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Revision: 97192
Author: s.aibar
Date: 2014-11-27T16:35:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/FGNet/R/3_functionalNetwork.R
Added  /trunk/madman/Rpacks/FGNet/data/GOEvidenceCodes.RData
Added data/GOEvidenceCodes.RData, node color bug with missign values
Revision: 97191
Author: khansen
Date: 2014-11-27T16:25:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/minfi/NAMESPACE
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 60f27376794cdf8e00860999909f4e69f7887802

    adding import of getGEO

Committed by: ririzarr
Author Name: ririzarr
Commit date: 2014-11-27 11:25:40 -0500
Author date: 2014-11-27 11:25:40 -0500
Revision: 97189
Author: a.oles
Date: 2014-11-27T15:19:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBImage/NAMESPACE
Modified  /trunk/madman/Rpacks/EBImage/R/Image.R
Fix to previous commit
Revision: 97187
Author: j.zhu
Date: 2014-11-27T14:00:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/SRAdb/DESCRIPTION
Bump the version to 1.20.5
Revision: 97186
Author: stvjc
Date: 2014-11-27T13:13:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/R/allS4.R
Modified  /trunk/madman/Rpacks/gQTLstats/R/storeStats.R
Modified  /trunk/madman/Rpacks/gQTLstats/man/filtFDR.Rd
Modified  /trunk/madman/Rpacks/gQTLstats/vignettes/gQTLstats.Rmd
handle manual propagation of filtering in enumerateByFDR
Revision: 97185
Author: stvjc
Date: 2014-11-27T11:54:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/R/storeStats.R
Modified  /trunk/madman/Rpacks/gQTLstats/man/directPlot.Rd
Modified  /trunk/madman/Rpacks/gQTLstats/man/enumerateByFDR.Rd
introduce filter parameter for enumerateByFDR
Revision: 97184
Author: maechler
Date: 2014-11-27T08:08:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/codetoolsBioC/R/findExternalDeps.R
Added  /trunk/madman/Rpacks/codetoolsBioC/TODO.org
first note about TODOs /  bug
Revision: 97182
Author: d.strbenac
Date: 2014-11-27T07:00:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/R/selectionPlot.R
Accidentally deleted code in selectionPlot reinstated.
Revision: 97181
Author: khansen
Date: 2014-11-27T05:44:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/minfi/NAMESPACE
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 43d04a9281d6aedc3d1fabccc3d190c8853e362a

    adding read.450k.GEO

Committed by: ririzarr
Author Name: ririzarr
Commit date: 2014-11-27 00:44:14 -0500
Author date: 2014-11-27 00:44:14 -0500
Revision: 97180
Author: khansen
Date: 2014-11-27T05:41:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/minfi/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 68f4680c0ac3c0fa8edc316ad1540ae6fd0b28a5

    adding read.450k.GEO

Committed by: ririzarr
Author Name: ririzarr
Commit date: 2014-11-27 00:41:13 -0500
Author date: 2014-11-27 00:41:13 -0500
Revision: 97179
Author: khansen
Date: 2014-11-27T05:39:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/minfi/DESCRIPTION
Modified  /trunk/madman/Rpacks/minfi/R/read.450k.R
Added  /trunk/madman/Rpacks/minfi/man/read.450k.GEO.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commits.

Commit information:

Commit id: 2775cedb2f37611b4a9016598d96ab9f2032528d

    adding read.450k.GEO

Committed by: ririzarr
Author Name: ririzarr
Commit date: 2014-11-27 00:39:35 -0500
Author date: 2014-11-27 00:39:35 -0500

Commit id: d844ec0e44b8caeba3c3e7c6e7c988d7e6d328d2

    adding read.450k.GEO

Committed by: ririzarr
Author Name: ririzarr
Commit date: 2014-11-27 00:39:26 -0500
Author date: 2014-11-27 00:39:26 -0500

Commit id: b22d36eda40d08c0e01f4a7bc0c0829ef7a9c5f6

    adding read.450k.GEO

Committed by: ririzarr
Author Name: ririzarr
Commit date: 2014-11-27 00:39:20 -0500
Author date: 2014-11-27 00:39:20 -0500
Revision: 97178
Author: khansen
Date: 2014-11-27T03:20:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rgraphviz/README.md
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: ad4e463c3cbe69793c15eee8037a35d33a9312e7

    Merge pull request #2 from benmarwick/patch-1

    tiny typo
Committed by: Kasper Daniel Hansen
Author Name: Kasper Daniel Hansen
Commit date: 2014-11-26 22:20:00 -0500
Author date: 2014-11-26 22:20:00 -0500

