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Revision: 93061
Author: r.castelo
Date: 2014-07-30T22:34:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/R/methods-VariantFilteringResults.R
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
Added github url to the DESCRIPTION file.
Revision: 93059
Author: m.love
Date: 2014-07-30T20:59:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/src/DESeq2.cpp
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Rcpp::checkUserInterrupt
Revision: 93055
Author: b.fischer
Date: 2014-07-30T18:36:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/rhdf5/CHANGES
Modified  /trunk/madman/Rpacks/rhdf5/R/h5checktype.R
Modified  /trunk/madman/Rpacks/rhdf5/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/rhdf5/man/H5F.Rd
Modified  /trunk/madman/Rpacks/rhdf5/DESCRIPTION
A warning is shown in high level function (h5read, h5write and others), if an open HDF5 handle already exists for the specified filename
Revision: 93054
Author: l.pantano
Date: 2014-07-30T18:12:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGreport/.travis.yml
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: ead27125d3c74cc7006c78e3ace5dc6f6b1b0ada
Commit message: problem installing r-base in travis
Committed by: Lorena Pantano
Author Name: Lorena Pantano
Commit date: 2014-07-30 14:12:16 -0400
Author date: 2014-07-30 14:12:16 -0400

Revision: 93053
Author: l.pantano
Date: 2014-07-30T17:52:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGreport/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 612b991dba3aea77e06b4ba0e12b6473e282f484
Commit message: new z version for some new files
Committed by: Lorena Pantano
Author Name: Lorena Pantano
Commit date: 2014-07-30 13:51:58 -0400
Author date: 2014-07-30 13:51:58 -0400

Revision: 93048
Author: a.oles
Date: 2014-07-30T15:44:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocStyle/R/html_document.R
version 1.3.6
- html_document: disable the default bootstrap theme
Revision: 93047
Author: g.yu
Date: 2014-07-30T15:42:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOSE/vignettes/DOSE.Rnw
Modified  /trunk/madman/Rpacks/DOSE/NEWS
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 857b0e2dee8383f47967671e6d9a59f5477fd35d
Commit message: update vignettes
Committed by: Guangchuang Yu
Author Name: Guangchuang Yu
Commit date: 2014-07-30 23:42:30 +0800
Author date: 2014-07-30 23:42:30 +0800

Revision: 93045
Author: a.oles
Date: 2014-07-30T15:02:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/man/markdown.Rd
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Added  /trunk/madman/Rpacks/BiocStyle/R/html_document.R
Modified  /trunk/madman/Rpacks/BiocStyle/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocStyle/vignettes/HtmlStyle.Rmd
version 1.3.5
- support for 'rmarkdown' html output
Revision: 93042
Author: g.yu
Date: 2014-07-30T14:18:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOSE/DESCRIPTION
Added  /trunk/madman/Rpacks/DOSE/man/enrichMap.Rd
Added  /trunk/madman/Rpacks/DOSE/R/enrichMap.R
Modified  /trunk/madman/Rpacks/DOSE/NAMESPACE
Modified  /trunk/madman/Rpacks/DOSE/NEWS
Modified  /trunk/madman/Rpacks/DOSE/R/gsea.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: b870ff5265f6d997eedada334b256f88584fb0c4
Commit message: enrichMap
Committed by: Guangchuang Yu
Author Name: Guangchuang Yu
Commit date: 2014-07-30 22:18:20 +0800
Author date: 2014-07-30 22:18:20 +0800

Revision: 93041
Author: g.finak
Date: 2014-07-30T14:00:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/MIMOSA/R/MIMOSA.R
Fix annotation bug in results
Revision: 93035
Author: g.klambauer
Date: 2014-07-30T08:17:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/dexus/inst/CITATION
Modified  /trunk/madman/Rpacks/dexus/DESCRIPTION
updated citation
Revision: 93034
Author: g.klambauer
Date: 2014-07-30T08:14:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/cn.mops/R/normalizeChromosomes.R
Modified  /trunk/madman/Rpacks/cn.mops/DESCRIPTION
Modified  /trunk/madman/Rpacks/cn.mops/R/getReadCountsFromBAM.R
Modified  /trunk/madman/Rpacks/cn.mops/R/referencecn.mops.R
Modified  /trunk/madman/Rpacks/cn.mops/R/segPlot.R
