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Revision: 106843
Author: t.girke
Date: 2015-07-28T16:53:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.R
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 7b825538f69b3aec89ab1fa538a63be9fa4dce4a

    fix for missing systemPipeRdata

Revision: 106842
Author: t.girke
Date: 2015-07-28T16:49:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/systemPipeR/README
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: fc33258eeb06c05a0c817e577b4c318055c69f0a

    fix for missing systemPipeRdata

Revision: 106839
Author: b.calder
Date: 2015-07-28T16:03:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/savR/CHANGES
Modified  /trunk/madman/Rpacks/savR/DESCRIPTION
Modified  /trunk/madman/Rpacks/savR/R/savR-package.R
Modified  /trunk/madman/Rpacks/savR/man/savR-package.Rd
merge master

From: R. Brent Calder <brent.calder@einstein.yu.edu>
Revision: 106838
Author: t.girke
Date: 2015-07-28T15:40:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 62ac22c6eae1024195a442d38fd6be2fc9f05043

    some edits

Revision: 106835
Author: p.moulos
Date: 2015-07-28T13:45:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/metaseqR/DESCRIPTION
Modified  /trunk/madman/Rpacks/metaseqR/NAMESPACE
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqR-package.R
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.annotation.R
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.argcheck.R
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.count.R
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.json.R
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.main.R
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.meta.R
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.plot.R
Modified  /trunk/madman/Rpacks/metaseqR/R/metaseqr.util.R
Modified  /trunk/madman/Rpacks/metaseqR/inst/NEWS
Modified  /trunk/madman/Rpacks/metaseqR/man/check.num.args.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/diagplot.de.heatmap.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/diagplot.edaseq.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/diagplot.filtered.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/diagplot.metaseqr.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/diagplot.noiseq.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/diagplot.pairs.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/diagplot.venn.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/diagplot.volcano.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/downsample.counts.Rd
Added  /trunk/madman/Rpacks/metaseqR/man/fisher.method.Rd
Added  /trunk/madman/Rpacks/metaseqR/man/fisher.method.perm.Rd
Added  /trunk/madman/Rpacks/metaseqR/man/fisher.sum.Rd
Added  /trunk/madman/Rpacks/metaseqR/man/make.avg.expression.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/metaseqR-package.Rd
Modified  /trunk/madman/Rpacks/metaseqR/man/metaseqr.Rd
Added one more output list member of the main pipeline (metaseqr) containing all the processed data in a way that can be easily used for further downstream analysis in R. Fixed broken dependency with removed CRAN package MADAM which was used for the Fisher p-value combination. The fix was done by copying the two required functions from the last MADAM archived version (1.2). Fixed a bug in make.sample.list which rendered the function unusable.
Revision: 106834
Author: b.calder
Date: 2015-07-28T13:45:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/savR/DESCRIPTION
Modified  /trunk/madman/Rpacks/savR/R/savR-methods.R
Modified  /trunk/madman/Rpacks/savR/R/savR-package.R
Modified  /trunk/madman/Rpacks/savR/README.md
Modified  /trunk/madman/Rpacks/savR/man/savR-package.Rd
Modified  /trunk/madman/Rpacks/savR/tests/testthat/test_load.R
workaround for ErrorMetricsOut.bin with lanes with no PhiX data.

From: R. Brent Calder <brent.calder@einstein.yu.edu>
Revision: 106833
Author: b.calder
Date: 2015-07-28T13:44:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/savR/R/savR-methods.R
Modified  /trunk/madman/Rpacks/savR/tests/testthat/test_load.R
added check and test for empty binary files