Commit id: c721ceccff3e82f723e865aacb97d76d228a9d67

    tiny typo

Committed by: Ben Marwick
Author Name: Ben Marwick
Commit date: 2014-11-26 00:44:43 -0800
Author date: 2014-11-26 00:44:43 -0800
Revision: 97177
Author: stvjc
Date: 2014-11-27T02:37:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/man/directPlot.Rd
Modified  /trunk/madman/Rpacks/gQTLstats/man/eqBox2.Rd
Modified  /trunk/madman/Rpacks/gQTLstats/man/filtFDR.Rd
Modified  /trunk/madman/Rpacks/gQTLstats/man/storeToStats.Rd
basic fixes
Revision: 97175
Author: k.oneill
Date: 2014-11-27T01:56:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowType/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowType/R/flowType.R
Modified  /trunk/madman/Rpacks/flowType/inst/NEWS
Bugfix to get correct partitions matrix when more than one threshold is used
Revision: 97174
Author: khansen
Date: 2014-11-27T01:53:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/affxparser/DESCRIPTION
Modified  /trunk/madman/Rpacks/affxparser/NEWS
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: ce9dcb162962668a77f7ba5a62008edc4cf0cc2b

    Bumped version. Going live with bug fixes of readPgf().

Committed by: hb
Author Name: hb
Commit date: 2014-11-26 17:53:13 -0800
Author date: 2014-11-26 17:53:13 -0800
Revision: 97171
Author: d.strbenac
Date: 2014-11-27T00:00:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/R/KullbackLeiblerSelection.R
Type argument removed from KullbackLeiblerSelection.
Revision: 97169
Author: l.gatto
Date: 2014-11-26T23:12:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/synapter/DESCRIPTION
Merge branch 'master' into local-hedgehog
Revision: 97167
Author: l.gatto
Date: 2014-11-26T23:10:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/synapter/DESCRIPTION
Modified  /trunk/madman/Rpacks/synapter/NEWS
Modified  /trunk/madman/Rpacks/synapter/R/synapter-class.R
Modified  /trunk/madman/Rpacks/synapter/R/utils.R
Merge branch 'master' into local-hedgehog
Revision: 97165
Author: hpages
Date: 2014-11-26T22:10:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
minor speed improvement and memory footprint reduction during preprocessing
Revision: 97163
Author: j.zhu
Date: 2014-11-26T22:08:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/SRAdb/R/getFASTQinfo.R
Changed table name of fastqlist to fastq
Revision: 97160
Author: d.tenenbaum
Date: 2014-11-26T21:04:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/R453Plus1Toolbox/DESCRIPTION
Modified  /trunk/madman/Rpacks/R453Plus1Toolbox/NAMESPACE
remove levels from IRanges imports
Revision: 97159
Author: r.nicolle
Date: 2014-11-26T20:59:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/CoRegNet/DESCRIPTION
Modified  /trunk/madman/Rpacks/CoRegNet/NAMESPACE
Modified  /trunk/madman/Rpacks/CoRegNet/R/coRegnet.R
Modified  /trunk/madman/Rpacks/CoRegNet/R/netInference.R
Modified  /trunk/madman/Rpacks/CoRegNet/inst/unitTests/test_coregnet.R
Added  /trunk/madman/Rpacks/CoRegNet/man/.Rhistory
Modified  /trunk/madman/Rpacks/CoRegNet/man/hLICORN.Rd
Deleted  /trunk/madman/Rpacks/CoRegNet/src/Makevars
Deleted  /trunk/madman/Rpacks/CoRegNet/src/chargement.c
Added  /trunk/madman/Rpacks/CoRegNet/src/comblicorn.c
Deleted  /trunk/madman/Rpacks/CoRegNet/src/licorn.c
Deleted  /trunk/madman/Rpacks/CoRegNet/src/prototypes.h
Deleted  /trunk/madman/Rpacks/CoRegNet/src/pvalue.c
Deleted  /trunk/madman/Rpacks/CoRegNet/src/score.c
Deleted  /trunk/madman/Rpacks/CoRegNet/src/structure.c
Added  /trunk/madman/Rpacks/CoRegNet/vignettes/.Rhistory
Added  /trunk/madman/Rpacks/CoRegNet/vignettes/CoRegNet.Rmd
Deleted  /trunk/madman/Rpacks/CoRegNet/vignettes/CoRegNet.Rnw
Added  /trunk/madman/Rpacks/CoRegNet/vignettes/CoRegNet.html
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 3303359fed8950f46027b127dbbaf03593645c69

    New LICORN

    used the R package a priori all through the LICORN (searching for core
    too) and created a new C code to compute MAE. Just missing the
    automatic definition of parameters.

