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: 97854
Author: t.triche
Date: 2014-12-22T17:13:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/methylumi/DESCRIPTION
Modified  /trunk/madman/Rpacks/methylumi/vignettes/methylumi450k.Rnw
Fixed another stupid mistake of mine (--tjt)
Revision: 97852
Author: v.obenchain
Date: 2014-12-22T17:00:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/ensemblVEP/DESCRIPTION
Modified  /trunk/madman/Rpacks/ensemblVEP/NEWS
Modified  /trunk/madman/Rpacks/ensemblVEP/R/AllClasses.R
Modified  /trunk/madman/Rpacks/ensemblVEP/R/methods-VEPParam-class.R
Modified  /trunk/madman/Rpacks/ensemblVEP/R/runtimeOptions.R
Modified  /trunk/madman/Rpacks/ensemblVEP/man/VEPParam-class.Rd
Modified  /trunk/madman/Rpacks/ensemblVEP/man/runtimeOptions.Rd
changes for Ensembl version 78:
- add VEPParam78 class
- add 'flag_pick', 'flag_pick_allele', 'pick_order' and 'tsl' flags
Revision: 97851
Author: k.horan
Date: 2014-12-22T16:01:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChemmineR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChemmineR/NAMESPACE
Modified  /trunk/madman/Rpacks/ChemmineR/R/AllClasses.R
Modified  /trunk/madman/Rpacks/ChemmineR/R/draw_sdf.r
Modified  /trunk/madman/Rpacks/ChemmineR/R/sim.R
Modified  /trunk/madman/Rpacks/ChemmineR/inst/unitTests/test_general.R
Modified  /trunk/madman/Rpacks/ChemmineR/man/cmp.parse.Rd
Modified  /trunk/madman/Rpacks/ChemmineR/src/fingerprints.cc
Commit made by the Bioconductor Git-SVN bridge.
Consists of 0 commit.

Commit information:


Revision: 97850
Author: p.moulos
Date: 2014-12-22T15:15:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/metaseqR/DESCRIPTION
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqR-package.R
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.main.R
Modified  /trunk/madman/Rpacks/metaseqR/R/zzz.R
Modified  /trunk/madman/Rpacks/metaseqR/inst/NEWS
Fixed small bug when checking if weights with the PANDORA method (see CITATION) equal 1. Added a welcome message with a warning about the usage of baySeq.
Revision: 97846
Author: r.castelo
Date: 2014-12-22T14:58:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/qpgraph/DESCRIPTION
Modified  /trunk/madman/Rpacks/qpgraph/R/qpgraph.R
Bugfix on the calculation of distributions of limited-order partial correlations.
Revision: 97845
Author: a.franceschini
Date: 2014-12-22T14:26:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/scsR/DESCRIPTION
Modified  /trunk/madman/Rpacks/scsR/R/scsR_utils.R
bug fix on biostrings
Revision: 97844
Author: whuber
Date: 2014-12-22T12:27:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/arrayQualityMetrics/DESCRIPTION
Modified  /trunk/madman/Rpacks/arrayQualityMetrics/R/writereport.r
Fixed a scoping/evaluation problem in the call to 'gridsvg'