From: R. Brent Calder <brent.calder@einstein.yu.edu>
Revision: 106832
Author: g.yu
Date: 2015-07-28T12:46:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/vignettes/ChIPseeker.Rmd
update vignette
Revision: 106831
Author: f.mueller
Date: 2015-07-28T11:25:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/RnBeads/R/RnBiseqSet-class.R
status check fix for not disk dumped objects
Revision: 106830
Author: f.mueller
Date: 2015-07-28T10:37:33+00:00
Paths:
Added  /trunk/madman/Rpacks/RnBeads/inst/extdata/chromSizes/hg38.chrom.sizes
added chrom.sizes for exporting hg38 data
Revision: 106829
Author: t.le
Date: 2015-07-28T02:52:13+00:00
Paths:
Added  /trunk/madman/Rpacks/miRLAB/miRLAB_0.99.3.tar.gz
Add ValidateAll GOBP and KEGG
Revision: 106827
Author: l.gatto
Date: 2015-07-28T01:24:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLInterfaces/NAMESPACE
import hwriter::hwrite
Revision: 106826
Author: l.gatto
Date: 2015-07-28T01:24:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLInterfaces/DESCRIPTION
Modified  /trunk/madman/Rpacks/MLInterfaces/NEWS
import hwriter::hwrite
Revision: 106825
Author: l.gatto
Date: 2015-07-28T01:24:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLInterfaces/R/pv.R
complete fun arg name
Revision: 106824
Author: l.gatto
Date: 2015-07-28T01:24:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLInterfaces/man/hclustWidget.Rd
add missing arg doc
Revision: 106823
Author: l.gatto
Date: 2015-07-28T01:24:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLInterfaces/R/performance-analytics.R
fix mis-used ... in perf-analytics methods
Revision: 106822
Author: l.gatto
Date: 2015-07-28T01:24:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLInterfaces/R/performance-analytics.R
fix naAs0 propagation
Revision: 106821
Author: l.gatto
Date: 2015-07-28T01:23:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLInterfaces/R/performance-analytics.R
more naAs0 propagation
Revision: 106820
Author: l.gatto
Date: 2015-07-28T01:23:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLInterfaces/DESCRIPTION
Modified  /trunk/madman/Rpacks/MLInterfaces/NEWS
Modified  /trunk/madman/Rpacks/MLInterfaces/R/performance-analytics.R
fix conflicts
Revision: 106819
Author: x.zheng
Date: 2015-07-28T00:57:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/gdsfmt/src/gdsfmt.cpp
Commit made by the Bioconductor Git-SVN bridge.

Commit id: fb74f1f97da55b2ad1445dcbe9839aa7309d7834

    missing a line (seems a github bug)

Revision: 106818
Author: x.zheng
Date: 2015-07-28T00:55:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/gdsfmt/R/gdsfmt-main.r
Modified  /trunk/madman/Rpacks/gdsfmt/README.md
Modified  /trunk/madman/Rpacks/gdsfmt/man/addfile.gdsn.Rd
Modified  /trunk/madman/Rpacks/gdsfmt/man/addfolder.gdsn.Rd
Modified  /trunk/madman/Rpacks/gdsfmt/man/readex.gdsn.Rd
Modified  /trunk/madman/Rpacks/gdsfmt/src/gdsfmt.cpp
Commit made by the Bioconductor Git-SVN bridge.

