtbls2
Commit: 9ba3d81a6c409d63db4162794120925f1f7b19ac
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2014-03-18 10:23:35
Commit message:

 Added Rmd version of Vignette
 
Package: mtbls2
Commit: 617174f313f43931d835ddde0c475468f543de84
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2014-03-18 09:29:06
Commit message:

 rerun MTBLS2 with different parameters
 
Package: mtbls2
Commit: 6343432a160bd7b1530344940b6b39b991b0e6e1
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2014-03-18 09:28:04
Commit message:

 reasonable mzTab files
 
Package: mtbls2
Commit: 98e39208c6212dd8bda4358f4e34512a65918087
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2014-03-04 16:33:36
Commit message:

 First skeleton for exporting mzTab
 
Package: mtbls2
Commit: 06c69f2fc1a9c5bbb76493cfb2143377adc86324
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2014-01-14 07:54:41
Commit message:

 Before upgrading to MTBLS config 2013
 
Package: mtbls2
Commit: cb0074e7f537820987c8a03cfc2801a2947573b4
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2013-07-17 07:51:53
Commit message:

 First full mzQuantML export for MTBLS2
 
Package: mtbls2
Commit: 3a9d61e82c709d4aaec89cb9f937015e7ba04b08
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2013-07-16 15:19:46
Commit message:

 Add forward references between SmallMolecule and Feature
 
Package: mtbls2
Commit: a20d7c5272bb974c4779a53890993208ae9fd55e
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2013-07-15 22:34:28
Commit message:

 Generated mzQ for faahKO
 
Package: mtbls2
Commit: e460248766b21c28914fbb5c3f9011c4a7f7ddb3
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2013-07-15 22:33:22
Commit message:

 Now with DataMatrix
 
Package: mtbls2
Commit: be527e905656c1772fbe4ae83c2985c3e9ecd89c
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2013-07-15 21:19:55
Commit message:

 write proper FeatureLists
 
Package: mtbls2
Commit: 54ba70f688bcec775df48512cc14855443280201
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2013-07-15 09:34:49
Commit message:

 include 
 
    
  
    
Package: mtbls2
Commit: b3802a2d1c18dfd25caa9b223b2ad0ab3d2a3771
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2013-07-13 20:44:00
Commit message:

 successfully validates, but no data yet
 
Package: mtbls2
Commit: b96a8f528139ee4829195daee4436ccf438c4539
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2013-07-12 08:09:19
Commit message:

 validates with xmllint agains mzQuantML_1_0_0.xsd
 
Package: mtbls2
Commit: 690536a1e1cdbfd2d733a03ba37cf7f408a391f9
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2013-03-15 22:00:05
Commit message:

 header for mtbls2, minimal set of quantification and featurelists
 
Package: mtbls2
Commit: d5cfc72dbb36a400a15a6e2b231210381fa98184
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-09-22 13:05:06
Commit message:

 Added bibliography, polished text
 
Package: mtbls2
Commit: d5185394d7e8219d54ee6003287ba84a0ed8a401
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-09-22 11:35:31
Commit message:

 fixed some more line length thingies,
removed comment
 
Package: mtbls2
Commit: 4525ec620ca11f9fc725cc6f7bf965801d4b0ff2
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-09-21 15:44:13
Commit message:

 re-leyout vignette to fit lines, final assignment in update() avoids full printing of whole ISA object
 
Package: mtbls2
Commit: 2e0a082ffd0f18d4748022a781b1540855c8678f
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-09-21 11:56:36
Commit message:

 update authors list, hide library preload
 
Package: mtbls2
Commit: 7c8cc3419e41cf71f9a9035f6244493c36a3e5db
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-08-31 13:19:55
Commit message:

 updated
 
Package: mtbls2
Commit: a4de8f428ba9f7b185484385871556f90f8544ec
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-08-31 09:36:48
Commit message:

 Merge branch 'master' of github.com:sneumann/mtbls2
 
Package: mtbls2
Commit: deb8c3ad7d059c8bf77d78ce786f1f7bb174649c
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-08-31 09:36:43
Commit message:

 some wording
 
Package: mtbls2
Commit: 05384a0ebac98aee27538a5d559c1dbfc3e811d2
Author: sneumann <sneumann@ipb-halle.de>
Date: 2012-08-31 09:19:56
Commit message:

 Merge pull request #5 from agbeltran/master

Changed a variable name 
Package: mtbls2
Commit: f357e60bd73af64e84d5930a7a9ffd20c63c42d6
Author: Alejandra Gonzalez-Beltran <alejandra.gonzalez.beltran@gmail.com>
Date: 2012-08-30 15:09:54
Commit message:

 Updated to latest Risa code
 
Package: mtbls2
Commit: 30fbf53375aee2e81668182ec927646ae01127a7
Author: Alejandra Gonzalez-Beltran <alejandra.gonzalez.beltran@gmail.com>
Date: 2012-08-02 12:28:06
Commit message:

 Changed function name from addAssayMetadata to updateAssayMetadata
 
Package: mtbls2
Commit: fd9746f0aa99a455f50a80fa62bbaa56bd88ef44
Author: Alejandra Gonzalez-Beltran <alejandra.gonzalez.beltran@gmail.com>
Date: 2012-07-31 20:24:14
Commit message:

 Changed variable name
 
Package: mtbls2
Commit: ed72c1f15c486ecf124c27acfb7682e1a0b0e59e
Author: sneumann <sneumann@ipb-halle.de>
Date: 2012-07-30 11:44:07
Commit message:

 Merge pull request #4 from agbeltran/master

Changed package name from ISA2R to Risa 
Package: mtbls2
Commit: ed0d5b25118ed9588fcea6f225bce44111b35440
Author: Alejandra Gonzalez-Beltran <alejandra.gonzalez.beltran@gmail.com>
Date: 2012-07-30 10:43:37
Commit message:

 Changed package name from ISA2R to Risa
 
Package: mtbls2
Commit: 23192a062e6065d32ff54d457f1de681e10cb190
Author: sneumann <sneumann@ipb-halle.de>
Date: 2012-07-26 17:38:05
Commit message:

 Merge pull request #3 from agbeltran/master

Completed vignette with code to augment ISATab assay file after analysis and update process function name 
Package: mtbls2
Commit: 02847a5e63f7ac8978d82eb9e835c53b9a6bf752
Author: Alejandra Gonzalez-Beltran <alejandra.gonzalez.beltran@gmail.com>
Date: 2012-07-26 16:34:31
Commit message:

 Update to latest ISA2R version: changed function name to processAssayXcmsSet; added functions to add metadata back to the assay file and write the updated assay file to disk
 
Package: mtbls2
Commit: 3df45896cc65b5d9639ddf29ac352c92badd090f
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-07-25 19:09:15
Commit message:

 Improve (La)Text part
 
Package: mtbls2
Commit: b811bc1371acdcef39cd9bd6a672c44f6b313f17
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-07-25 13:09:05
Commit message:

 Some more text in the vignette
 
Package: mtbls2
Commit: e65984a5c6dbbb2d50275625e1cce51bf881581a
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-07-24 20:44:06
Commit message:

 remove unused library, and add temporary hack to speed up vignette (requires xcms >=1.33.14)
 
Package: mtbls2
Commit: bbe1bc7796c96fc78de6aacf46d88aa5886757b5
Author: sneumann <sneumann@ipb-halle.de>
Date: 2012-07-24 19:09:54
Commit message:

 Merge pull request #2 from agbeltran/master

Pull request with updates to current ISA2R code 
Package: mtbls2
Commit: 8fdd0ffb688ba2faf0778f908388b862aaba514b
Author: Alejandra Gonzalez-Beltran <alejandra.gonzalez.beltran@gmail.com>
Date: 2012-07-24 18:57:09
Commit message:

 Updating vignetted to the latest ISA2R code
 
Package: mtbls2
Commit: 0c3ff8f30f795961f12efda74f8feef3154b21cb
Author: sneumann <sneumann@ipb-halle.de>
Date: 2012-07-24 17:09:25
Commit message:

 Merge pull request #1 from proccaserra/patch-1

Fixing typo in header: s/Organisim/Organism/ 
Package: mtbls2
Commit: 8d4259ea31d1bff99ba36e51c284c123279ee0fb
Author: Philippe <proccaserra@gmail.com>
Date: 2012-07-24 15:25:22
Commit message:

 Fixing typo in header: s/Organisim/Organism/ 
Package: mtbls2
Commit: 6f50fde271022e13fb4f8aee99668bdf977b8d5a
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-07-24 14:50:43
Commit message:

 cleaned up MTBLS2.Rnw vignette
 
Package: mtbls2
Commit: 2f8f81f2e543203ac528dbe9ad996640b24d78d5
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-07-24 12:37:14
Commit message:

 Merge branch 'master' of github.com:sneumann/mtbls2
 
Package: mtbls2
Commit: 212120eb578b09f27921743dd3eb03200b84f3bb
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-07-24 12:36:24
Commit message:

 Clarify that this is only a reduced data set
 
Package: mtbls2
Commit: e0ec59f01c8385ffc61421f4366ab79f06399292
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-07-24 12:33:46
Commit message:

 Also after workshop
 
Package: mtbls2
Commit: 05247914602e76f7d05cc1b9fb6c18ee50f5ff18
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-07-24 11:49:44
Commit message:

 commit after the Workshop
 
Package: mtbls2
Commit: 4f5abed520519f2cd447b15669363308643eb7c9
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-05-22 09:33:53
Commit message:

 empty strings for zeros
 
Package: mtbls2
Commit: d895025dc642433acfe410b3d7ee6cde1af0fdde
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-05-22 09:19:56
Commit message:

 re-export without zero scores
 
Package: mtbls2
Commit: 92c3aad8ff23168f9869725760dfe67a2b943905
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-05-22 09:16:46
Commit message:

 use official supplemental filename
 
Package: mtbls2
Commit: 42774d549bbe37294b0655273d7c26e2bc4edc58
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-05-22 06:47:10
Commit message:

 removed numbered N/A
 
Package: mtbls2
Commit: ad3c03eec4a6093ba55bef982d29af4ca8b6a353
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-05-10 14:38:41
Commit message:

 Import Steffen's Version of MTBLS2
 
Package: mtbls2
Commit: abd90c804905094bf151f34429cd86c59c96c695
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2012-05-10 14:36:25
Commit message:

 first commit
 
Package: ATACseqQC
Commit: fc7b0bcee10cb7e7f6208b27aa6d1dc483eff4b0
Author: Jianhong Ou <jianhongou@riboimager.research.duhs.duke.edu>
Date: 2018-01-19 15:14:14
Commit message:

 remove SRAdb from dependence because it is not support WINDOWS.
 