Revision: 97842
Author: whuber
Date: 2014-12-22T11:24:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/arrayQualityMetrics/DESCRIPTION
Made explicit the dependency on gridSVG >= 1.4-3, see also https://support.bioconductor.org/p/63781/
Revision: 97841
Author: hpages
Date: 2014-12-22T01:40:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
fetchExtendedChromInfoFromUCSC() now supports danRer7
Revision: 97840
Author: hpages
Date: 2014-12-22T01:23:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
fetchExtendedChromInfoFromUCSC() now supports susScr2
Revision: 97839
Author: hpages
Date: 2014-12-22T01:13:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
fetchExtendedChromInfoFromUCSC() now supports susScr3
Revision: 97838
Author: hpages
Date: 2014-12-22T00:13:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
fetchExtendedChromInfoFromUCSC() now supports rheMac2
Revision: 97837
Author: t.triche
Date: 2014-12-21T21:45:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/methylumi/DESCRIPTION
Deleted  /trunk/madman/Rpacks/methylumi/R/subset450kas27k.R
remove subset450kas27k.R (was causing build to fail)
Revision: 97836
Author: m.love
Date: 2014-12-21T20:40:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/NAMESPACE
Modified  /trunk/madman/Rpacks/DESeq2/R/core.R
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeq.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeq2-package.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeqDataSet.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeqResults.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeqTransform.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/coef.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/collapseReplicates.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/counts.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/design.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/dispersionFunction.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/dispersions.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/estimateBetaPriorVar.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/estimateDispersions.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/estimateDispersionsGeneEst.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/estimateSizeFactors.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/estimateSizeFactorsForMatrix.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/fpkm.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/fpm.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/makeExampleDESeqDataSet.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/nbinomLRT.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/nbinomWaldTest.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/normalizationFactors.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/normalizeGeneLength.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/plotCounts.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/plotDispEsts.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/plotMA.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/plotPCA.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/replaceOutliers.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/results.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/rlog.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/show.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/sizeFactors.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/summary.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/varianceStabilizingTransformation.Rd
putting full back in, for matrix input later
Revision: 97835
Author: hpages
Date: 2014-12-21T20:10:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
fetchExtendedChromInfoFromUCSC() now supports rheMac3
Revision: 97834
Author: hpages
Date: 2014-12-21T20:01:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/rankSeqlevels.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
fetchExtendedChromInfoFromUCSC() now supports galGal3
Revision: 97833
Author: a.franceschini
Date: 2014-12-21T19:33:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/STRINGdb/DESCRIPTION
Modified  /trunk/madman/Rpacks/STRINGdb/R/rstring.R
bug fix on get aliases
Revision: 97831
Author: whuber
Date: 2014-12-21T14:47:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/arrayQualityMetrics/DESCRIPTION
Modified  /trunk/madman/Rpacks/arrayQualityMetrics/R/arrayQualityMetrics.r
Modified  /trunk/madman/Rpacks/arrayQualityMetrics/R/writereport.r
Now using fully grDevices::dev.off() and gridSVG::dev.off() to avoid any potential confusion with name masking.
Expanded some comments.

Revision: 97826
Author: c.panse
Date: 2014-12-20T11:37:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/specL/man/specLSet-class.Rd
man page cosmetics
Revision: 97824
Author: jq.sun
Date: 2014-12-20T04:35:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCC/DESCRIPTION
Modified  /trunk/madman/Rpacks/TCC/NEWS
Modified  /trunk/madman/Rpacks/TCC/R/TCC.R
Modified  /trunk/madman/Rpacks/TCC/R/TCC.estimateDE.R
Modified  /trunk/madman/Rpacks/TCC/R/TCC.public.R
add MA coordinaets into results of DE analysis for paired two group
Revision: 97823
Author: h.bengtsson
Date: 2014-12-20T02:43:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/aroma.light/NEWS
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: a1e37247fbee813d1cbf86070da562f955d49ee5

    Backported 2.3.1 to 2.2.1; hence updated NEWS

Committed by: hb
Author Name: hb
Commit date: 2014-12-19 18:43:04 -0800
Author date: 2014-12-19 18:43:04 -0800
Revision: 97821
Author: m.jiang
Date: 2014-12-20T01:14:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowWorkspace/R/AllClasses.R
Modified  /trunk/madman/Rpacks/flowWorkspace/R/GatingSet-Methods.R
Modified  /trunk/madman/Rpacks/flowWorkspace/R/flowJoWorkspace-Methods.R
Modified  /trunk/madman/Rpacks/flowWorkspace/inst/tests/expect_result/flowJoWorkspace_expect.rds
Modified  /trunk/madman/Rpacks/flowWorkspace/inst/tests/flowJoWorkspace-testSuite.R
Modified  /trunk/madman/Rpacks/flowWorkspace/man/flowJoWorkspace-class.Rd
Modified  /trunk/madman/Rpacks/flowWorkspace/man/getKeywords.Rd
Modified  /trunk/madman/Rpacks/flowWorkspace/vignettes/flowWorkspace.Rnw
Commit made by the Bioconductor Git-SVN bridge.
Consists of 4 commits.