Commit id: b5a6f62af2ab9e0cd4cf90e9a21e258d9240a708

    optimize "readex.gdsn" when 'sel' is numeric

Revision: 106817
Author: a.lun
Date: 2015-07-28T00:40:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/diffHic/DESCRIPTION
Modified  /trunk/madman/Rpacks/diffHic/NAMESPACE
Modified  /trunk/madman/Rpacks/diffHic/R/boxPairs.R
Modified  /trunk/madman/Rpacks/diffHic/R/classes.R
Modified  /trunk/madman/Rpacks/diffHic/R/clusterPairs.R
Modified  /trunk/madman/Rpacks/diffHic/R/compartmentalize.R
Modified  /trunk/madman/Rpacks/diffHic/R/connectCounts.R
Modified  /trunk/madman/Rpacks/diffHic/R/consolidatePairs.R
Modified  /trunk/madman/Rpacks/diffHic/R/correctedContact.R
Modified  /trunk/madman/Rpacks/diffHic/R/filterPeaks.R
Modified  /trunk/madman/Rpacks/diffHic/R/filters.R
Modified  /trunk/madman/Rpacks/diffHic/R/getDistance.R
Modified  /trunk/madman/Rpacks/diffHic/R/h5utils.R
Modified  /trunk/madman/Rpacks/diffHic/R/marginCounts.R
Modified  /trunk/madman/Rpacks/diffHic/R/mergePairs.R
Added  /trunk/madman/Rpacks/diffHic/R/neighborCounts.R
Deleted  /trunk/madman/Rpacks/diffHic/R/neighbourCounts.R
Modified  /trunk/madman/Rpacks/diffHic/R/normalizeCNV.R
Modified  /trunk/madman/Rpacks/diffHic/R/plotPlaid.R
Modified  /trunk/madman/Rpacks/diffHic/R/prepPseudoPairs.R
Modified  /trunk/madman/Rpacks/diffHic/R/preparePairs.R
Modified  /trunk/madman/Rpacks/diffHic/R/savePairs.R
Modified  /trunk/madman/Rpacks/diffHic/R/squareCounts.R
Modified  /trunk/madman/Rpacks/diffHic/R/totalCounts.R
Modified  /trunk/madman/Rpacks/diffHic/inst/NEWS.Rd
Added  /trunk/madman/Rpacks/diffHic/inst/tests/test-empty.R
Added  /trunk/madman/Rpacks/diffHic/inst/tests/test-empty.Rout.save
Modified  /trunk/madman/Rpacks/diffHic/inst/tests/test-neighbor.R
Modified  /trunk/madman/Rpacks/diffHic/inst/tests/test-neighbor.Rout.save
Modified  /trunk/madman/Rpacks/diffHic/man/DNaseHiC.Rd
Modified  /trunk/madman/Rpacks/diffHic/man/boxPairs.Rd
Modified  /trunk/madman/Rpacks/diffHic/man/compartmentalize.Rd
Modified  /trunk/madman/Rpacks/diffHic/man/correctedContact.Rd
Modified  /trunk/madman/Rpacks/diffHic/man/enrichedPairs.Rd
Modified  /trunk/madman/Rpacks/diffHic/man/filterPeaks.Rd
Added  /trunk/madman/Rpacks/diffHic/man/neighborCounts.Rd
Deleted  /trunk/madman/Rpacks/diffHic/man/neighbourCounts.Rd
Modified  /trunk/madman/Rpacks/diffHic/man/plotDI.Rd
Modified  /trunk/madman/Rpacks/diffHic/man/plotPlaid.Rd
Modified  /trunk/madman/Rpacks/diffHic/src/count_background.cpp
Added  /trunk/madman/Rpacks/diffHic/src/neighbors.cpp
Added  /trunk/madman/Rpacks/diffHic/src/neighbors.h
Deleted  /trunk/madman/Rpacks/diffHic/src/neighbours.cpp
Deleted  /trunk/madman/Rpacks/diffHic/src/neighbours.h
Modified  /trunk/madman/Rpacks/diffHic/src/quadrant_bg.cpp
Renamed neighborCounts, switched to seq_* coding style.
Revision: 106814
Author: a.lun
Date: 2015-07-27T23:52:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/csaw/DESCRIPTION
Modified  /trunk/madman/Rpacks/csaw/R/basefun.R
Modified  /trunk/madman/Rpacks/csaw/R/checkBimodality.R
Modified  /trunk/madman/Rpacks/csaw/R/consolidateSizes.R
Modified  /trunk/madman/Rpacks/csaw/R/correlateReads.R
Modified  /trunk/madman/Rpacks/csaw/R/detailRanges.R
Modified  /trunk/madman/Rpacks/csaw/R/dumpPE.R
Modified  /trunk/madman/Rpacks/csaw/R/extractReads.R
Modified  /trunk/madman/Rpacks/csaw/R/filterWindows.R
Modified  /trunk/madman/Rpacks/csaw/R/getPESizes.R
Modified  /trunk/madman/Rpacks/csaw/R/normalizeCounts.R
Modified  /trunk/madman/Rpacks/csaw/R/overlapStats.R
Modified  /trunk/madman/Rpacks/csaw/R/profileSites.R
Modified  /trunk/madman/Rpacks/csaw/R/regionCounts.R
Modified  /trunk/madman/Rpacks/csaw/R/strandedCounts.R
Modified  /trunk/madman/Rpacks/csaw/R/windowCounts.R
Modified  /trunk/madman/Rpacks/csaw/inst/NEWS.Rd
Added  /trunk/madman/Rpacks/csaw/inst/tests/test-empty.R
Added  /trunk/madman/Rpacks/csaw/inst/tests/test-empty.Rout.save
Modified  /trunk/madman/Rpacks/csaw/man/detailRanges.Rd
Modified  /trunk/madman/Rpacks/csaw/man/profileSites.Rd
Modified  /trunk/madman/Rpacks/csaw/man/wwhm.Rd
Modified  /trunk/madman/Rpacks/csaw/src/annotator.cpp
Modified  /trunk/madman/Rpacks/csaw/src/best_in_cluster.cpp
Modified  /trunk/madman/Rpacks/csaw/src/find_maxima.cpp
Modified  /trunk/madman/Rpacks/csaw/src/get_cluster_stats.cpp
Modified  /trunk/madman/Rpacks/csaw/src/get_rle_counts.cpp
Modified  /trunk/madman/Rpacks/csaw/src/merge_windows.cpp
Modified  /trunk/madman/Rpacks/csaw/vignettes/csaw.Rnw
Rejigged code to use seq_*, improved behaviour on empty inputs.
Revision: 106811
Author: s.arora
Date: 2015-07-27T23:24:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/NAMESPACE
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/UCSCTrackUpdateChecker.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/ahmToJson.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeChEA.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEnsemblFasta.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEnsemblGtfToGRanges.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeInparanoid8ToDbs.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeNCBIToOrgDbs.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/trackWithAuxiliaryTableToGRangesRecipe.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/updateResources.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/webAccessFunctions.R
code update