segplot and normalization
Revision: 93030
Author: jq.sun
Date: 2014-07-30T03:18:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCC/R/ROKU.R
Modified  /trunk/madman/Rpacks/TCC/DESCRIPTION
bugfix for ROKU
Revision: 93028
Author: v.obenchain
Date: 2014-07-30T02:57:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFiles/vignettes/GenomicFiles.Rnw
Modified  /trunk/madman/Rpacks/GenomicFiles/DESCRIPTION
edits to vignette
Revision: 93027
Author: v.obenchain
Date: 2014-07-30T02:14:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
bump version to 0.99.z
Revision: 93026
Author: v.obenchain
Date: 2014-07-30T01:47:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/vignettes/Overview.Rnw
edits to vignette
Revision: 93021
Author: b.fischer
Date: 2014-07-29T22:09:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/rhdf5/CHANGES
Modified  /trunk/madman/Rpacks/rhdf5/src/H5F.c
Modified  /trunk/madman/Rpacks/rhdf5/NAMESPACE
Modified  /trunk/madman/Rpacks/rhdf5/src/H5F.h
Modified  /trunk/madman/Rpacks/rhdf5/src/wrap.c
Modified  /trunk/madman/Rpacks/rhdf5/DESCRIPTION
Modified  /trunk/madman/Rpacks/rhdf5/R/H5F.R
Added low level functions H5Fis_hdf5, H5Fget_filesize, and H5Fget_name
Revision: 93019
Author: g.pau
Date: 2014-07-29T18:32:10+00:00
Paths:
Added  /trunk/madman/Rpacks/HTSeqGenie/man/findVariantFile.Rd
Added  /trunk/madman/Rpacks/HTSeqGenie/man/isSparse.Rd
added HTSeqGenie/man/findVariantFile.Rd HTSeqGenie/man/isSparse.Rd
Revision: 93018
Author: m.jiang
Date: 2014-07-29T18:02:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/COMPASS/man/metadata.Rd
Modified  /trunk/madman/Rpacks/COMPASS/R/utils.R
Modified  /trunk/madman/Rpacks/COMPASS/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 377ad5d3e1f9fc9be6a6c8fc53e0a5c495667c65
Commit message: fix docs for metadata<-
Committed by: mikejiang
Author Name: mikejiang
Commit date: 2014-07-29 10:49:27 -0700
Author date: 2014-07-29 10:49:27 -0700

Revision: 93014
Author: d.tenenbaum
Date: 2014-07-29T14:03:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/affycoretools/DESCRIPTION
bump version to number higher than before (after it was bumped in the wrong
direction)
Revision: 93013
Author: hpages
Date: 2014-07-29T06:06:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/vignettes/GenomicRangesHOWTOs.Rnw
describe input data only once, in the introduction
Revision: 93012
Author: p.haverty
Date: 2014-07-29T05:38:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/bigmemoryExtras/DESCRIPTION
Edited github url
Revision: 93011
Author: p.haverty
Date: 2014-07-29T05:38:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/genoset/DESCRIPTION
Edited github url
Revision: 93010
Author: p.haverty
Date: 2014-07-29T05:32:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/genoset/DESCRIPTION
Added github url
Revision: 93009
Author: p.haverty
Date: 2014-07-29T05:31:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/bigmemoryExtras/DESCRIPTION
Added github url
Revision: 93004
Author: g.yu
Date: 2014-07-29T03:06:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/NEWS
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 2ee14fc72722fdf87868e5216ada0c722e4031ba
Commit message: update NEWS
Committed by: Guangchuang Yu
Author Name: Guangchuang Yu
Commit date: 2014-07-29 11:05:35 +0800
Author date: 2014-07-29 11:05:35 +0800

Revision: 93003
Author: g.yu
Date: 2014-07-29T03:04:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/man/getGenomicAnnotation.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/man/enrichAnnoOverlap.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/man/enrichPeakOverlap.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChIPseeker/man/annotatePeak.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: e07df5ca0969a42911bb618e2236eb3f57462b48
Commit message: update man files
Committed by: Guangchuang Yu
Author Name: Guangchuang Yu
Commit date: 2014-07-29 11:03:48 +0800
Author date: 2014-07-29 11:03:48 +0800

Revision: 93002
Author: hpages
Date: 2014-07-29T02:53:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/man/TxDb-class.Rd