Commit information:

Commit id: 1fdfb65bfa277a246541352aa6d1386ea4ad4d18

    Merge branch 'trunk'

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-12-19 17:14:21 -0800
Author date: 2014-12-19 17:14:21 -0800

Commit id: f1628fa84da971ed5f787c134f00ffca0ea6ad71

    close #172

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-12-19 17:14:15 -0800
Author date: 2014-12-19 16:05:49 -0800

Commit id: 250c93bfcb8ff4526c5c72b201419b71e99692dc

    Merge branch 'trunk'

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-12-19 17:13:48 -0800
Author date: 2014-12-19 17:13:48 -0800

Commit id: cd0749d29355cc45d6bb62075482c9522c3291cb

    close #172

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-12-19 17:13:42 -0800
Author date: 2014-12-19 16:05:49 -0800
Revision: 97819
Author: h.bengtsson
Date: 2014-12-19T20:31:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biobase/DESCRIPTION
# Bumped version
Revision: 97818
Author: h.bengtsson
Date: 2014-12-19T20:30:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/Biobase/man/rowQ.Rd
Rd correction: rowMedians() is not using rowQ() - that changed years ago.
Revision: 97817
Author: x.zheng
Date: 2014-12-19T20:15:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/SNPRelate/R/AllUtilities.R
Modified  /trunk/madman/Rpacks/SNPRelate/README.md
Modified  /trunk/madman/Rpacks/SNPRelate/man/snpgdsSlidingWindow.Rd
Modified  /trunk/madman/Rpacks/SNPRelate/man/snpgdsVCF2GDS.Rd
Modified  /trunk/madman/Rpacks/SNPRelate/src/ConvToGDS.cpp
Modified  /trunk/madman/Rpacks/SNPRelate/src/R_GDS_Patch.h
Modified  /trunk/madman/Rpacks/SNPRelate/src/R_SNPRelate.c
Modified  /trunk/madman/Rpacks/SNPRelate/src/SNPRelate.cpp
Modified  /trunk/madman/Rpacks/SNPRelate/src/dGenGWAS.cpp
Modified  /trunk/madman/Rpacks/SNPRelate/src/dVect.cpp
Modified  /trunk/madman/Rpacks/SNPRelate/src/dVect.h
Modified  /trunk/madman/Rpacks/SNPRelate/src/genIBD.cpp
Modified  /trunk/madman/Rpacks/SNPRelate/src/genIBS.cpp
Modified  /trunk/madman/Rpacks/SNPRelate/src/genLD.cpp
Modified  /trunk/madman/Rpacks/SNPRelate/src/genPCA.cpp
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 97d381583f8633c7ca3eb6f8ca2531d0ebf7bfd4

    Copyright [Year]

Committed by: Xiuwen Zheng
Author Name: Xiuwen Zheng
Commit date: 2014-12-19 12:15:13 -0800
Author date: 2014-12-19 12:15:13 -0800
Revision: 97816
Author: m.jiang
Date: 2014-12-19T18:45:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowWorkspace/R/merge-GatingSet.R
Modified  /trunk/madman/Rpacks/flowWorkspace/vignettes/HowToMergeGatingSet.Rmd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 1b647ee09d939990db674c64a88936bf85ad77cd

    Merge branch 'trunk'

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-12-19 10:45:04 -0800
Author date: 2014-12-19 10:45:04 -0800

Commit id: 72c9abaa799461aabeab09f01b0251582449aef8

    fix vignette error

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-12-19 10:33:49 -0800
Author date: 2014-12-19 10:33:49 -0800
Revision: 97815
Author: a.franceschini
Date: 2014-12-19T18:30:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/scsR/R/scsR_utils.R
bug fix on Biostring
Revision: 97814
Author: p.stempor
Date: 2014-12-19T18:05:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 7752b532f193d6dd428f94fd9306295d22a59f2a

    Merge branch 'master' of github.com:Przemol/seqplots

Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-12-19 10:09:35 -0800
Author date: 2014-12-19 10:09:35 -0800

Commit id: 5b6d7900b56c54cf10b0ecdf0d9d616770803e2b

    version bump to 1.1.6

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-19 18:05:16 +0000
Author date: 2014-12-19 18:05:16 +0000
Revision: 97813
Author: p.stempor
Date: 2014-12-19T18:03:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 91129d22fd8bcd5c12169dfbb81f3b5b90e3436c

    Merge branch 'master' of github.com:Przemol/seqplots

Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-12-19 10:07:58 -0800
Author date: 2014-12-19 10:07:58 -0800

Commit id: 3fac78f35b95da313cc2af4ab3f6c3af29f4b11b

    biocViews added to DESCRIPTION, version bump to 1.1.6

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-19 18:03:36 +0000
Author date: 2014-12-19 18:03:36 +0000
Revision: 97812
Author: p.stempor
Date: 2014-12-19T17:57:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commits.