- correct NAMESPACE imports using codetoolsBioC::writeNamespaceImport()
- remove require() calls from code as it leads to warning
- remove package from multiple fields to remove note
- remove ::: calls to the AnnotationHubData's namespace in its code.
- rearrange the Depends, Imports and Suggests field of the DESCRIPTION file.


Revision: 106810
Author: t.girke
Date: 2015-07-27T22:46:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.R
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 09a76de55d03e5a02aea82bf325af55cf8b45bf9

    some edits

Revision: 106809
Author: m.smith
Date: 2015-07-27T22:06:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/IONiseR/R/readSummary.R
Modified  /trunk/madman/Rpacks/IONiseR/R/summaryPlots.R
Read type plot added
Revision: 106808
Author: s.arora
Date: 2015-07-27T21:49:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/AnnotationHubMetadata-class.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeBioPaxImporter.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEnsemblGtfToGRanges.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeInparanoid8ToDbs.R
Deleted  /trunk/madman/Rpacks/AnnotationHubData/inst/extdata/goldenpath
Deleted  /trunk/madman/Rpacks/AnnotationHubData/inst/extdata/pub
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/unitTests/test_AnnotationHubMetadata.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/unitTests/test_EnsemblImportPreparer-classes.R
Deleted  /trunk/madman/Rpacks/AnnotationHubData/man/rtrackLayerImport.Rd
code update

- remove leftover code to scree biopax level 3 files.
- correct the format of recipe string for Inparanoid recipe.
- correct base url for gtf files.
- update .checkThatGenomeLooksReasonable() because genome can
be 'inparanoid8 genome' or 'NA_character_' and currentc code check
does not handle that.
- clean up
  - remove inst/extdata/goldenpath and inst/extdata/pub
  (they contained super long paths which were not used in any way)
  - remove man/rtrackLayerImport.Rd