Package: ATACseqQC
Commit: abbdefd52a00bf272e1c426e548f7a01aa40e507
Author: jianhong <jianhong.ou@gmail.com>
Date: 2018-01-18 17:36:47
Commit message:

 remove SRAdb from dependence
 
Package: ATACseqQC
Commit: 0d2429d64c6b8b9269d282fd93b5547ac7af5b2c
Author: Jianhong Ou <jianhongou@dhcp-152-16-223-142.research.duhs.duke.edu>
Date: 2018-01-16 22:18:56
Commit message:

 fix a bug in distanceDyad
 
Package: ATACseqQC
Commit: 4133d5470fb0cc6ea48df9a32b02a59de8b8dfc9
Author: Jianhong Ou <jianhongou@dhcp-152-16-223-142.research.duhs.duke.edu>
Date: 2018-01-16 22:04:15
Commit message:

 update vPlot.
 
Package: brgedata
Commit: a0173f3e1c32fbc50bad83805e5ece0850c26955
Author: Carlos Ruiz <yocra3@gmail.com>
Date: 2018-01-19 15:12:02
Commit message:

 Solve problem with dependencies. Bump version
 
Package: Hiiragi2013
Commit: 1e7d7d4a00efed12a15cd0896880cd1f9fd97e37
Author: aoles <andrzej.oles@gmail.com>
Date: 2018-01-19 14:56:40
Commit message:

 Update call to BiocStyle format function
 
Package: BiocStyle
Commit: 18c0e098854fc87a10e760cf16a5dba5c29c2b18
Author: aoles <andrzej.oles@gmail.com>
Date: 2018-01-19 14:49:31
Commit message:

 version 2.7.8
- add 'relative_path' argument to 'pdf_document' (closes https://github.com/Bioconductor/BiocStyle/issues/32)
- fix message for defunct functions
 
Package: qpgraph
Commit: 4cb368a8237f8ac2b5cf9975c192372754ce78a6
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2018-01-19 14:30:24
Commit message:

 Added argument marginalization argument to qpPathWeight().
 
Package: apeglm
Commit: 9cfa048094eb6903add57d9bad86a3701da75ca6
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-01-19 14:11:00
Commit message:

 working on methode nbinomR
 
Package: rDGIdb
Commit: c2f0d305133799f1be342b7028fbd3813c37c6ef
Author: Thomas Thurnherr <texblog@gmail.com>
Date: 2018-01-19 13:07:20
Commit message:

 Version bump of devel according to guidelines
 
Package: esetVis
Commit: 4242096d7434fefe05166dbe969f2ffb09be18cf
Author: lcougnaud <laure.cougnaud@openanalytics.eu>
Date: 2018-01-19 12:45:04
Commit message:

 increase version higher than internal repository
 
Package: BiocStyle
Commit: 1f32d5af093816a0721ccbee100fe180d36c9db7
Author: aoles <andrzej.oles@gmail.com>
Date: 2018-01-19 09:51:54
Commit message:

 version 2.7.7
- some further cleanup to package code and documentation
 
Package: Biostrings
Commit: 1eca6e2c4c3405cdcb6ba3fd8a83a04a9706596d
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-19 05:13:39
Commit message:

 minor tweak to "show" method for PairwiseAlignments objects
 
Package: cytofkit
Commit: 2a9fac33d2d9140fd68629063f281c3bab3d8be3
Author: MattMyint <matthewmyint1993@gmail.com>
Date: 2018-01-12 09:34:50
Commit message:

 global scaling fixes
 
Package: PureCN
Commit: f95e754ce43912f93bc8ecbea67b78a9c954d38a
Author: lima1 <mriester@gmx.de>
Date: 2018-01-19 01:42:42
Commit message:

 Throw exception when normalDB is outdated.
 
Package: PureCN
Commit: ec6f11d9108b33e000a1229b8160ed60189eaaf0
Author: Markus Riester <markus.riester@novartis.com>
Date: 2018-01-18 18:28:37
Commit message:

 Replaced voom normalization with GATK4's tangent normalization (https://github.com/lima1/PureCN/issues/18)
 
Package: PureCN
Commit: 36ccafcffe32d7890e7afaf8be927652918c4cfb
Author: Markus Riester <markus.riester@novartis.com>
Date: 2018-01-16 04:56:56
Commit message:

 Added support for GATK4 CollectFragmentCounts in readCoverageFile.
 
Package: Biostrings
Commit: 750f92a0fcaef5fa998876db628ac3ca091806d9
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-19 00:19:08
Commit message:

 Add the alignedPattern() and alignedSubject() getters for extracting
the aligned patterns and subjects from a PairwiseAlignments object.