Commit information:

Commit id: b9e0749f0f230326eca82731754aa6e36d7de7ac

    Merge branch 'master' of github.com:Przemol/seqplots

Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-12-19 10:01:14 -0800
Author date: 2014-12-19 10:01:14 -0800

Commit id: 046411a623a616ff0eac4dcdba7499acf1712232

    version bump to 1.1.5

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-19 17:56:51 +0000
Author date: 2014-12-19 17:56:51 +0000

Commit id: cc85fba74b733c0b71217f50da7893cb46cdd02e

    package name removed from title

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-19 17:46:26 +0000
Author date: 2014-12-19 17:46:26 +0000
Revision: 97811
Author: stvjc
Date: 2014-12-19T17:48:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/NAMESPACE
facet_grid is needed
Revision: 97810
Author: stvjc
Date: 2014-12-19T17:48:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/NAMESPACE
minor changes
Revision: 97809
Author: p.stempor
Date: 2014-12-19T17:43:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/R/int_heatmapPlotWrapper.R
Modified  /trunk/madman/Rpacks/seqplots/man/heatmapPlotWrapper.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: abfbf59f6f3488c9c17e20e056b1105a666dfb1d

    Merge branch 'master' of github.com:Przemol/seqplots

Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-12-19 09:47:59 -0800
Author date: 2014-12-19 09:47:59 -0800

Commit id: ebec3cb719003d5a9fc2de017d99a28935e1eb61

    docs update for heatmap wrapper function

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-19 17:43:38 +0000
Author date: 2014-12-19 17:43:38 +0000
Revision: 97808
Author: p.stempor
Date: 2014-12-19T17:39:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/DESCRIPTION
Modified  /trunk/madman/Rpacks/seqplots/NAMESPACE
Modified  /trunk/madman/Rpacks/seqplots/R/seqplots-package.R
Modified  /trunk/madman/Rpacks/seqplots/man/ggHeatmapPlotWrapper.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/heatmapPlotWrapper.Rd
Modified  /trunk/madman/Rpacks/seqplots/man/imPlot2.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 76211996dcd6788d5963c862d7e4bd5e92be404b

    Merge branch 'master' of github.com:Przemol/seqplots

Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-12-19 09:43:12 -0800
Author date: 2014-12-19 09:43:12 -0800

Commit id: 5089c497459034668b3c3924298c2aa1b6bbb7cc

    ggplot2 and reshape2 packages added to DESCRIPTION and  NAMESPACE, docs updated

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-19 17:38:48 +0000
Author date: 2014-12-19 17:38:48 +0000
Revision: 97807
Author: p.stempor
Date: 2014-12-19T17:16:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/afterHTMLgridrender.js
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: e74a7640fa33dbf53f5d1a12583ac59fbc7ae218

    Merge branch 'master' of github.com:Przemol/seqplots

Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-12-19 09:20:52 -0800
Author date: 2014-12-19 09:20:52 -0800

Commit id: c76020db8f15152365ede6bbb0bf16e42edad80d

    [js] removed redundant tooltip call

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-19 17:16:31 +0000
Author date: 2014-12-19 17:16:31 +0000
Revision: 97806
Author: p.stempor
Date: 2014-12-19T17:05:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/renderHTMLgrid.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/js/afterHTMLgridrender.js
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 6603b8995eaff74abb24231b329ca9dbb076deb6

    Merge branch 'master' of github.com:Przemol/seqplots

Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-12-19 09:09:26 -0800
Author date: 2014-12-19 09:09:26 -0800

Commit id: 36af8a5f8c298db465e2e775a89e079ab0c599f5

    button creating labels from row/columns text inputs, better tooltips for html grid