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/TxDb-class.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/NAMESPACE
finally remove TranscriptDb class
Revision: 93001
Author: m.lawrence
Date: 2014-07-29T02:51:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/R/eval-utils.R
fix subset(x, i) on zero column DataFrame
Revision: 92998
Author: hpages
Date: 2014-07-29T02:07:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPpeakAnno/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChIPpeakAnno/man/assignChromosomeRegion.Rd
Modified  /trunk/madman/Rpacks/ChIPpeakAnno/R/assignChromosomeRegion.R
follow renaming of TranscriptDb class -> TxDb
Revision: 92997
Author: v.obenchain
Date: 2014-07-29T01:31:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/inst/unitTests/test_mapCoords-methods.R
Modified  /trunk/madman/Rpacks/GenomicRanges/R/mapCoords-methods.R
add arg to .orderElementsByTranscription() to control if
ranges on neg strand are ordered large-to-small
Revision: 92990
Author: hpages
Date: 2014-07-29T00:05:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/casper/DESCRIPTION
Modified  /trunk/madman/Rpacks/casper/R/makeTranscriptDbFromGFF.R
Modified  /trunk/madman/Rpacks/casper/NAMESPACE
Modified  /trunk/madman/Rpacks/casper/man/procGenome.Rd
Modified  /trunk/madman/Rpacks/casper/R/procGenome.R
follow renaming of TranscriptDb class -> TxDb
Revision: 92986
Author: hpages
Date: 2014-07-28T23:48:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/man/getGenomicAnnotation.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/R/plotAnno.R
Modified  /trunk/madman/Rpacks/ChIPseeker/man/enrichAnnoOverlap.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/man/plotAnnoBar.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/man/peakHeatmap.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/vignettes/ChIPseeker.Rnw
Modified  /trunk/madman/Rpacks/ChIPseeker/R/plotTagMatrix.R
Modified  /trunk/madman/Rpacks/ChIPseeker/R/plotDistToTSS.R
Modified  /trunk/madman/Rpacks/ChIPseeker/R/tagMatrix.R
Modified  /trunk/madman/Rpacks/ChIPseeker/R/enrichOverlap.R
Modified  /trunk/madman/Rpacks/ChIPseeker/man/plotAvgProf2.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/R/vennplot.R
Modified  /trunk/madman/Rpacks/ChIPseeker/man/plotAnnoPie.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/man/getPromoters.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/man/shuffle.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/R/annotatePeak.R
Modified  /trunk/madman/Rpacks/ChIPseeker/R/utilities.R
Modified  /trunk/madman/Rpacks/ChIPseeker/R/getGenomicAnnotation.R
Modified  /trunk/madman/Rpacks/ChIPseeker/man/plotDistToTSS.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/man/enrichPeakOverlap.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChIPseeker/man/vennplot.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/man/annotatePeak.Rd
follow renaming of TranscriptDb class -> TxDb
Revision: 92985
Author: hpages
Date: 2014-07-28T23:37:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/seqinfo.Rd
Modified  /trunk/madman/Rpacks/GenomeInfoDb/man/seqlevels-wrappers.Rd
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/seqinfo.R
Modified  /trunk/madman/Rpacks/GenomeInfoDb/R/seqlevels-wrappers.R
follow renaming of TranscriptDb class -> TxDb
Revision: 92984
Author: hpages
Date: 2014-07-28T23:33:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/flipflop/vignettes/flipflop.Rnw
follow renaming of TranscriptDb class -> TxDb
Revision: 92981
Author: hpages
Date: 2014-07-28T23:23:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipseq/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipseq/R/context.R
follow renaming of TranscriptDb class -> TxDb
Revision: 92980
Author: hpages
Date: 2014-07-28T23:22:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/Gviz/R/Gviz-methods.R
Modified  /trunk/madman/Rpacks/Gviz/DESCRIPTION
Modified  /trunk/madman/Rpacks/Gviz/TODO
Modified  /trunk/madman/Rpacks/Gviz/man/GeneRegionTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/NAMESPACE
Modified  /trunk/madman/Rpacks/Gviz/vignettes/Gviz.Rnw
follow renaming of TranscriptDb class -> TxDb
Revision: 92979
Author: hpages