Revision: 106807
Author: m.love
Date: 2015-07-27T20:19:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2.Rnw
remove gplots, add pheatmap
Revision: 106806
Author: t.girke
Date: 2015-07-27T19:17:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 8c898dc3e47f28f191dffa4dad7074ee6fdd399c

    some edits

Revision: 106805
Author: t.girke
Date: 2015-07-27T18:53:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.R
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 6b78c030b22e6571c1412d0f3ed76b88dbf32557

    some edits

Revision: 106804
Author: t.girke
Date: 2015-07-27T18:50:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4133403210a9d31691b5c6e4c0ca6641aba1a64f

    some edits

Revision: 106803
Author: t.girke
Date: 2015-07-27T18:44:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 0eb9c914010767265c6cc4bc3021a4f34f524c4c

    some edits

Revision: 106802
Author: t.girke
Date: 2015-07-27T18:44:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: acab5de7dbcc7b932d67c34e0113c668aad29c4d

    some edits

Revision: 106801
Author: t.girke
Date: 2015-07-27T18:42:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.R
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4a86626d49c268f0349b3ad707c4b3e916b8aa7f

    some edits

Revision: 106798
Author: t.girke
Date: 2015-07-27T15:52:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/SystemPipeR_Workflow.png
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 9f1778b8198fc501e70aa642086f79cb51dbf17c

    some edits

Revision: 106797
Author: t.girke
Date: 2015-07-27T15:48:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/SystemPipeR_Workflow.png
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 428037a4446d2a798325245ad315701fed945648

    some edits

Revision: 106796
Author: f.mueller
Date: 2015-07-27T15:26:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/RnBeads/R/annotations.R
further compatibility when loading data using hg38 reference
Revision: 106795
Author: m.love
Date: 2015-07-27T15:19:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2.Rnw
fixing latex error
Revision: 106794
Author: d.gatti
Date: 2015-07-27T15:09:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOQTL/NAMESPACE
Deleted  /trunk/madman/Rpacks/DOQTL/R/get.chr.lengths.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: f957c0308342a52ba72140544a98cc2cf0c8f0fb

    Updated NAMESPACE to remove non-existing functions.

Revision: 106793
Author: t.girke
Date: 2015-07-27T14:18:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4fa2f0bbc7d00fb9ef1e8ec6d6b43f605cdada6f

    some edits

Revision: 106792
Author: t.girke
Date: 2015-07-27T14:16:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 254a8925067e9eab856ac1cf442950213d2d16b6

    some edits

Revision: 106791
Author: t.girke
Date: 2015-07-27T14:15:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: a7583d767d82c52d28db61472f7375fa801034c2

    some edits

Revision: 106790
Author: t.girke
Date: 2015-07-27T14:12:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 2c8ed15382b32c372b7d54457c5c4166e111c53e

    some edits

Revision: 106789
Author: t.girke
Date: 2015-07-27T14:11:46+00:00
Paths:
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.R
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: c539ea634bc79dcce28504182b07e7de1997e8da

    some edits

Revision: 106787
Author: c.determan
Date: 2015-07-27T13:32:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/OmicsMarkeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/OmicsMarkeR/R/training.R
Modified  /trunk/madman/Rpacks/OmicsMarkeR/vignettes/OmicsMarkeR-concordance.tex
Modified  /trunk/madman/Rpacks/OmicsMarkeR/vignettes/OmicsMarkeR.log
Modified  /trunk/madman/Rpacks/OmicsMarkeR/vignettes/OmicsMarkeR.pdf
Modified  /trunk/madman/Rpacks/OmicsMarkeR/vignettes/OmicsMarkeR.synctex.gz
Modified  /trunk/madman/Rpacks/OmicsMarkeR/vignettes/OmicsMarkeR.tex
Commit made by the Bioconductor Git-SVN bridge.

Commit id: b712278bc86b7490420cbbeff095c2d5c2a8bcda

    Removed 'scale' argument from svm.  Was causing categories to be convert to numbers and messing with labels.  Incremented subversion and updated dates.