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-19 17:05:05 +0000
Author date: 2014-12-19 17:05:05 +0000
Revision: 97804
Author: p.moulos
Date: 2014-12-19T16:19:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/metaseqR/DESCRIPTION
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqR-package.R
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.stat.R
Modified  /trunk/madman/Rpacks/metaseqR/inst/CITATION
Modified  /trunk/madman/Rpacks/metaseqR/inst/NEWS
Applied a temporary fix for a bug in the usage of ... in the internals of edgeR when using GLM. Updated CITATION, NEWS etc.
Revision: 97803
Author: j.meys
Date: 2014-12-19T15:55:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/unifiedWMWqPCR/DESCRIPTION
Modified  /trunk/madman/Rpacks/unifiedWMWqPCR/NAMESPACE
Modified  /trunk/madman/Rpacks/unifiedWMWqPCR/R/unifiedWMWqPCR-package.R
Modified  /trunk/madman/Rpacks/unifiedWMWqPCR/inst/CITATION
Modified  /trunk/madman/Rpacks/unifiedWMWqPCR/inst/NEWS
Modified  /trunk/madman/Rpacks/unifiedWMWqPCR/man/unifiedWMWqPCR-package.Rd
Updating the CITATION information and the help page of the package itself
to include the publication in Bioinformatics.
Upping the minor version number.
Revision: 97802
Author: t.martin
Date: 2014-12-19T15:21:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/coMET/DESCRIPTION
Modified  /trunk/madman/Rpacks/coMET/NEWS
Modified  /trunk/madman/Rpacks/coMET/R/BiofeatureGraphics.R
Modified  /trunk/madman/Rpacks/coMET/inst/doc/coMET.pdf
Modified  /trunk/madman/Rpacks/coMET/inst/doc/coMET_manual.pdf
Modified  /trunk/madman/Rpacks/coMET/man/coMET-package.Rd
Modified  /trunk/madman/Rpacks/coMET/vignettes/coMET.pdf
Modified  /trunk/madman/Rpacks/coMET/vignettes/figure/minimal-cometPlot-1.pdf
Modified  /trunk/madman/Rpacks/coMET/vignettes/figure/minimal-cometPlot_nopval-1.pdf
Modified  /trunk/madman/Rpacks/coMET/vignettes/figure/minimal-cometwebPlot-1.pdf
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: a9edf52a244b8923386d7200c2570800c5521c77

    Merge branch 'master' of https://github.com/TiphaineCMartin/coMET

Committed by: Tiphaine Martin
Author Name: Tiphaine Martin
Commit date: 2014-12-19 15:20:49 +0000
Author date: 2014-12-19 15:20:49 +0000

Commit id: 873ece50a853e299a702109bd3f956d961c7cc71

    Update version 0.99.7 related to the change of ENSEMBL mart

Committed by: Tiphaine Martin
Author Name: Tiphaine Martin
Commit date: 2014-12-19 15:16:46 +0000
Author date: 2014-12-19 15:16:46 +0000
Revision: 97801
Author: p.stempor
Date: 2014-12-19T15:12:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/www/upload/js/main.js
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 16b5cd237faf1a24fb58cd56a4dc36374c80fa81

    Merge branch 'master' of github.com:Przemol/seqplots

Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-12-19 07:16:29 -0800
Author date: 2014-12-19 07:16:29 -0800

Commit id: be64520725c4af5d2d0f06d080e8b1754a0072f8

    Fixed browser navigation message cooke setup

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-19 15:12:02 +0000
Author date: 2014-12-19 15:12:02 +0000
Revision: 97800
Author: p.stempor
Date: 2014-12-19T15:11:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/server.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: ae21def4c5439fccc6147f29ec4878791f6cab15

    Merge branch 'master' of github.com:Przemol/seqplots

Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-12-19 07:15:44 -0800
Author date: 2014-12-19 07:15:44 -0800

Commit id: f3a37fe1fbfc9e58f5b628727c3a2589807be3b1

    "Disconnected from server" message do not show any more on explicit user exit

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-19 15:11:21 +0000
Author date: 2014-12-19 15:11:21 +0000
Revision: 97799
Author: p.stempor
Date: 2014-12-19T14:51:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/R/int_heatmapPlotWrapper.R
Modified  /trunk/madman/Rpacks/seqplots/R/int_imPlot2.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: d08e8218611cf2fecc7cc4c84a9f3316f45b01a6

    Merge branch 'master' of github.com:Przemol/seqplots

Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-12-19 06:55:48 -0800
Author date: 2014-12-19 06:55:48 -0800