Unlike aligned(pattern()) and aligned(subject()), alignedPattern()
and alignedSubject() do NOT trim globally aligned sequences. The
fact that aligned(pattern()) and aligned(subject()) trim the deleted
extremities of globally aligned sequences as been a nuisance and a
source of complain for many years. The addition of alignedPattern()
and alignedSubject() is a response to this.

The "show" method for PairwiseAlignments objects now uses
alignedPattern() and alignedSubject() internally to display the
untrimmed globally aligned pattern and subject.

The "as.character" method for PairwiseAlignmentsSingleSubject objects
was modified to do as.character(alignedPattern(x)) so does not trim
globally aligned patterns anymore.
 
Package: GENESIS
Commit: e9f54c813269922bb6e6a75c549c8f0ca4e8f64d
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2018-01-18 21:19:58
Commit message:

 version bump
 
Package: GENESIS
Commit: fdd56eb39b340a337f9a48eb365e96a0e1754ebd
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2018-01-18 21:17:16
Commit message:

 fix missing file links in man pages
 
Package: S4Vectors
Commit: 60e9d32bda4617ad9362dc81fb4b1fce6eae2db2
Author: Michael Lawrence <michafla@gene.com>
Date: 2018-01-18 21:16:39
Commit message:

 prepare_objects_to_concatenate() in .concatenate_vectors()
 
Package: BiocCheck
Commit: cdfffcd49b8e2abf0f7c758c98b6a5a4743fcc62
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-01-18 20:39:39
Commit message:

 version bump & contributor
 
Package: BiocCheck
Commit: 1c8cdf3d4bdd152fe558cee4b8883aa37d026ea6
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-01-18 20:39:24
Commit message:

 remove unused code
 
Package: BiocCheck
Commit: 65bd6bffba5b7c32d118e4a977919d4a9db186ac
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-01-18 20:38:52
Commit message:

 parse only .R files for library(), sapply(), etc.
 
Package: CrispRVariants
Commit: b9b733e5fc94392f71bf659545ca94750d23dc8d
Author: Helen Lindsay <helen.lindsay@uzh.ch>
Date: 2018-01-18 20:28:19
Commit message:

 Easier specification of plotting order
 
Package: chimeraviz
Commit: c924e0d3f3e484cc854b4b92b9deb8ba05a525e2
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2018-01-18 20:02:09
Commit message:

 Bump version to trigger build
 
Package: chimeraviz
Commit: 276e38cfc319c6adae0d5979ddd8e8ca6c54d9a1
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2018-01-13 17:26:29
Commit message:

 Support the latest output version from STAR-Fusion
 
Package: BiocFileCache
Commit: ca1a4824d895a345a5fceaec93a53687d37313dd
Author: lshep <shepherl@gmail.com>
Date: 2018-01-18 19:39:58
Commit message:

 Fix a test

   - access time changed because of access, compare all values but this
 
Package: GWASTools
Commit: e57a2df7f571fe3518020deb73c883c108920031
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2018-01-18 19:25:03
Commit message:

 version bump
 
Package: GWASTools
Commit: 343ea244ce303a7eed906b0c39403ad78da3499e
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2018-01-18 19:20:30
Commit message:

 fix links to other packages in man pages
 
Package: XVector
Commit: 31f780777e421d223eca259641098f228818219d
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-18 17:37:28
Commit message:

 The "concatenateObjects" method for XVector objects must set the 'offset'
slot of the returned object to 0L.
 
Package: BPRMeth
Commit: bf3691bf16d9bee349159a77c5e62ee3540d9f4f
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-18 17:25:07
Commit message:

 Bump version
 
Package: BPRMeth
Commit: c221ae878a16678f7d77820e4d481aa13ac710f3
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-18 17:24:36
Commit message:

 Fix VB implementation numerical issue with Gamma priors
 
Package: BPRMeth
Commit: cdc84c0040a245df3193b84bebdefa19a3c0c615
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-18 14:34:51
Commit message:

 Minor changes in VB implementation
 
Package: annotatr
Commit: c4b4858ef649a5a9ac447d3171f5b33b01d7599d
Author: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Date: 2018-01-18 16:34:12
Commit message:

 Suggest TxDb and OrgDb packages

* This saves users some space with package installations.
* The requireNamespace() approach is taken with an error indicating which package needs to be installed. 
Package: annotatr
Commit: fbae1e0b3940fd496b84e1fc23b3be6a0176a13e
Author: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Date: 2018-01-18 16:06:57
Commit message:

 Bugfix: For builtin_ functions, need to use annotatr::

* This solves a problem I didn't originally understand that was posed in the Bioc support forums. 
Package: ndexr
Commit: cde4facdd0f254bfe338f8dd111e5f3d2450d703
Author: Florian J. Auer <florian.auer@med.uni-goettingen.de>
Date: 2018-01-18 15:48:39
Commit message:

 fixed build error caused by 'metadata:properties' now being optional
 
Package: qpgraph
Commit: 791f057d9cc4815fda0d5c36189fbf9d559ae2f2
Author: [rcastelo] <[robert.castelo@upf.edu]>
Date: 2018-01-18 15:41:45
Commit message:

 Added a qpPathWeight-dspMatrix method.
 