Committed by: RemyNicolle
Author Name: RemyNicolle
Commit date: 2014-11-24 17:36:09 +0100
Author date: 2014-11-24 17:36:09 +0100
Revision: 97158
Author: z.ji
Date: 2014-11-26T20:49:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSCA/inst/shiny/server.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 37762ab1a3409e9d8302a2a3ec1b9b07e5595ac5

    Fixing bug of more than 3 genesets

Committed by: Zhicheng Ji
Author Name: Zhicheng Ji
Commit date: 2014-11-26 15:49:49 -0500
Author date: 2014-11-26 15:49:49 -0500
Revision: 97156
Author: maechler
Date: 2014-11-26T20:48:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/codetoolsBioC/R/findExternalDeps.R
tweaks -> vapply(); findExternalDeps() shorter local variable names
Revision: 97155
Author: mtmorgan
Date: 2014-11-26T20:44:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/minfi/DESCRIPTION
Modified  /trunk/madman/Rpacks/minfi/NAMESPACE
remove unknown import 'featuredata'
Revision: 97154
Author: maechler
Date: 2014-11-26T20:43:18+00:00
Paths:
Added  /trunk/madman/Rpacks/codetoolsBioC/tests
Added  /trunk/madman/Rpacks/codetoolsBioC/tests/findExt-stats4.R
add some tests
Revision: 97153
Author: z.ji
Date: 2014-11-26T20:29:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSCA/DESCRIPTION
Modified  /trunk/madman/Rpacks/GSCA/NAMESPACE
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: ad48dfb5e147e5a3187ca431288d10a796a5c459

    Disabling all 3 dimensional features.

Committed by: Zhicheng Ji
Author Name: Zhicheng Ji
Commit date: 2014-11-26 15:29:02 -0500
Author date: 2014-11-26 15:29:02 -0500
Revision: 97152
Author: z.ji
Date: 2014-11-26T20:19:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSCA/inst/shiny/server.R
Modified  /trunk/madman/Rpacks/GSCA/inst/shiny/ui.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: ff1df7d5c95a37d93ba4ea46258638e87880c08f

    reversing UI settings

Committed by: Zhicheng Ji
Author Name: Zhicheng Ji
Commit date: 2014-11-26 15:19:19 -0500
Author date: 2014-11-26 15:19:19 -0500
Revision: 97150
Author: l.goldstein
Date: 2014-11-26T19:22:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/SGSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/SGSeq/R/convert.R
Modified  /trunk/madman/Rpacks/SGSeq/man/convertToTxFeatures.Rd
convertToTxFeatures supports transcript and gene names for GRangesList input
Revision: 97147
Author: p.haverty
Date: 2014-11-26T17:09:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/genoset/DESCRIPTION
Modified  /trunk/madman/Rpacks/genoset/NAMESPACE
Modified  /trunk/madman/Rpacks/genoset/R/bounds.R
Modified  /trunk/madman/Rpacks/genoset/R/genoset-class.R
Modified  /trunk/madman/Rpacks/genoset/R/rangeSummaries.R
Modified  /trunk/madman/Rpacks/genoset/src/genoset.h
Added  /trunk/madman/Rpacks/genoset/src/init.c
Version: 1.21.2. .Call now uses registration
Revision: 97146
Author: stvjc
Date: 2014-11-26T15:24:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/R/allS4.R
Modified  /trunk/madman/Rpacks/gQTLstats/R/storeStats.R
Added  /trunk/madman/Rpacks/gQTLstats/data
Added  /trunk/madman/Rpacks/gQTLstats/data/filtFDR.rda
Added  /trunk/madman/Rpacks/gQTLstats/data/rawFDR.rda
adding some provenance materials into the FDR objects
Revision: 97143
Author: j.ou
Date: 2014-11-26T14:47:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/dagLogo/DESCRIPTION
Modified  /trunk/madman/Rpacks/dagLogo/NEWS
Modified  /trunk/madman/Rpacks/dagLogo/vignettes/dagLogo.Rnw
 try to catch the error when mart server does not work.
Revision: 97142
Author: hpages
Date: 2014-11-26T12:07:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicAlignments/DESCRIPTION
Bump version because of new 'algorithm' arg added to countOverlaps() generic and
methods defined in IRanges and GenomicRanges.
Revision: 97141
Author: hpages
Date: 2014-11-26T11:54:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/findOverlaps-methods.R
add 'algorithm' argument to countOverlaps() methods
Revision: 97140
Author: hpages
Date: 2014-11-26T11:21:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/Hits-class-leftovers.R
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/R/findOverlaps-methods.R
Modified  /trunk/madman/Rpacks/IRanges/inst/unitTests/test_NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Add 'algorithm' argument to countOverlaps() generic and methods so the user
can choose between "intervaltree" and "nclist" (i.e. IntervalTree- and
NCList-based algos). Like for findOverlaps(), "intervaltree" remains the
default for now.
Revision: 97139
Author: hpages
Date: 2014-11-26T09:18:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/findOverlaps-methods.R
resync with latest changes in NCList code in IRanges
Revision: 97138
Author: hpages
Date: 2014-11-26T09:07:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/R/findOverlaps-methods.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
more code cleanup
Revision: 97135
Author: hpages
Date: 2014-11-26T04:58:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/inst/unitTests/test_NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
- Rename internal helper NCList_find_overlaps_by_group_and_combine() ->
  NCList_find_overlaps_in_groups().
- Internal helpers findOverlaps_NCList() and findOverlaps_NCLists() now support
  "on-the-fly preprocessing".
- Code cleanup.
Revision: 97134
Author: stvjc
Date: 2014-11-26T03:54:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/R/filters.R
bad bug in regressOut
Revision: 97133
Author: mtmorgan
Date: 2014-11-26T02:32:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/bsseq/DESCRIPTION
Modified  /trunk/madman/Rpacks/bsseq/NAMESPACE
Modified  /trunk/madman/Rpacks/bsseq/R/utils.R
Modified  /trunk/madman/Rpacks/bsseq/man/BSseq-class.Rd
re-implement assayNames function as method