Commit id: 5b211c9023c565731c485a6c01e5e03abd5e4a97

    dendrogram is plotted for hierarchically clustered heatmap

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-19 14:51:28 +0000
Author date: 2014-12-19 14:51:28 +0000
Revision: 97797
Author: hpages
Date: 2014-12-19T10:28:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
fix regression introduced at previous commit
Revision: 97796
Author: hpages
Date: 2014-12-19T10:11:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/assembly-utils.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/rankSeqlevels.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
fetchExtendedChromInfoFromUCSC() now supports panTro4, panTro3, and panTro2
Revision: 97793
Author: hpages
Date: 2014-12-19T07:17:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/Seqinfo-class.Rd
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
fetchExtendedChromInfoFromUCSC() now supports mm8
Revision: 97792
Author: hpages
Date: 2014-12-19T07:04:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/assembly-utils.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchSequenceInfo.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
fetchExtendedChromInfoFromUCSC() now supports canFam3, canFam2, and canFam1
Revision: 97791
Author: hpages
Date: 2014-12-19T06:40:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/Seqinfo-class.Rd
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
fetchExtendedChromInfoFromUCSC() now supports ce10, ce6, ce4, and ce2
Revision: 97790
Author: hpages
Date: 2014-12-19T05:59:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/Seqinfo-class.Rd
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
fetchExtendedChromInfoFromUCSC() now supports bosTau6, bosTau7, and bosTau8
Revision: 97789
Author: hpages
Date: 2014-12-19T05:23:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchSequenceInfo.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
More tweaks and improvements to fetchExtendedChromInfoFromUCSC():
- Drop the trailing "s" from column names "UCSC_seqlevels", "UCSC_seqlengths",
  and "NCBI_seqlevels" in the returned data frame.
- For UCSC seqlevels with no corresponding NCBI seqlevels, obtain SequenceRole
  information from the base of knowledge included in GenomeInfoDb.
Revision: 97787
Author: s.gogarten
Date: 2014-12-19T00:44:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/GWASTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/GWASTools/R/chromIntensityPlot.R
Modified  /trunk/madman/Rpacks/GWASTools/R/plinkUtils.R
make colors of chromIntensityPlot match anomStatsPlot, replace 'netcdf' with 'genoData' in plinkCheck
Revision: 97786
Author: hpages
Date: 2014-12-18T23:28:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/assembly-utils.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchSequenceInfo.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
More tweaks to fetchExtendedChromInfoFromUCSC():
- Add 'quiet' arg.
- In case the genome is not based on an NCBI assembly (e.g. sacCer2), the rows
  are now sorted by UCSC seqlevel rank as determined by rankSeqlevels().
- No more attempt at guessing the UCSC genome name (e.g. "rn6") when the
  genome is specified as a RefSeq or GenBank accession (e.g. "GCF_000001895.5"
  or "GCA_000001895.5"). Was a neat feature but we have no use case for this.
Revision: 97785
Author: mtmorgan
Date: 2014-12-18T23:19:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/R/testPairedEndBam.R
Modified  /trunk/madman/Rpacks/Rsamtools/man/testPairedEndBam.Rd
tweak testPairedEndBam

- respect user-specified yieldSize
- report progress
Revision: 97783
Author: j.paulson
Date: 2014-12-18T23:15:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/metagenomeSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/MRexperiment2biom.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/cumNorm.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/cumNormMat.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/MRcoefs.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/MRcounts.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/MRexperiment2biom.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/MRfulltable.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/MRtable.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/aggregateByTaxonomy.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/biom2MRexperiment.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/calcNormFactors.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/calculateEffectiveSamples.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/correctIndices.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/correlationTest.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/cumNorm.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/cumNormMat.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/cumNormStat.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/cumNormStatFast.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/doCountMStep.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/doEStep.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/doZeroMStep.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/expSummary.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/exportMat.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/exportStats.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/filterData.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/fitDO.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/fitMeta.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/fitPA.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/fitSSTimeSeries.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/fitTimeSeries.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/fitZig.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/getCountDensity.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/getEpsilon.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/getNegativeLogLikelihoods.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/getPi.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/getZ.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/isItStillActive.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/libSize.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/load_biom.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/load_meta.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/load_metaQ.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/load_phenoData.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/makeLabels.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/newMRexperiment.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/normFactors.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/plotBubble.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/plotClassTimeSeries.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/plotCorr.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/plotFeature.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/plotGenus.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/plotMRheatmap.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/plotOTU.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/plotOrd.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/plotRare.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/plotTimeSeries.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/posteriorProbs.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/ssFit.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/ssIntervalCandidate.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/ssPerm.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/ssPermAnalysis.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/trapz.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/uniqueFeatures.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/zigControl.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: b0e9aea9c099fd72f4b2804cc116e742fb9d2803