Package: rhdf5
Commit: 762af749e83d5a1c9fb14b0cfa828f82429b4621
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-01-18 15:30:24
Commit message:

 Adding platform specific print statments for 64bit ints.
 
Package: rhdf5
Commit: 8530a8fa40125d48875f01c6721d3dee79a1dcef
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-01-18 13:30:16
Commit message:

 Experiment with windows specific print statements
 
Package: rhdf5
Commit: 5cef56e10152469253a692a4f1b8ed4ad3222f2a
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-01-12 16:33:35
Commit message:

 Added tests for h5closeAll()
 
Package: ndexr
Commit: 2d8a91afcb1ec26fa15efae4ce2fa161113b6a14
Author: Florian J. Auer <florian.auer@med.uni-goettingen.de>
Date: 2018-01-18 15:16:45
Commit message:

 fixed build error caused by 'metadata:properties' now being optional
 
Package: omicsPrint
Commit: dba2cdcbfcb98a152e8947486aa360d403db6d52
Author: DavyCats <davycats.dc@gmail.com>
Date: 2018-01-18 09:10:16
Commit message:

 handle NA in phasing
 
Package: BiocFileCache
Commit: 51c044801d26f8bbca54df97fac9cb16c72dfc28
Author: lshep <shepherl@gmail.com>
Date: 2018-01-18 14:01:33
Commit message:

 Fix .httr_get_cache_info

  - updating to return etag and last_modified time, need to update error patch to have same structure
 
Package: BiocFileCache
Commit: e58d870545543c5e7dcd59f320a353aa95ecd423
Author: lshep <shepherl@gmail.com>
Date: 2018-01-18 13:10:48
Commit message:

 bfcinfo and bfcquery display full rpath

   - rpath will still be stored as relative but display fully
 
Package: BiocFileCache
Commit: 53fd3d69e33397c825e824a88ac4c034a7a4356a
Author: lshep <shepherl@gmail.com>
Date: 2018-01-18 12:14:54
Commit message:

 Add section in vignette

   - for best practice when using within a package
 
Package: BiocFileCache
Commit: bfda0df8a7eb0244f3e2cd431afcf8ef1d2b71cf
Author: lshep <shepherl@gmail.com>
Date: 2018-01-18 11:55:42
Commit message:

 Merge branch 'convertFromDF'
 
Package: BiocFileCache
Commit: 0b722783985635b1ade39c0903df366500a530ba
Author: lshep <shepherl@gmail.com>
Date: 2018-01-16 19:59:32
Commit message:

 Add function makeBFCfromDF

  - converts a data.frame to a BiocFileCache object
 
Package: BiocStyle
Commit: c070ef71d4a46b96892cec6f16ff4fc1cb593dfa
Author: aoles <andrzej.oles@gmail.com>
Date: 2018-01-18 12:01:59
Commit message:

 version 2.7.6
- switch documentation to roxygen2
 
Package: oposSOM
Commit: dd2904e6a5472d358fd89c25021d148ed06c63cb
Author: hloefflerwirth <wirth@izbi.uni-leipzig.de>
Date: 2018-01-18 10:15:53
Commit message:

 oposSOM 1.17.1: Crucial fix for unstable ensembl database availability.
oposSOM 1.17.0: Bumped version number by Bioconductor + few minor changes.
oposSOM 1.15.3: Bugfixes for Chromosome Expression Plots and PCM.
oposSOM 1.15.2: Bugfixes for Chromosome Expression Plots and ICA.
 
Package: synapter
Commit: bd1c294deaac81d2daab37f5c8986b9777cb15e1
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-17 20:43:30
Commit message:

 Fix charges argument in .requantifyTheoreticalDistribution
 
Package: synapter
Commit: a18bcd4af745c0e4cb3e986d81b307ee99b457dd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-17 20:31:25
Commit message:

 Use  instead of
 
Package: synapter
Commit: e57f0aa8af33f6b0b006c7143deb0fb24722ab62
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-17 20:24:02
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: synapter
Commit: 68c480d1ceeea8ff71c99e68f45b8b96c49e0a2b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-05-29 19:03:15
Commit message:

 bump version and update NEWS.md
 
Package: synapter
Commit: b41a33d114d761b1833ee2644840cf86487f38da
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-05-29 18:55:48
Commit message:

 partly revert 95f4094, because MSnbase:::utils.applyColumnwiseByGroup is gone
 
Package: synapter
Commit: 331e3ee74844330b1c16e4d030efdfc5797ac397
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-19 11:08:12
Commit message:

 remove travis badge for 2.0 branch [ci skip]
 
Package: synapter
Commit: 6613b5bc6032f7b02df0536bce5bf410ea5b0cf5
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-19 09:17:34
Commit message:

 update show,MasterPeptides to check of there's a fragmentlibrary slot before trying to access it
 