Date: 2014-07-28T23:19:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantTools/R/callableGenes.R
Modified  /trunk/madman/Rpacks/VariantTools/DESCRIPTION
follow renaming of TranscriptDb class -> TxDb
Revision: 92978
Author: hpages
Date: 2014-07-28T23:17:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/rtracklayer/man/BEDFile-class.Rd
Modified  /trunk/madman/Rpacks/rtracklayer/man/GFFFile-class.Rd
follow renaming of TranscriptDb class -> TxDb
Revision: 92977
Author: hpages
Date: 2014-07-28T23:16:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/man/spViewPerFeature.Rd
follow renaming of TranscriptDb class -> TxDb
Revision: 92976
Author: hpages
Date: 2014-07-28T23:15:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/gmapR/NAMESPACE
Modified  /trunk/madman/Rpacks/gmapR/man/GmapGenome-class.Rd
Modified  /trunk/madman/Rpacks/gmapR/DESCRIPTION
Modified  /trunk/madman/Rpacks/gmapR/R/GmapGenome-class.R
follow renaming of TranscriptDb class -> TxDb
Revision: 92975
Author: hpages
Date: 2014-07-28T23:13:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/CompGO/R/fullPipeline.R
Modified  /trunk/madman/Rpacks/CompGO/man/annotateBedFromDb.Rd
Modified  /trunk/madman/Rpacks/CompGO/DESCRIPTION
follow renaming of TranscriptDb class -> TxDb
Revision: 92974
Author: hpages
Date: 2014-07-28T23:11:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/R/createAnnotationFile.R
follow renaming of TranscriptDb class -> TxDb
Revision: 92973
Author: hpages
Date: 2014-07-28T23:08:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/QuasR/DESCRIPTION
Modified  /trunk/madman/Rpacks/QuasR/man/qCount.Rd
Modified  /trunk/madman/Rpacks/QuasR/vignettes/QuasR.Rnw
Modified  /trunk/madman/Rpacks/QuasR/R/qCount.R
follow renaming of TranscriptDb class -> TxDb
Revision: 92972
Author: hpages
Date: 2014-07-28T23:03:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/easyRNASeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/easyRNASeq/man/easyRNASeq-package.Rd
Modified  /trunk/madman/Rpacks/easyRNASeq/R/easyRNASeq-package.R
follow renaming of TranscriptDb class -> TxDb
Revision: 92971
Author: hpages
Date: 2014-07-28T23:01:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationForge/vignettes/MakingNewAnnotationPackages.Rnw
follow renaming of TranscriptDb class -> TxDb
Revision: 92970
Author: hpages
Date: 2014-07-28T23:00:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/waveTiling/man/plotWfm.Rd
Modified  /trunk/madman/Rpacks/waveTiling/vignettes/waveTiling-vignette.Rnw
Modified  /trunk/madman/Rpacks/waveTiling/man/getNonAnnotatedRegions.Rd
Modified  /trunk/madman/Rpacks/waveTiling/DESCRIPTION
Modified  /trunk/madman/Rpacks/waveTiling/man/getSigGenes.Rd
follow renaming of TranscriptDb class -> TxDb
Revision: 92968
Author: hpages
Date: 2014-07-28T22:51:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/RNASeqGenie/R/appendOverlappingExons.R
Modified  /trunk/madman/Rpacks/RNASeqGenie/DESCRIPTION
Modified  /trunk/madman/Rpacks/RNASeqGenie/R/processGsnapResults.R
follow renaming of TranscriptDb class -> TxDb
Revision: 92967
Author: hpages
Date: 2014-07-28T22:48:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/qpgraph/R/eQTLnetworkEstimationParam-methods.R
Modified  /trunk/madman/Rpacks/qpgraph/DESCRIPTION
follow renaming of TranscriptDb class -> TxDb
Revision: 92965
Author: hpages
Date: 2014-07-28T22:47:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/cummeRbund/R/database-setup.R
follow renaming of TranscriptDb class -> TxDb
Revision: 92963
Author: m.carlson
Date: 2014-07-28T22:43:52+00:00
Paths:
Added  /trunk/madman/Rpacks/OncoSimulR/src/OncoSimul.h
Added  /trunk/madman/Rpacks/ballgown/R/stattest.R
Added  /trunk/madman/Rpacks/STAN/man/humanCD4T_flags_ex.Rd
Added  /trunk/madman/Rpacks/ballgown/vignettes/greycite.bib
Added  /trunk/madman/Rpacks/ballgown/man/dirs.Rd
Added  /trunk/madman/Rpacks/STAN/man/getViterbi.Rd
Added  /trunk/madman/Rpacks/missMethyl/R/plottingFunctions.R
Added  /trunk/madman/Rpacks/STAN/man/humanCD4T_initCovs.Rd
Added  /trunk/madman/Rpacks/STAN/R/AllClasses.R
Added  /trunk/madman/Rpacks/missMethyl
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample11/t_data.ctab