    fixing documentation

Committed by: nosson
Author Name: nosson
Commit date: 2014-12-18 18:15:00 -0500
Author date: 2014-12-18 18:15:00 -0500
Revision: 97782
Author: v.obenchain
Date: 2014-12-18T22:07:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
version bump
Revision: 97781
Author: v.obenchain
Date: 2014-12-18T22:07:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/coordinate-mapping-methods.R
Modified  /trunk/madman/Rpacks/GenomicRanges/inst/unitTests/test_coordinate-mapping-methods.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/coordinate-mapping-methods.Rd
cody tidy for mapToTranscript()
Revision: 97780
Author: hpages
Date: 2014-12-18T21:30:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
clarify ordering of rows in fetchExtendedChromInfoFromUCSC() output
Revision: 97779
Author: hpages
Date: 2014-12-18T21:23:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchSequenceInfo.R
Simplify implementation of 'Seqinfo(genome="some genome")' by using
fetchExtendedChromInfoFromUCSC() behind the scene. As a consequence, the
returned Seqinfo object is now ordered like the data frame returned by
fetchExtendedChromInfoFromUCSC().
Revision: 97778
Author: j.paulson
Date: 2014-12-18T21:14:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/metagenomeSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/metagenomeSeq/vignettes/metagenomeSeq.Rnw
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 1df28aa250ffe8cc0fdae7affa76ae7820bb66d6

    Updating vignette

Committed by: nosson
Author Name: nosson
Commit date: 2014-12-18 16:14:42 -0500
Author date: 2014-12-18 16:14:42 -0500
Revision: 97777
Author: hpages
Date: 2014-12-18T21:03:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomeInfoDb/NAMESPACE
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd
A couple of tweaks to fetchExtendedChromInfoFromUCSC():
- Fix it for rn6 genome.
- Order rows of returned data frame first by sequence role (assembled-molecule,
  alt-scaffold, unlocalized-scaffold, unplaced-scaffold, pseudo-scaffold), then
  by UCSC seqlevel rank (as determined by rankSeqlevels()).
Revision: 97775
Author: hpages
Date: 2014-12-18T20:52:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/assembly-utils.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/fetchExtendedChromInfoFromUCSC.R
- Rename internal helper lookup_refseq_assembly_id() ->
  lookup_refseq_assembly_accession().
- Make internal helper fetch_assembly_report() fail with a better error message
  when no RefSeq assembly accession can be found for the supplied 'assembly'.
Revision: 97773
Author: j.paulson
Date: 2014-12-18T20:52:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/metagenomeSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/metagenomeSeq/vignettes/metagenomeSeq.Rnw
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: a64166717b135ee26206cad7021ee04613381675

    Updated documentation

Committed by: nosson
Author Name: nosson
Commit date: 2014-12-18 15:52:04 -0500
Author date: 2014-12-18 15:52:04 -0500
Revision: 97772
Author: mtmorgan
Date: 2014-12-18T20:28:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/NAMESPACE
clean up NAMESPACE import

- import all used read*StringSet functions
Revision: 97771
Author: mtmorgan
Date: 2014-12-18T20:28:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/Rsamtools/R/testPairedEndBam.R
Modified  /trunk/madman/Rpacks/Rsamtools/inst/unitTests/test_testPairedEndBam.R
Modified  /trunk/madman/Rpacks/Rsamtools/man/testPairedEndBam.Rd
testPairedEndBam() code clean-up

- no more 'fast' option -- iterate through file until paired-end read
  found
- restore yieldSize to (reference class) BamFile
- revert DOS line endings
- S4 methods have identical signatures; document (simple) alternatives
  in arguments section rather than usage
- don't indent usage() (displays poorly in text documentation)
- minor doc tweaks
Revision: 97770
Author: k.horan
Date: 2014-12-18T20:27:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChemmineR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChemmineR/src/fingerprints.cc
Commit made by the Bioconductor Git-SVN bridge.
Consists of 0 commit.

Commit information:


Revision: 97769
Author: p.stempor
Date: 2014-12-18T19:46:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/R/int_heatmapPlotWrapper.R
Modified  /trunk/madman/Rpacks/seqplots/R/plotHeatmap.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/LOCAL/server_plotHeatmap.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/mcDoParallel_plotting.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/server.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 4 commits.