- on GenomicRanges::assayNames
- argument changed (from 'object' to 'x')
Revision: 97132
Author: mtmorgan
Date: 2014-11-26T02:31:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/NAMESPACE
Modified  /trunk/madman/Rpacks/GenomicRanges/NEWS
Modified  /trunk/madman/Rpacks/GenomicRanges/R/SummarizedExperiment-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/SummarizedExperiment-class.Rd
improve access to assay names

- assayNames, assayNames<- generic and methods
- document consequences of withDimnames with respect to performance
Revision: 97131
Author: c.trapnell
Date: 2014-11-26T01:42:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/monocle/DESCRIPTION
Modified  /trunk/madman/Rpacks/monocle/R/methods-CellDataSet.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 4dec230a283407fb72a1760ed067b5b220115e78

    fixed a few minor problems that screw up the vignette

Committed by: ctrapnell
Author Name: ctrapnell
Commit date: 2014-11-25 17:41:45 -0800
Author date: 2014-11-25 17:41:45 -0800
Revision: 97129
Author: v.obenchain
Date: 2014-11-26T00:49:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicAlignments/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicAlignments/src/cigar_utils.c
fix off by one error when processing 'S' in query_locs_to_ref_locs()
Revision: 97128
Author: s.arora
Date: 2014-11-25T23:29:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/DESCRIPTION
Modified  /trunk/madman/Rpacks/biocViews/R/recommendBiocViews.R
code update