Added  /trunk/madman/Rpacks/STAN
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample13/i2t.ctab
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample15/t_data.ctab
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample09/e2t.ctab
Added  /trunk/madman/Rpacks/STAN/src/EmissionFunction.cpp
Added  /trunk/madman/Rpacks/ballgown/tests/testthat/test-constructor.R
Added  /trunk/madman/Rpacks/OncoSimulR/src/OncoSimul.cpp
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample19/t_data.ctab
Added  /trunk/madman/Rpacks/STAN/man/yeastTF_databychrom_ex.Rd
Added  /trunk/madman/Rpacks/ballgown/inst/extdata
Added  /trunk/madman/Rpacks/STAN/man/bdHMM-class.Rd
Added  /trunk/madman/Rpacks/STAN/man/humanCD4T_initMeans.Rd
Added  /trunk/madman/Rpacks/OncoSimulR/inst/NEWS
Added  /trunk/madman/Rpacks/ballgown/R/pctOverlap.R
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample04/e_data.ctab
Added  /trunk/madman/Rpacks/STAN/src/JointlyIndependent.h
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Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample18/i2t.ctab
Added  /trunk/madman/Rpacks/ballgown/man/pData.Rd
Added  /trunk/madman/Rpacks/ballgown/R/getAttributeField.R
Added  /trunk/madman/Rpacks/STAN/R/bdHMMTransMatOptim.R
Added  /trunk/madman/Rpacks/STAN/man/yeastTF_initCovs.Rd
Added  /trunk/madman/Rpacks/STAN/inst
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample10/e_data.ctab
Added  /trunk/madman/Rpacks/STAN/R/bdConstraints.R
Added  /trunk/madman/Rpacks/ballgown/man/mergedDate.Rd
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample14/e_data.ctab
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample12/i_data.ctab
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample18/e_data.ctab
Added  /trunk/madman/Rpacks/ballgown/man/annotate_assembly.Rd
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample16/i_data.ctab
Added  /trunk/madman/Rpacks/STAN/data/yeastTF_probeAnno_ex.rda
Added  /trunk/madman/Rpacks/OncoSimulR/man/poset.Rd
Added  /trunk/madman/Rpacks/STAN/data/humanCD4T_signal_ex.rda
Added  /trunk/madman/Rpacks/missMethyl/man/missMethyl-package.Rd
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample11/i2t.ctab
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample07/e2t.ctab
Added  /trunk/madman/Rpacks/ballgown/man/plotLatentTranscripts.Rd
Added  /trunk/madman/Rpacks/ballgown/man/eexpr.Rd
Added  /trunk/madman/Rpacks/STAN/data/yeastTF_databychrom_ex.rda
Added  /trunk/madman/Rpacks/ballgown/man/gffReadGR.Rd
Added  /trunk/madman/Rpacks/STAN/src/matUtils.cpp
Added  /trunk/madman/Rpacks/STAN/data/yeastTF_SGDGenes.rda
Added  /trunk/madman/Rpacks/ballgown/inst
Added  /trunk/madman/Rpacks/STAN/man/yeastTF_SGDGenes.Rd
Added  /trunk/madman/Rpacks/ballgown/man/last.Rd
Added  /trunk/madman/Rpacks/ballgown/man/stattest.Rd
Added  /trunk/madman/Rpacks/STAN/R/logdiwish.R
Added  /trunk/madman/Rpacks/STAN/src/MemoryAllocation.h
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample02/t_data.ctab
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample20/i2t.ctab
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample16/e2t.ctab
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample06/t_data.ctab
Added  /trunk/madman/Rpacks/ballgown/inst/extdata/sample04/i2t.ctab
Added  /trunk/madman/Rpacks/missMethyl/man/getLeveneResiduals.Rd
Added  /trunk/madman/Rpacks/ballgown/R/last.R
Added  /trunk/madman/Rpacks/STAN/src/InitialProbability.h
Adds OncoSimulR, missMethyl, ballgown and STAN to the repos.
Revision: 92962
Author: hpages
Date: 2014-07-28T22:37:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/biomvRCNS/vignettes/biomvRCNS.Rnw
Modified  /trunk/madman/Rpacks/biomvRCNS/man/biomvRhsmm.Rd
Modified  /trunk/madman/Rpacks/biomvRCNS/DESCRIPTION
Modified  /trunk/madman/Rpacks/biomvRCNS/R/biomvRhsmm.R
Modified  /trunk/madman/Rpacks/biomvRCNS/man/sojournAnno.Rd
follow renaming of TranscriptDb class -> TxDb
Revision: 92961
Author: hpages
Date: 2014-07-28T22:34:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggbio/DESCRIPTION
need to have testthat in the Suggests field (used in the testing suite)

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