Subversion Logs
This is a list of recent commits to the development branch
of the Bioconductor Subversion repository.
This list is also available as an RSS feed. (release branch)
Revision: 76777
Author: a.honkela
Date: Tue, 21 May 2013 12:13:19 GMT
Paths:
tigre 1.15.1: bug fixes to non-cascade model (identical to tigre 1.14.1)
Revision: 76775
Author: r.stojnic
Date: Tue, 21 May 2013 10:58:04 GMT
Paths:
Fixed a typo
Revision: 76772
Author: radivot
Date: Tue, 21 May 2013 09:50:44 GMT
Paths:
fixed sod example. Source of integration instability was my clipping of negative concentrations to zero. So I fixed simulate to no longer do this.
Revision: 76771
Author: t.yin
Date: Tue, 21 May 2013 05:47:50 GMT
Paths:
fix tracks bugs for labeling and remove Grob class subclass, this may be confusing
Revision: 76770
Author: t.yin
Date: Tue, 21 May 2013 03:56:42 GMT
Paths:
add fix arguments
Revision: 76768
Author: h.bengtsson
Date: Tue, 21 May 2013 02:08:09 GMT
Paths:
Version: 1.33.1 [2013-05-20]
o Same updates as in release v1.32.1.
Version: 1.32.1 [2013-05-20]
o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
Revision: 76766
Author: h.bengtsson
Date: Tue, 21 May 2013 01:05:52 GMT
Paths:
Version: 1.31.2 [2013-05-20]
o Same updates as in v1.30.2.
Version: 1.30.2 [2013-05-20]
o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
Revision: 76765
Author: y.liao
Date: Mon, 20 May 2013 23:48:58 GMT
Paths:
minor improvement of featureCounts
Revision: 76764
Author: t.yin
Date: Mon, 20 May 2013 18:51:14 GMT
Paths:
fix major broken issues of tracks function, need to support old accessor API too I guess though
Revision: 76761
Author: j.hon
Date: Mon, 20 May 2013 17:59:40 GMT
Paths:
rgl moved from Depends into Suggests
Revision: 76760
Author: radivot
Date: Mon, 20 May 2013 17:48:31 GMT
Paths:
added sodNatural.R, but I can't seem to make it work
Revision: 76759
Author: j.muller
Date: Mon, 20 May 2013 17:36:52 GMT
Paths:
CHANGES IN VERSION 1.5.3
------------------------
NEW FEATURES
o meltPeak can return loess smoothed scores.
Revision: 76758
Author: l.chavez
Date: Mon, 20 May 2013 17:20:23 GMT
Paths:
Manual distance=1 update
Revision: 76757
Author: p.haverty
Date: Mon, 20 May 2013 17:13:02 GMT
Paths:
Fixed roxygen2 segments family see also
Revision: 76756
Author: p.haverty
Date: Mon, 20 May 2013 17:10:14 GMT
Paths:
Now importing width from GenomicRanges
Revision: 76755
Author: p.haverty
Date: Mon, 20 May 2013 16:34:38 GMT
Paths:
IRanges now both Depends and Imports
Revision: 76754
Author: t.yates
Date: Mon, 20 May 2013 15:57:12 GMT
Paths:
Fix for transcriptCoordsToGenome
* ANNMAP112:
Up to v1.3.1
Added NEWS of fix
Fix for ANNMAP-112 use as.integer rather than as.numeric
Unit test for ANNMAP-112 bug with transcript/protein CoordsToGenome
Revision: 76753
Author: y.liao
Date: Mon, 20 May 2013 15:55:12 GMT
Paths:
minor improvement of featureCounts
Revision: 76751
Author: radivot
Date: Mon, 20 May 2013 12:01:57 GMT
Paths:
added SOD model and curtoNatural.R to models. Removed need for reversible flag in SBMLR model files.