Package: synapter
Commit: 8a5c39544564924eb84885039beb17a9b0ba33e3
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-11 16:04:58
Commit message:

 add news back
 
Package: synapter
Commit: 9dc214408847f7a388af0b72f16030024f369113
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-11 15:08:16
Commit message:

 fix news version
 
Package: synapter
Commit: d8e263bd833c0ede484d623b29b770c9f770e867
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-11 15:06:55
Commit message:

 only news md
 
Package: synapter
Commit: a402debc5b3e5e306764df58ed9920a96113842e
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-11 15:05:46
Commit message:

 update news
 
Package: synapter
Commit: 5bc07eaf28125f615227751bdbf0787ea4e1256e
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-07 07:02:27
Commit message:

 add files to inst/doc to fix vignette build
 
Package: synapter
Commit: 9444fa764f09ae35faaf71f46fd38f27a4ece37b
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-06 15:52:39
Commit message:

 add/update links to github page
 
Package: synapter
Commit: 9cf05d77c49ed3f120a0fbf1aea81a270365a262
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 11:10:23
Commit message:

 add unit test for .cumsumIntensities
 
Package: synapter
Commit: 4bca1ebe8c653249ab3163d72f7de81dadedf1e9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 11:03:56
Commit message:

 add unit test for filterEmptyFragments
 
Package: synapter
Commit: 177ae8be4d084a5aa08a232253e57876319f4020
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 10:52:34
Commit message:

 add unit tests for .getSpectrum and .sumAllPeakCounts
 
Package: synapter
Commit: 5812a7877ffa43f99e745e914b865fe1e6e13bbc
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 10:07:58
Commit message:

 add @noRd to avoid warning about invalid documentation path
 
Package: synapter
Commit: b08e483b5325cc705d82cab0a089ed59c4eae366
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 10:03:32
Commit message:

 add docs/ directory; closes #132
 
Package: synapter
Commit: 95451aa350a9cd799dee544732540a812726f5aa
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 09:49:32
Commit message:

 add branch-specific gitignores as described at https://lgatto.github.io/branch-specific-gitignore/
 
Package: synapter
Commit: 9eb9d03510b5d3c28ddfe3f4a018f25cb02281a7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 09:13:55
Commit message:

 remove biocView GUI
 
Package: synapter
Commit: eca574414cf639219552a1cf6b95a9e3fb41acf0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 08:57:01
Commit message:

 avoid NOTE: \examples lines wider than 100 characters
 
Package: synapter
Commit: 608ba0e0fcd3e42cdd781c607e5ead61330dd013
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-04 10:36:35
Commit message:

 remove results="asis"
 
Package: synapter
Commit: 6a960aa1f571e107af672a9999bd636d8b36c59c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-04 09:36:44
Commit message:

 use synobj2RData() to access synobj2
 
Package: synapter
Commit: 05bd448142c1f7d854a67509bb3b2f1b0b26802f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-04 09:32:19
Commit message:

 Revert "replace synobj2 by synobj3"

This reverts commit 91f6a71e741ef08ebfaa3cb0859b7525fedab3f2.
 
Package: synapter
Commit: f73e92a2107723025f35ee47f2b290544b179f62
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-04 08:34:00
Commit message:

 Merge branch '2.0' of github.com:lgatto/synapter into 2.0
 
Package: synapter
Commit: 8c33fe29d8f509e4a47ff8c9979fe229a62def81
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-04 08:32:12
Commit message:

 suggest synapterdata 1.13.2
 
Package: synapter
Commit: aa512d0381755c57c2a71cdf4a439db25bb32a7c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-03 22:54:45
Commit message:

 Merge branch '2.0' of github.com:lgatto/synapter into 2.0
 
Package: synapter
Commit: b6bd69c3fede570e6f5d3259aa701a4cf7eddd5e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-03 22:54:37
Commit message:

 limit output to the first 13 lines
 
Package: synapter
Commit: 7771324d6deea55669d14d4deb6a63cfd2bdc11b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-03 22:13:01
Commit message:

 adapt mergeMaster unit test to new span.rt/span.int arguments
 
Package: synapter
Commit: 7e7d81e266d38da1cd05d05019eb19d3e1fa6cab
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-03 22:03:09
Commit message:

 fix class version assignment
 
Package: synapter
Commit: 91f6a71e741ef08ebfaa3cb0859b7525fedab3f2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-03 21:58:31
Commit message:

 replace synobj2 by synobj3
 
Package: synapter
Commit: da20825e06521aebba88753b55b9c02dc16df541
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-03 14:05:30
Commit message:

 depend on synapterdata 1.13.1 for synobj3
 
Package: synapter
Commit: ccbd8414fcf674e9992d0e2afb6a519f1c209160
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-03-24 13:00:51
Commit message:

 replace (m)apply by for loops
 
Package: synapter
Commit: 5cf9a32b717eab176d04d0886b1ba307c914f086
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-03-24 12:27:27
Commit message:

 fix calculateGridPerformance for categories with 0 occurence; fix #134
 
Package: synapter
Commit: b6088c5dd543ee64a142a632f856b34501ba73a0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-03-12 16:51:57
Commit message:

 set missedCleavages=2 as default for synergise2
 
Package: synapter
Commit: 42a08518d52cdbd81440ce2694e5316a01b29b77
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-03-04 21:40:18
Commit message:

 rerun roxygen
 
Package: synapter
Commit: b51c9a32bd62a7fe3ed7a96620dc22b90e66aa2a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-03-04 21:40:04
Commit message:

 add span.rt and span.int to makeMaster
 
Package: synapter
Commit: f9154667a0c6b333bfc7e07162e880a7a183a7d6
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-02-08 01:16:39
Commit message:

 define constant for classVersion to avoid regression in .isCurrent
 
Package: synapter
Commit: e0cbdf7906e60dcf2602ae7730c04303d430607b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-25 13:05:50
Commit message:

 extend performance report [ci skip]
 