Revision: 106786
Author: a.conesa
Date: 2015-07-27T10:07:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/maSigPro/man/p.vector.Rd
p.vector updated help file
Revision: 106785
Author: z.gu
Date: 2015-07-27T10:03:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/ComplexHeatmap/vignettes/ComplexHeatmap.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: d82f99e734bd45cb60f4bac96d05d851b07b6faf

    Update ComplexHeatmap.Rmd

Revision: 106784
Author: a.conesa
Date: 2015-07-27T09:50:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/maSigPro/R/p.vector.R
Modified  /trunk/madman/Rpacks/maSigPro/man/p.vector.Rd
p.vector: redundant lines removed and updated help file
Revision: 106783
Author: e.thevenot
Date: 2015-07-27T09:30:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/ropls/DESCRIPTION
Modified  /trunk/madman/Rpacks/ropls/NEWS
Modified  /trunk/madman/Rpacks/ropls/man/ropls-package.Rd
version bumped to be taken into account
Revision: 106782
Author: e.thevenot
Date: 2015-07-27T09:18:28+00:00
Paths:
Deleted  /trunk/madman/Rpacks/ropls/R/roplsF.R
Added  /trunk/madman/Rpacks/ropls/inst/doc/ropls.pdf
Deleted  /trunk/madman/Rpacks/ropls/inst/unitTests/test_roplsF.R
Deleted  /trunk/madman/Rpacks/ropls/man/roplsF.Rd
missing files committed
Revision: 106781
Author: z.gu
Date: 2015-07-27T08:59:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/ComplexHeatmap/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 0032751570e3ae2d3fa05761b39c8bcc172d190d

    Update DESCRIPTION

Revision: 106780
Author: a.conesa
Date: 2015-07-27T07:49:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/maSigPro/R/PlotGroups.R
Modified  /trunk/madman/Rpacks/maSigPro/R/p.vector.R
Modified  /trunk/madman/Rpacks/maSigPro/R/see.genes.R
Small changes:
p.vector: redundant lines removed
PlotGroups: ylab, new argument for graphs
see.genes: hclust distance default Ward changed for Ward.D 
Revision: 106779
Author: t.girke
Date: 2015-07-27T03:30:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: b8c44535fa21504a7ac3af3576e58b4da5373031

    some edits

Revision: 106778
Author: t.girke
Date: 2015-07-27T01:24:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 30b1b335c16f5a161b4c313facbf1857831d3897

    some edits

Revision: 106776
Author: t.girke
Date: 2015-07-27T00:28:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: a922e63df2d2e20249af03b91c2cd64f56a0e3e5

    some edits

Revision: 106775
Author: t.girke
Date: 2015-07-27T00:26:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/README.md
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rmd
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.html
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 3357623684c30cba7dbfdc345ddaabd77b2986c4

    some edits

Revision: 106774
Author: t.girke
Date: 2015-07-27T00:20:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: b07666ba7c632c6d7382181db2685531c4d7bc18

    some edits

Revision: 106773
Author: t.girke
Date: 2015-07-27T00:16:01+00:00
Paths:
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/heatmap1.png
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: f0e6e464f1c18bdb423ff27f9c942ae743eac898

    some edits

Revision: 106772
Author: t.girke
Date: 2015-07-27T00:09:25+00:00
Paths:
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/GOslimbarplotMF.png
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: f04d55c1a91aa5f5b2f9b53817dd6cdd604efa40

    some edits

Revision: 106771
Author: t.girke
Date: 2015-07-26T23:18:05+00:00
Paths:
Deleted  /trunk/madman/Rpacks/systemPipeR/vignettes/sample_tree.png
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 34ee41bcf948e45136fd6a25c4a6b82535d16f88

    some edits

Revision: 106770
Author: t.girke
Date: 2015-07-26T23:11:00+00:00
Paths:
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/SystemPipeR_Workflow.png
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/fastqReport.png
Added  /trunk/madman/Rpacks/systemPipeR/vignettes/sample_tree.png
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.R
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.pdf
Commit made by the Bioconductor Git-SVN bridge.