Revision: 76750
Author: j.hon
Date: Mon, 20 May 2013 09:52:05 GMT
Paths:
Stric rgl dependency
Revision: 76748
Author: y.liao
Date: Mon, 20 May 2013 00:00:00 GMT
Paths:
removed wrong message from featureCounts
Revision: 76747
Author: g.yu
Date: Mon, 20 May 2013 05:33:44 GMT
Paths:
enrichGO and enrichKEGG support rat organism <2013-05-20, Mon>
Revision: 76746
Author: p.murrell
Date: Mon, 20 May 2013 00:00:00 GMT
Paths:
add "start" option for "arrowLoc"
Revision: 76745
Author: p.murrell
Date: Mon, 20 May 2013 00:00:00 GMT
Paths:
add "both" option for "arrowLoc"; bug fix for conversion from Hypregraph to graphBPH
Revision: 76744
Author: y.liao
Date: Sun, 19 May 2013 23:30:44 GMT
Paths:
removed wrong message from featureCounts
Revision: 76743
Author: t.yin
Date: Sun, 19 May 2013 22:51:54 GMT
Paths:
update manual of tracks
Revision: 76742
Author: t.yin
Date: Sun, 19 May 2013 22:51:33 GMT
Paths:
add test folder and file
Revision: 76741
Author: t.yin
Date: Sun, 19 May 2013 22:50:35 GMT
Paths:
update test
Revision: 76740
Author: t.yin
Date: Sun, 19 May 2013 22:50:20 GMT
Paths:
update NAMESPACE
Revision: 76739
Author: t.yin
Date: Sun, 19 May 2013 22:36:24 GMT
Paths:
tweak and move around functions
Revision: 76738
Author: t.yin
Date: Sun, 19 May 2013 22:34:38 GMT
Paths:
remove ggplot,Any
Revision: 76737
Author: t.yin
Date: Sun, 19 May 2013 22:34:14 GMT
Paths:
add numericORNULL
Revision: 76736
Author: t.yin
Date: Sun, 19 May 2013 22:32:02 GMT
Paths:
fix a typo
Revision: 76735
Author: t.yin
Date: Sun, 19 May 2013 22:31:40 GMT
Paths:
add Plot Class
Revision: 76734
Author: t.yin
Date: Sun, 19 May 2013 22:31:18 GMT
Paths:
add Grob class
Revision: 76733
Author: t.yin
Date: Sun, 19 May 2013 21:28:40 GMT
Paths:
add test directory
Revision: 76732
Author: t.yin
Date: Sun, 19 May 2013 21:24:56 GMT
Paths:
add Cache class
Revision: 76731
Author: t.yin
Date: Sun, 19 May 2013 21:24:28 GMT
Paths:
add Tracked class
Revision: 76730
Author: mtmorgan
Date: Sun, 19 May 2013 12:13:41 GMT
Paths:
quieten warnings from Snapshot
- use seqlevels<-
- avoid setting scales in update() -- bug in lattice??
Revision: 76728
Author: mtmorgan
Date: Sun, 19 May 2013 04:01:52 GMT
Paths:
DESCRIPTION and NEWS update
Revision: 76727
Author: mtmorgan
Date: Sun, 19 May 2013 02:36:24 GMT
Paths:
trim*,character-methods using filterFastq
Revision: 76726
Author: mtmorgan
Date: Sun, 19 May 2013 02:35:41 GMT
Paths:
filterFastq methods
Revision: 76725
Author: mtmorgan
Date: Sat, 18 May 2013 19:19:18 GMT
Paths:
write 0-length fastq files
Revision: 76724
Author: mtmorgan
Date: Sat, 18 May 2013 19:16:25 GMT
Paths:
encoding,QualityScore-methods
Revision: 76723
Author: mtmorgan
Date: Sat, 18 May 2013 19:06:16 GMT
Paths:
alphabet and encoding methods for XStringQuality
Revision: 76722
Author: hpages
Date: Sat, 18 May 2013 04:56:45 GMT
Paths:
small tweaks to vignette
Revision: 76721
Author: radivot
Date: Sat, 18 May 2013 03:09:57 GMT
Paths:
got it to pass check with VV additions
Revision: 76720
Author: hpages
Date: Sat, 18 May 2013 02:01:51 GMT
Paths:
Use new RNAseqData.HeLa.bam.chr14 dataset in the vignette instead of
TBX20BamSubset.