Package: synapter
Commit: bf56392fd92ed573b44fbc515ed65ddb0a03d52a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-25 13:05:28
Commit message:

 just print performance2 if verbose=TRUE; [ci skip]
 
Package: synapter
Commit: d5ddba1fcd4b479eea36e81617559d39c638cfd5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-22 17:10:40
Commit message:

 set IisL=FALSE; closes #133
 
Package: synapter
Commit: a0f5a3d65d2b48743fd060be25f7586fd3dcedb2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-18 23:16:44
Commit message:

 fix header level [ci skip]
 
Package: synapter
Commit: b4a0bf2edd1d74f8a90baa2fc2d6da99c7cf2627
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-18 15:22:05
Commit message:

 don't validate MSnExp in .spectrumXml2spectra; see also lgatto/MSnbase#183
 
Package: synapter
Commit: 43f256fc43201c863ad20862a7b61761f4bcafe9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 22:41:19
Commit message:

 add Authors@R [ci skip]
 
Package: synapter
Commit: ef25be92cb1b582f86f202b1a6142d31d31c6266
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 22:17:59
Commit message:

 first synapter2 vignette draft; see #124
 
Package: synapter
Commit: c8d9122e5174b6d2860e76c56708eddba5561ff0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 21:48:14
Commit message:

 plotIntensity instead of plotRt
 
Package: synapter
Commit: 68327e31770011a93ab1c4e16f4e7146170a5b3a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 19:46:26
Commit message:

 fix correctIntensity call in requantify
 
Package: synapter
Commit: 5b909548032af90094bd4d4067bc900ece5e42f0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 19:36:05
Commit message:

 allow synapterPlgsAgreement for MSnSets with just 1 sample
 
Package: synapter
Commit: a9983a09172033e13088b41c0a0ec3c56d4b9280
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 18:43:14
Commit message:

 fix unit tests for verbose=TRUE
 
Package: synapter
Commit: fa57c514b60420c6588148420e4c021e0449b4a9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 17:06:36
Commit message:

 replace verbose=TRUE by verbose=interactive()
 
Package: synapter
Commit: 726b5f86d18aa1fe4c0ccfd2d8bb74921c6f5a00
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 17:04:19
Commit message:

 fix object name
 
Package: synapter
Commit: 5a31811f16643ba3ee3ef5b203254441cb460c43
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 13:58:28
Commit message:

 pass grid.imdiffs.* arguments to .synergise
 
Package: synapter
Commit: e52a3f0c06b3531ed8ed42800a86bcbc4b66d81f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 13:02:18
Commit message:

 add first stub synapter2 vignette [ci skip]
 
Package: synapter
Commit: 3117da1f091c6b4ba5392c4f0be15a938a971778
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 12:54:24
Commit message:

 append newline
 
Package: synapter
Commit: 9d8e07fc31011239bd1a079ccac563505ddaafe7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 12:03:24
Commit message:

 correct file path for create_synobj2.R
 
Package: synapter
Commit: 43c2173c7e1b2e5994716e82bcd0ec486ed768df
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 12:03:04
Commit message:

 don't use svg to save space
 
Package: synapter
Commit: c9f5978f22cc4b7b6b6a7974954d3722b3b45a1b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 11:59:35
Commit message:

 modelIntensity just works after findEMRTs
 
Package: synapter
Commit: f05fd59cec1a05678c9eae66a15c8a9db87ef5b7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 11:45:36
Commit message:

 add synapter2workflow flowchart; closes #130
 
Package: synapter
Commit: d1ef702d0e30cd121c17602496253f8c875addfe
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 09:10:09
Commit message:

 add fragment library hint to NEWS.md [ci skip]
 
Package: synapter
Commit: c381ee6fbcd369e4e2159a73c12b73b9eec097a3
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 08:55:38
Commit message:

 replace NEWS by NEWS.md [ci skip]; closes #79
 
Package: synapter
Commit: a91a214c5982bf197fd5dc5af554c066ccdbc94d
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 08:54:31
Commit message:

 add NEWS.md and docs to .Rbuildignore [ci skip]
 
Package: synapter
Commit: cfd766e3f4fd59c84c69398ceac05c1369b3ed71
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 08:06:20
Commit message:

 coding style [ci skip]
 
Package: synapter
Commit: 512fa2415a952abf29613a03219863a9c5991f83
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 08:05:30
Commit message:

 Revert "remove useless comparison"

This reverts commit 415b5997f9a0cc6f07a5ab3c5004d525970b06ec.
 