correct logic for recommendBiocViews
Revision: 97127
Author: stvjc
Date: 2014-11-25T22:48:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/R/storeStats.R
fixed up enumerateByFDR to include fdr
Revision: 97126
Author: hpages
Date: 2014-11-25T22:16:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
Resync with latest improvements to
IRanges:::NCList_find_overlaps_by_group_and_combine().
Revision: 97125
Author: hpages
Date: 2014-11-25T22:12:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/IRanges.h
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
Modified  /trunk/madman/Rpacks/IRanges/src/R_init_IRanges.c
More optimization of NCList_find_overlaps_by_group_and_combine() by avoiding
copying the input data to temporary buffers.
Revision: 97124
Author: m.love
Date: 2014-11-25T21:00:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/NAMESPACE
Modified  /trunk/madman/Rpacks/DESeq2/R/AllClasses.R
Modified  /trunk/madman/Rpacks/DESeq2/R/core.R
Modified  /trunk/madman/Rpacks/DESeq2/R/methods.R
Modified  /trunk/madman/Rpacks/DESeq2/R/plots.R
Modified  /trunk/madman/Rpacks/DESeq2/R/results.R
Modified  /trunk/madman/Rpacks/DESeq2/R/rlogTransformation.R
Modified  /trunk/madman/Rpacks/DESeq2/R/varianceStabilizingTransformation.R
Modified  /trunk/madman/Rpacks/DESeq2/inst/unitTests/test_results.R
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeq.Rd
Added  /trunk/madman/Rpacks/DESeq2/man/DESeq2-package.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeqDataSet.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/DESeqResults.Rd
Added  /trunk/madman/Rpacks/DESeq2/man/DESeqTransform.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/coef.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/estimateDispersions.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/estimateSizeFactors.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/normalizationFactors.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/results.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/rlog.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/sizeFactors.Rd
Modified  /trunk/madman/Rpacks/DESeq2/man/varianceStabilizingTransformation.Rd
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2.Rnw
adding BiocGenerics plotPCA import and fixing many man pages
Revision: 97123
Author: stvjc
Date: 2014-11-25T20:14:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLstats/NAMESPACE
Added  /trunk/madman/Rpacks/gQTLstats/R/queryVCF.R
Modified  /trunk/madman/Rpacks/gQTLstats/R/storeStats.R
Modified  /trunk/madman/Rpacks/gQTLstats/vignettes/gQTLstats.Rmd
enumeration tools are in
Revision: 97120
Author: m.carlson
Date: 2014-11-25T19:26:20+00:00
Paths:
Added  /trunk/madman/Rpacks/PROPER
Added  /trunk/madman/Rpacks/PROPER/DESCRIPTION
Added  /trunk/madman/Rpacks/PROPER/NAMESPACE
Added  /trunk/madman/Rpacks/PROPER/R
Added  /trunk/madman/Rpacks/PROPER/R/DEdetection.R
Added  /trunk/madman/Rpacks/PROPER/R/plots.R
Added  /trunk/madman/Rpacks/PROPER/R/power.R
Added  /trunk/madman/Rpacks/PROPER/R/simOptions.2grp.R
Added  /trunk/madman/Rpacks/PROPER/R/simOptions.util.R
Added  /trunk/madman/Rpacks/PROPER/R/simfuns.R
Added  /trunk/madman/Rpacks/PROPER/data
Added  /trunk/madman/Rpacks/PROPER/data/GE.human.RData
Added  /trunk/madman/Rpacks/PROPER/data/bottomly.RData
Added  /trunk/madman/Rpacks/PROPER/data/cheung.RData
Added  /trunk/madman/Rpacks/PROPER/data/datalist
Added  /trunk/madman/Rpacks/PROPER/data/gilad.RData
Added  /trunk/madman/Rpacks/PROPER/data/maqc.RData
Added  /trunk/madman/Rpacks/PROPER/data/pbmc.RData
Added  /trunk/madman/Rpacks/PROPER/doc
Added  /trunk/madman/Rpacks/PROPER/doc/NEWS
Added  /trunk/madman/Rpacks/PROPER/doc/PROPER.pdf
Added  /trunk/madman/Rpacks/PROPER/inst
Added  /trunk/madman/Rpacks/PROPER/inst/CITATION
Added  /trunk/madman/Rpacks/PROPER/man
Added  /trunk/madman/Rpacks/PROPER/man/RNAseq.SimOptions.2grp.Rd
Added  /trunk/madman/Rpacks/PROPER/man/comparePower.Rd
Added  /trunk/madman/Rpacks/PROPER/man/historicalData.Rd
Added  /trunk/madman/Rpacks/PROPER/man/plotPowerHist.Rd
Added  /trunk/madman/Rpacks/PROPER/man/plots.Rd
Added  /trunk/madman/Rpacks/PROPER/man/power.seqDepth.Rd
Added  /trunk/madman/Rpacks/PROPER/man/runSims.Rd
Added  /trunk/madman/Rpacks/PROPER/man/simRNAseq.Rd
Added  /trunk/madman/Rpacks/PROPER/man/summaryPower.Rd
Added  /trunk/madman/Rpacks/PROPER/vignettes
Added  /trunk/madman/Rpacks/PROPER/vignettes/FDC.pdf
Added  /trunk/madman/Rpacks/PROPER/vignettes/PROPER.Rnw
Added  /trunk/madman/Rpacks/PROPER/vignettes/TD.pdf
Added  /trunk/madman/Rpacks/PROPER/vignettes/all.pdf
Added  /trunk/madman/Rpacks/PROPER/vignettes/filter.pdf
Added  /trunk/madman/Rpacks/PROPER/vignettes/powers.pdf
Modified  /trunk/madman/Rpacks/bioc_3.1.manifest
Adds PROPER to the repos.
Revision: 97119
Author: n.servant
Date: 2014-11-25T18:30:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/HiTC/NEWS
change in setEnvDisplay to fix x11 bug. S. Thomas
Revision: 97118
Author: n.servant
Date: 2014-11-25T18:28:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/HiTC/DESCRIPTION
Modified  /trunk/madman/Rpacks/HiTC/R/mapC.R
change in setEnvDisplay to fix x11 bug. S. Thomas
Revision: 97117
Author: j.hill
Date: 2014-11-25T17:41:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/sangerseqR/inst/PolyPeakParser/polypeakfunctions.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: c3db4732e690dcca1519bd895051659236e59117