Commit id: e631c13f6e578f1cef5eae55fe3fe8e3fbd9e087

    some edits

Revision: 106769
Author: n.leng
Date: 2015-07-26T22:16:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/EBSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/EBSeq/NEWS
Modified  /trunk/madman/Rpacks/EBSeq/R/MedianNorm.R
Modified  /trunk/madman/Rpacks/EBSeq/man/MedianNorm.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: a2fb2c802f7cd779f9076b64c16999b03ca02cf0

    update news


Commit id: 98c0851c50f4dd04a2cbc643b6c20489b2922a2a

    boost

Revision: 106768
Author: z.gu
Date: 2015-07-26T21:46:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/gtrellis/NEWS
Modified  /trunk/madman/Rpacks/gtrellis/R/layout.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 8644d048ec4ab186a9bb2fb5a84acbbcd627a329

    rm file


Commit id: 57a50f82d3d9df14fb318e4b6784fc29f795f2f2

    correct unit in x-axis

Revision: 106767
Author: f.klein
Date: 2015-07-26T18:37:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/FourCSeq/inst/CITATION
changed names in added citation
Revision: 106766
Author: f.klein
Date: 2015-07-26T18:34:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/FourCSeq/DESCRIPTION
Added  /trunk/madman/Rpacks/FourCSeq/inst/CITATION
Modified  /trunk/madman/Rpacks/FourCSeq/vignettes/FourCSeq.Rnw
Modified  /trunk/madman/Rpacks/FourCSeq/vignettes/literature.bib
added Bioinformatic citation
Revision: 106764
Author: stvjc
Date: 2015-07-26T15:06:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLInterfaces/DESCRIPTION
Modified  /trunk/madman/Rpacks/MLInterfaces/R/MLIConverters.R
Modified  /trunk/madman/Rpacks/MLInterfaces/R/MLIPredicters.R
needed special casing for kernlab::predict
Revision: 106763
Author: stvjc
Date: 2015-07-26T14:33:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLInterfaces/DESCRIPTION
Modified  /trunk/madman/Rpacks/MLInterfaces/NAMESPACE
deal with RColorBrewer
Revision: 106762
Author: stvjc
Date: 2015-07-26T13:10:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/gQTLstats/R/filters.R
Modified  /trunk/madman/Rpacks/gQTLstats/man/eqBox2.Rd
minor changes to pass check
Revision: 106761
Author: x.zheng
Date: 2015-07-26T08:02:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/SeqArray/DESCRIPTION
Modified  /trunk/madman/Rpacks/SeqArray/NEWS
Modified  /trunk/madman/Rpacks/SeqArray/R/Internal.R
Modified  /trunk/madman/Rpacks/SeqArray/R/Methods.R
Modified  /trunk/madman/Rpacks/SeqArray/README.md
Modified  /trunk/madman/Rpacks/SeqArray/src/ConvVCF2GDS.cpp
Modified  /trunk/madman/Rpacks/SeqArray/src/Methods.cpp
Modified  /trunk/madman/Rpacks/SeqArray/src/SeqArray.cpp
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 92c34f2188bacc0921472ad53a30b6b64d3204a0