Package: synapter
Commit: 893f68742146c84a44422033a1e44503696ea39b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-16 20:44:47
Commit message:

 remove wrong eval=FALSE
 
Package: synapter
Commit: 415b5997f9a0cc6f07a5ab3c5004d525970b06ec
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-16 19:02:11
Commit message:

 remove useless comparison
 
Package: synapter
Commit: 7564bd7bd166b1610caf92a36b75240abff5c566
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-16 13:57:08
Commit message:

 convert synapter vignette to markdown
 
Package: synapter
Commit: 2bb31fb19f45faf76eebd149b36190ed3157e1f6
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-14 17:01:21
Commit message:

 convert fragmentmatching vignette to markdown
 
Package: synapter
Commit: 43edaf8d6958049bbd74149c622cb4ff4840ff63
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-23 13:41:52
Commit message:

 avoid unnecessary copy in calculateGridPerformance [ci skip]
 
Package: synapter
Commit: 517237ea364783cbb5563886564e881f05692100
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-22 21:21:05
Commit message:

 Merge branch 'master' into 2.0 [ci skip]
 
Package: synapter
Commit: 0028c401a44cc43accdd741385239d3eb722b91f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-22 21:02:50
Commit message:

 add identfragments/quantspectra to synergise2 documentation
 
Package: synapter
Commit: 89bd40990dcec338063deefc91207ea3667ad7f7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-22 20:45:21
Commit message:

 include sessionInfo in reports
 
Package: synapter
Commit: 6d7910b846224a9aed74a459bd873bfa3dab84a3
Author: Laurent <lg390@cam.ac.uk>
Date: 2016-12-22 11:01:14
Commit message:

 update readme
 
Package: synapter
Commit: bbbfc1934e22f8c285645abbeb129100c8127aa0
Author: Laurent <lg390@cam.ac.uk>
Date: 2016-12-22 10:24:08
Commit message:

 ignore travis config when building pkg
 
Package: synapter
Commit: 704c22ab2abb8afc90b251d8957b97749288c013
Author: Laurent <lg390@cam.ac.uk>
Date: 2016-12-22 10:23:29
Commit message:

 add travis config file
 
Package: synapter
Commit: 60fe95fe6343172cf5f7b92023f89b72518c4366
Author: Laurent Gatto <lg390@cam.ac.uk>
Date: 2016-12-22 10:20:48
Commit message:

 Merge pull request #131 from lgatto/travis

add .travis.yml 
Package: synapter
Commit: 1bdef7dc504ca5b0d34b36ac33c219d54fc81b61
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-22 09:39:42
Commit message:

 add .travis.yml
 
Package: synapter
Commit: 267986e43a39bd71f574bcb566e3454d7ce9f249
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-08 21:07:57
Commit message:

 remove duplicated rescueEMRTs call
 
Package: synapter
Commit: 151cdcb5e81cdf6b1326ba28cda092356dba583e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-08 15:19:58
Commit message:

 fix brackets
 
Package: synapter
Commit: 1deacfe3b5f76953986d5b5f02e4f91e6f2332e0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-02 20:13:02
Commit message:

 don't write useless rownames to csv
 
Package: synapter
Commit: b7b03df0640985c3c7de3f501e44c0f68cbe9543
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-02 20:10:12
Commit message:

 reset defaults for fm.min{Common,Delta} and fix calculation of their threshold selection; fixes #128
 
Package: synapter
Commit: 496c9ffbabfea2421d711d848a3572d75e59ec85
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-02 19:46:21
Commit message:

 set IisL=TRUE as default in synergise2
 
Package: synapter
Commit: 5056230acbc2f01d02d1efd7695cfda859d61950
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-11-18 11:27:57
Commit message:

 replace default Spectrum2 ctor by C level replacement; see lgatto/MSnbase#171
 
Package: synapter
Commit: b6972770ef860d94c41bc8a9430982fd97525cf5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 17:59:06
Commit message:

 export synergise2
 
Package: synapter
Commit: bafb30d1a4b5ef1dd83945733ba8e564a8c648ff
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 16:55:37
Commit message:

 remove Makefile for vignettes
 
Package: synapter
Commit: 78eefd164f506924e818a54c8e02f37fbd533c3a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 16:55:17
Commit message:

 add missing space
 
Package: synapter
Commit: e31f8ecdad47b80dee673b13475d304ad4386819
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 16:53:37
Commit message:

 fix fragment filtering log message
 
Package: synapter
Commit: b906a278a36f3298f793a62dfa3b2ed1487a54b2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 16:12:02
Commit message:

 filter fragments by intensity in synergise2
 
Package: synapter
Commit: 0ff943f7864c42a033e0bda028cd7e60bab3d982
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 15:53:30
Commit message:

 fix tempdir call
 
Package: synapter
Commit: 0de2a243658073e56f3372e85c41c952c44a7942
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 15:19:34
Commit message:

 remove GUI from vignette
 
Package: synapter
Commit: 80a21877042f21d7ddafa381a3b2eae60d10a90e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 15:14:13
Commit message:

 remove useless NEWS entries
 

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