Commit information:

Commit id: f79a159f0db5f001a1c5184edea92da1f663b996

    Merge branch 'master' of github.com:Przemol/seqplots

Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-12-18 11:50:41 -0800
Author date: 2014-12-18 11:50:41 -0800

Commit id: a3ccc90ef16ebad0ba9d6d84d1d25f6effc0dea5

    reproducible clustering - seed is taken from previous heatmap

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-18 19:46:22 +0000
Author date: 2014-12-18 19:46:22 +0000

Commit id: 60e2b7b0f861637c9d49e0d3b099163527db8baf

    fix for hclust plus automatic handle off dendrogram panel plotting

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-18 19:44:53 +0000
Author date: 2014-12-18 19:44:53 +0000

Commit id: 661bd8236ce71a1df74ad4abada6efd31d7a8590

    possibility to plot dendrograms as first panel, still requires some work

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-18 19:43:10 +0000
Author date: 2014-12-18 19:43:10 +0000
Revision: 97767
Author: hpages
Date: 2014-12-18T19:42:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/assembly-utils.R
Update internal helper .fetch_assembly_summary() after NCBI renamed the 1st
field of their 2 assembly summaries from "assembly_id" to "assembly_accession".
Revision: 97766
Author: n.hayden
Date: 2014-12-18T17:36:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/R/methods-ScanBamParam.R
Accommodate the same deprecated bitname specified multiple times
Revision: 97765
Author: m.boenn
Date: 2014-12-18T17:32:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/geecc/DESCRIPTION
Modified  /trunk/madman/Rpacks/geecc/NAMESPACE
Modified  /trunk/madman/Rpacks/geecc/R/concub-class.R
Modified  /trunk/madman/Rpacks/geecc/R/geecc.R
Modified  /trunk/madman/Rpacks/geecc/R/littlehelpers.R
Modified  /trunk/madman/Rpacks/geecc/man/concub-class.Rd
Adaptions regarding empty variables
Revision: 97763
Author: p.stempor
Date: 2014-12-18T14:10:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/functions/LOCAL/server_plotHeatmap.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/server.R
Modified  /trunk/madman/Rpacks/seqplots/inst/seqplots/ui.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: b755ecbed6465a0c3c241b818c75a7735b9ff561

    Merge branch 'master' of github.com:Przemol/seqplots

Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-12-18 06:14:59 -0800
Author date: 2014-12-18 06:14:59 -0800

Commit id: 0ba072741ce1faf501d92b46904c2727756be3a4

    GUI controls for making clustering reputable and selecting a single cluster for plotting

Committed by: przemol
Author Name: przemol
Commit date: 2014-12-18 14:10:42 +0000
Author date: 2014-12-18 14:10:42 +0000
Revision: 97762
Author: f.klein
Date: 2014-12-18T12:05:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/FourCSeq
Modified  /trunk/madman/Rpacks/FourCSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/FourCSeq/R/functions.R
Modified  /trunk/madman/Rpacks/FourCSeq/vignettes/FourCSeq.Rnw
getZScores: added check if viewpoint information is provided
vignette: added subsection on how to manually add the information about the viewpoint position
Revision: 97760
Author: d.rambaldi
Date: 2014-12-18T10:01:28+00:00
Paths:
Added  /trunk/madman/Rpacks/flowFit/flowFit.Rproj
RStudio project
Revision: 97759
Author: d.rambaldi
Date: 2014-12-18T10:01:04+00:00
Paths:
Added  /trunk/madman/Rpacks/flowFit/.Rbuildignore
R build ignore file
Revision: 97758
Author: d.rambaldi
Date: 2014-12-18T09:30:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowFit/DESCRIPTION
Version 1.5.1
Revision: 97757
Author: d.rambaldi
Date: 2014-12-18T09:30:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowFit/R/flowFit-internal.R
Fixed and inconsistency on keyword names. In flowSet coming from flowJo the channel names:  became AF405-A in keywords. Added a new match in .getKeywordValue()
Revision: 97756
Author: b.friedman
Date: 2014-12-18T07:37:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnalysisPageServer/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnalysisPageServer/R/rook.analysis.page.server.R
Modified  /trunk/madman/Rpacks/AnalysisPageServer/man/kill.process.Rd
remove xref to fork package in man pages to silence R CMD check warning
Revision: 97755
Author: hpages
Date: 2014-12-18T07:05:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
Added  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/BSgenome.Rnorvegicus.UCSC.rn6-seed
Modified  /trunk/madman/Rpacks/BSgenome/inst/extdata/GentlemanLab/ForgeAll.R
add seed file for rn6 genome

Source Code & Build Reports »

Source code is stored in svn (user: readonly, pass: readonly).

Software packages are built and checked nightly. Build reports:

 

Development Version »

Bioconductor packages under development:


Developer Resources:

Fred Hutchinson Cancer Research Center