    Fixed bug in Poly Peak Parser when reverse compliment reference sequence is provided.

Committed by: Jonathon Hill
Author Name: Jonathon Hill
Commit date: 2014-11-25 10:41:11 -0700
Author date: 2014-11-25 10:41:11 -0700
Revision: 97114
Author: j.hill
Date: 2014-11-25T16:32:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/sangerseqR/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 96d4a5b87a7868c4fc3df3995cd241f06a72c546

    Changed version number.

Committed by: Jonathon Hill
Author Name: Jonathon Hill
Commit date: 2014-11-25 09:32:26 -0700
Author date: 2014-11-25 09:32:26 -0700
Revision: 97113
Author: j.hill
Date: 2014-11-25T16:24:40+00:00
Paths:
Added  /trunk/madman/Rpacks/sangerseqR/CITATION
Modified  /trunk/madman/Rpacks/sangerseqR/DESCRIPTION
Modified  /trunk/madman/Rpacks/sangerseqR/NAMESPACE
Modified  /trunk/madman/Rpacks/sangerseqR/R/ReadFileFunctions.R
Modified  /trunk/madman/Rpacks/sangerseqR/R/sangerseqmethods.R
Modified  /trunk/madman/Rpacks/sangerseqR/man/PolyPeakParser.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/abif-class.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/chromatogram.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/makeBaseCalls.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/read.abif.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/read.scf.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/readsangerseq.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/sangerseq-class.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/sangerseqAccessors.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/scf-class.Rd
Modified  /trunk/madman/Rpacks/sangerseqR/man/setAllelePhase.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 99194c06436383fc217f0ee501bb97b515f6703a

    Merge commit 'd531c69bec363581f286f314443ec57bac715038'

    Conflicts:
        DESCRIPTION

Committed by: Jonathon Hill
Author Name: Jonathon Hill
Commit date: 2014-11-25 09:24:30 -0700
Author date: 2014-11-25 09:24:30 -0700

Commit id: 5697d751ea34eacff55d0919135c09b0155491f2

    Fixed errors with opening some .ab1 files.

Committed by: Jonathon Hill
Author Name: Jonathon Hill
Commit date: 2014-11-24 15:44:13 -0700
Author date: 2014-11-24 15:44:13 -0700
Revision: 97112
Author: k.rue-albrecht
Date: 2014-11-25T16:01:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOexpress/DESCRIPTION
Modified  /trunk/madman/Rpacks/GOexpress/NEWS
Modified  /trunk/madman/Rpacks/GOexpress/R/analysis.R
Modified  /trunk/madman/Rpacks/GOexpress/R/post_analysis.R
Modified  /trunk/madman/Rpacks/GOexpress/R/toolkit.R
Modified  /trunk/madman/Rpacks/GOexpress/data/microarray2dataset.RData
Modified  /trunk/madman/Rpacks/GOexpress/data/prefix2dataset.RData
Modified  /trunk/madman/Rpacks/GOexpress/man/GOexpress-package.Rd
Modified  /trunk/madman/Rpacks/GOexpress/man/expression_plot_symbol.Rd
Modified  /trunk/madman/Rpacks/GOexpress/man/expression_profiles_symbol.Rd
Modified  /trunk/madman/Rpacks/GOexpress/man/microarray2dataset.Rd
Modified  /trunk/madman/Rpacks/GOexpress/man/prefix2dataset.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 0b0e943a1a47f8570bfca484c9b7fea3bd229275

    Devel 1.1.3. Included methods to generate the prefix2dataset and microarray2dataset tables to make life easier when Ensembl Biomart is updated. Updated the tables themselves with latest Ensembl species and microarray additions. Also included some additional information in those tables, and updated the methods dealing with them.