Revision: 76719
Author: y.liao
Date: Fri, 17 May 2013 23:53:47 GMT
Paths:
minor updated
Revision: 76718
Author: y.liao
Date: Fri, 17 May 2013 23:53:21 GMT
Paths:
minor updated
Revision: 76717
Author: y.liao
Date: Fri, 17 May 2013 23:46:03 GMT
Paths:
minor updated
Revision: 76716
Author: radivot
Date: Fri, 17 May 2013 23:33:29 GMT
Paths:
Added in the rest of VV's changes, i.e. from SBMLR on github
Revision: 76715
Author: l.chavez
Date: Fri, 17 May 2013 21:55:54 GMT
Paths:
MEDIPS.mergeFrames trim parameter
Revision: 76714
Author: p.haverty
Date: Fri, 17 May 2013 20:21:10 GMT
Paths:
Updated tests for rangeSegMeanLength and Rd
Revision: 76713
Author: m.lawrence
Date: Fri, 17 May 2013 17:46:48 GMT
Paths:
plotRangesLinkedToData now a generic, with a method for
SummarizedExperiment. Not tested at all.
Revision: 76703
Author: v.obenchain
Date: Fri, 17 May 2013 15:50:58 GMT
Paths:
Clean up how the default value is set for 'showHeaderLines' and 'showTailLine'.
Revision: 76702
Author: radivot
Date: Fri, 17 May 2013 15:02:04 GMT
Paths:
svn ignore RStudio project file added
Revision: 76701
Author: radivot
Date: Fri, 17 May 2013 15:01:03 GMT
Paths:
Vishak Venkateswaran has a branch of SBMLR up at github that I'm starting to go through. So far I added his changes to summary and simulate.
Revision: 76700
Author: m.stadler
Date: Fri, 17 May 2013 13:58:27 GMT
Paths:
update qAlign documentation with index storage locations
Revision: 76697
Author: r.day
Date: Fri, 17 May 2013 02:45:19 GMT
Paths:
expectedUtility:
added guarantee parameter,
corrected the format of the "details" block,
put quotes around "piHat".
Revision: 76696
Author: r.day
Date: Fri, 17 May 2013 02:41:27 GMT
Paths:
Corrected Vstart -> VStart
Added Ysigsq as @param
Removed references to global variables.
Removed test code outside of function.
Revision: 76695
Author: r.day
Date: Fri, 17 May 2013 02:39:42 GMT
Paths:
Corrected Vstart -> VStart
Added Ysigsq as @param
Removed references to global variables.
Removed test code outside of function.
Revision: 76694
Author: r.day
Date: Fri, 17 May 2013 02:38:23 GMT
Paths:
Corrected Vstart -> VStart
Added Ysigsq as @param
Removed references to global variables.
Removed test code outside of function.
Revision: 76693
Author: r.day
Date: Fri, 17 May 2013 02:25:35 GMT
Paths:
Replacing .First.lib by .onLoad
Revision: 76692
Author: y.liao
Date: Fri, 17 May 2013 00:00:00 GMT
Paths:
robust featureCount load_features
Revision: 76691
Author: y.liao
Date: Fri, 17 May 2013 00:00:00 GMT
Paths:
robust featureCount load_features
Revision: 76690
Author: hpages
Date: Fri, 17 May 2013 00:00:00 GMT
Paths:
Add 'max.plot.reads' arg to plotTranscripts(). Default is 200.
Revision: 76689
Author: v.obenchain
Date: Thu, 16 May 2013 23:01:42 GMT
Paths:
Fix bug in 'show' related to 'showHeaderLines' and 'showTailLines'.
Revision: 76684
Author: v.obenchain
Date: Thu, 16 May 2013 22:04:22 GMT
Paths:
Modify 'VCFRowID' argument to parseCSQToGRanges() to handle results returned in
any order or subset.
Revision: 76679
Author: mtmorgan
Date: Thu, 16 May 2013 21:12:43 GMT
Paths:
more efficient ref class constructor
- new empty instance, the update slots
Revision: 76678
Author: v.obenchain
Date: Thu, 16 May 2013 20:27:51 GMT
Paths:
- Replace calls to keepSeqlevels() and renameSeqlevels() with seqlevels().
- Header info is accessed twice in readVcf() which resulted in a double
(identical) warning if one was thrown. Now only a single warning is thrown.
Revision: 76677
Author: v.obenchain
Date: Thu, 16 May 2013 19:14:40 GMT
Paths:
Work on examples on 'seqinfo' man page and 'Seqinfo' unit tests.