Committed by: Kevin Rue
Author Name: Kevin Rue
Commit date: 2014-11-25 16:07:03 +0000
Author date: 2014-11-25 16:07:03 +0000
Revision: 97111
Author: h.fang
Date: 2014-11-25T15:34:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/supraHex/DESCRIPTION
Modified  /trunk/madman/Rpacks/supraHex/NAMESPACE
Modified  /trunk/madman/Rpacks/supraHex/R/sBMH.r
Modified  /trunk/madman/Rpacks/supraHex/R/sCompReorder.r
Modified  /trunk/madman/Rpacks/supraHex/R/sPipeline.r
Modified  /trunk/madman/Rpacks/supraHex/R/sTrainBatch.r
Modified  /trunk/madman/Rpacks/supraHex/R/sTrainSeq.r
Modified  /trunk/madman/Rpacks/supraHex/inst/NEWS
Modified  /trunk/madman/Rpacks/supraHex/inst/staticdocs/CITATIONs.md
Modified  /trunk/madman/Rpacks/supraHex/inst/staticdocs/INSTALLATIONs.md
Modified  /trunk/madman/Rpacks/supraHex/inst/staticdocs/INSTALLATIONs_pre.md
Modified  /trunk/madman/Rpacks/supraHex/inst/staticdocs/README.md
Modified  /trunk/madman/Rpacks/supraHex/inst/staticdocs/demo/Hiratani.r
Added  /trunk/madman/Rpacks/supraHex/inst/staticdocs/demo/ISMB2014.r
Modified  /trunk/madman/Rpacks/supraHex/inst/staticdocs/demo/List_demos.txt
Modified  /trunk/madman/Rpacks/supraHex/man/sBMH.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sCompReorder.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sDistance.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sDmat.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sDmatCluster.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sDmatMinima.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sHexDist.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sHexGrid.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sInitial.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sMapOverlay.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sNeighAny.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sNeighDirect.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sPipeline.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sTopology.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sTrainBatch.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sTrainSeq.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sTrainology.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/sWriteData.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visColoralpha.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visColorbar.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visColormap.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visCompReorder.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visDmatCluster.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visDmatHeatmap.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visHeatmap.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visHeatmapAdv.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visHexComp.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visHexGrid.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visHexMapping.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visHexMulComp.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visHexPattern.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visKernels.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visTreeBootstrap.Rd
Modified  /trunk/madman/Rpacks/supraHex/man/visVp.Rd
Bump to the version 1.5.1
Revision: 97110
Author: stvjc
Date: 2014-11-25T15:16:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLBase/DESCRIPTION
Modified  /trunk/madman/Rpacks/gQTLBase/vignettes/gQTLBase.Rmd
minor tweaks for geuvStore usage
Revision: 97109
Author: j.leek
Date: 2014-11-25T15:14:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/sva/R/num.sv.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: bdd97589736c45b64abfdea1d0ed780bf72083fe

    Merge branch 'master' of https://github.com/jtleek/sva-devel

Committed by: jtleek
Author Name: jtleek
Commit date: 2014-11-25 10:13:59 -0500
Author date: 2014-11-25 10:13:59 -0500

Commit id: 4b1d957d4744015ab40faa6fb7c49ee5ceb24fc7

    updated n.sv to do min(m,n) when using method=be

Committed by: jtleek
Author Name: jtleek
Commit date: 2014-11-25 10:13:44 -0500
Author date: 2014-11-25 10:13:44 -0500
Revision: 97107
Author: a.oles
Date: 2014-11-25T13:31:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBImage/DESCRIPTION
Modified  /trunk/madman/Rpacks/EBImage/R/Image.R
version 4.9.4
- as.Image: coerce subclasses to 'Image'
Revision: 97106
Author: c.bartenhagen
Date: 2014-11-25T11:41:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/RSVSim/DESCRIPTION
Modified  /trunk/madman/Rpacks/RSVSim/R/Main.R
Modified  /trunk/madman/Rpacks/RSVSim/R/Misc.R
Modified  /trunk/madman/Rpacks/RSVSim/R/Simulation.R
Bugfixing: 1.Loading TDs from masked BSGenome hg19 package. 2.Repeat bias weights messed up when user passes them via parameter
Revision: 97105
Author: smyth
Date: 2014-11-25T11:35:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/edgeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/edgeR/R/plotMDS.DGEList.R
plotMDS.DGEList now stores axislabel depending on distance method used.
Revision: 97104
Author: s.aibar
Date: 2014-11-25T11:32:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/FGNet/DESCRIPTION
Modified  /trunk/madman/Rpacks/FGNet/NEWS
Modified  /trunk/madman/Rpacks/FGNet/R/3_clustersDistance.R
Modified  /trunk/madman/Rpacks/FGNet/man/clustersDistance.Rd
3.1.8 Added argument 'clustMethod' to 'clustersDistance' and changed default clustering method to 'average'
Revision: 97103
Author: smyth
Date: 2014-11-25T11:28:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/limma/DESCRIPTION
Modified  /trunk/madman/Rpacks/limma/NAMESPACE
Modified  /trunk/madman/Rpacks/limma/R/arrayWeights.R
Modified  /trunk/madman/Rpacks/limma/R/neqc.R
Modified  /trunk/madman/Rpacks/limma/R/plotMDS.R
Modified  /trunk/madman/Rpacks/limma/R/plots-ma.R
Modified  /trunk/madman/Rpacks/limma/R/venn.R
Modified  /trunk/madman/Rpacks/limma/inst/doc/changelog.txt
Modified  /trunk/madman/Rpacks/limma/man/plotMDS.Rd
Modified  /trunk/madman/Rpacks/limma/man/plotma.Rd
Modified  /trunk/madman/Rpacks/limma/man/venn.Rd
25 Nov 2014: limma 3.23.2

- plotMDS() now stores 'axislabel', depending on the method used to
  compute distances, and using this for axis labels.

- vennDiagram now fills circles with specified colors.

- voomWithQualityWeights() now stores observation weights and array
  weights separately.

- plotMA method for EListRaw objects.

- nec() and neqc() now remove the Eb component if it exists in an
  EListRaw object.
Revision: 97101
Author: hpages
Date: 2014-11-25T10:46:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/kebabs/DESCRIPTION
Modified  /trunk/madman/Rpacks/kebabs/src/ByteStringVector.c
'seq' member was renamed 'ptr' in data structs Chars_holder, Ints_holder, and
Doubles_holder.
Revision: 97100
Author: hpages
Date: 2014-11-25T10:37:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/DESCRIPTION
Modified  /trunk/madman/Rpacks/ShortRead/src/alphabet.c
Modified  /trunk/madman/Rpacks/ShortRead/src/io.c
Modified  /trunk/madman/Rpacks/ShortRead/src/sampler.c
Modified  /trunk/madman/Rpacks/ShortRead/src/trim.c
'seq' member was renamed 'ptr' in data structs Chars_holder, Ints_holder, and
Doubles_holder.
Revision: 97099
Author: hpages
Date: 2014-11-25T10:29:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/DESCRIPTION
Modified  /trunk/madman/Rpacks/rtracklayer/src/twoBit.c
'seq' member was renamed 'ptr' in data structs Chars_holder, Ints_holder, and
Doubles_holder.
Revision: 97098
Author: hpages
Date: 2014-11-25T10:22:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/rSFFreader/DESCRIPTION
Modified  /trunk/madman/Rpacks/rSFFreader/src/SFF-io.c
'seq' member was renamed 'ptr' in data structs Chars_holder, Ints_holder, and
Doubles_holder.
Revision: 97097
Author: hpages
Date: 2014-11-25T10:16:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
Modified  /trunk/madman/Rpacks/Rsamtools/src/fafile.c
Modified  /trunk/madman/Rpacks/Rsamtools/src/utilities.c
'seq' member was renamed 'ptr' in data structs Chars_holder, Ints_holder, and
Doubles_holder.
Revision: 97096
Author: hpages
Date: 2014-11-25T09:58:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/GNCList-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/findOverlaps-methods.R
Modify findOverlaps_GNCList() to take advantage of support for "on-the-fly
preprocessing" in IRanges:::NCList_find_overlaps_by_group_and_combine().
This speeds up and reduce memory usage of findOverlaps() on GRanges objects
when algorithm="nclist" even more.
Revision: 97095
Author: hpages
Date: 2014-11-25T09:51:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/R/NCList-class.R
Modified  /trunk/madman/Rpacks/IRanges/src/NCList.c
NCList_find_overlaps_by_group_and_combine() now supports "on-the-fly
preprocessing". This will speedup and reduce memory usage of findOverlaps() on
GRanges objects when algorithm="nclist".

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