    fix a bug #7

Revision: 106760
Author: stvjc
Date: 2015-07-26T03:04:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLInterfaces/NAMESPACE
added import of predict.gbm
Revision: 106758
Author: e.thevenot
Date: 2015-07-25T23:13:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/ropls/DESCRIPTION
Modified  /trunk/madman/Rpacks/ropls/NAMESPACE
Modified  /trunk/madman/Rpacks/ropls/NEWS
Added  /trunk/madman/Rpacks/ropls/R/opls.R
Added  /trunk/madman/Rpacks/ropls/R/plot.opls.R
Added  /trunk/madman/Rpacks/ropls/R/predict.opls.R
Added  /trunk/madman/Rpacks/ropls/R/print.opls.R
Modified  /trunk/madman/Rpacks/ropls/R/strF.R
Modified  /trunk/madman/Rpacks/ropls/data/sacurine.rdata
Added  /trunk/madman/Rpacks/ropls/inst/doc
Added  /trunk/madman/Rpacks/ropls/inst/unitTests/test_opls.R
Added  /trunk/madman/Rpacks/ropls/man/opls.Rd
Added  /trunk/madman/Rpacks/ropls/man/plot.opls.Rd
Added  /trunk/madman/Rpacks/ropls/man/predict.opls.Rd
Modified  /trunk/madman/Rpacks/ropls/man/ropls-package.Rd
Modified  /trunk/madman/Rpacks/ropls/man/strF.Rd
Modified  /trunk/madman/Rpacks/ropls/vignettes/ropls.Rnw
The packaging was modified (but not the algorithms) to be consistent with other machine learning packages: 'opls' is now a class and the 'print', 'plot', 'predict', 'summary', 'fitted', 'coefficients' and 'residuals' methods are available (see the vignette)
Revision: 106757
Author: m.love
Date: 2015-07-25T17:13:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2.Rnw
how to ask questions
Revision: 106756
Author: c.panse
Date: 2015-07-25T09:14:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/specL/DESCRIPTION
Modified  /trunk/madman/Rpacks/specL/inst/NEWS
removed print cmd from read.bibliospec
Revision: 106755
Author: c.panse
Date: 2015-07-25T06:39:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/specL/R/read.bibliospec.R
removed print in read.bibliospec
Revision: 106754
Author: c.panse
Date: 2015-07-25T06:32:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/specL/DESCRIPTION
Modified  /trunk/madman/Rpacks/specL/R/read.bibliospec.R
buxfix read.bibliospec
Revision: 106753
Author: c.panse
Date: 2015-07-25T06:22:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/specL/R/read.bibliospec.R
bugfix intensity decomposition in read.bibliospec
Revision: 106751
Author: hpages
Date: 2015-07-25T01:15:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/BSgenome/DESCRIPTION
Modified  /trunk/madman/Rpacks/BSgenome/R/SNPlocs-class.R
fix bug in "snpsById" method for SNPlocs objects
Revision: 106750
Author: s.arora
Date: 2015-07-24T23:38:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/NAMESPACE
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/AnnotationHubMetadata-class.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeAnnotationHubResource.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEpigenomeRoadmap.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeHaemCode.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makedbSNPVCF.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/unitTests/test_EnsemblImportPreparer-classes.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/man/AnnotationHubMetadata-class.Rd
code update

- remove Packages listed in more than one of Depends,
   Imports, Suggests, Enhances
- update setClass and setMethod with 'where' arg
- update new argument in man page
- update failing unitTest
   - dbSNP had left over grep line.
   - haemcode was using old webaccess helper function
   - there can be two rdatapath - update if(cond) with any
   - epigenome roadmap - 'date' field was creating an issue

Revision: 106748
Author: m.alvarez
Date: 2015-07-24T22:56:24+00:00
Paths:
Added  /trunk/madman/Rpacks/viper/man/aracne2regulon4cnv.Rd
Added aracne2regulon4cnv.Rd
Revision: 106747
Author: m.alvarez
Date: 2015-07-24T22:55:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/viper/NAMESPACE
Added aracne2regulon4cnv.Rd and updated NAMESPACE
Revision: 106746
Author: m.alvarez
Date: 2015-07-24T22:53:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/viper/DESCRIPTION
Modified  /trunk/madman/Rpacks/viper/NEWS
Modified  /trunk/madman/Rpacks/viper/R/aracne.r
Added function aracne2regulon4cnv to parse ARACNe results generated by using different regulators and targets expression matrixes
Revision: 106745
Author: x.zheng
Date: 2015-07-24T22:18:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/SeqArray/DESCRIPTION
Modified  /trunk/madman/Rpacks/SeqArray/NEWS
Modified  /trunk/madman/Rpacks/SeqArray/R/Conversion.R
Modified  /trunk/madman/Rpacks/SeqArray/R/Utilities.R
Modified  /trunk/madman/Rpacks/SeqArray/README.md
Modified  /trunk/madman/Rpacks/SeqArray/inst/unitTests/test_examples.R
Modified  /trunk/madman/Rpacks/SeqArray/man/SeqArray-package.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqAlleleFreq.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqApply.Rd
Added  /trunk/madman/Rpacks/SeqArray/man/seqExport.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqGDS2SNP.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqGDS2VCF.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqGetData.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqGetFilter.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqInfoNewVar.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqMissing.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqNumAllele.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqOpen.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqOptimize.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqParallel.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqSetFilter.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqSetFilterChrom.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqSlidingWindow.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqSummary.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqTranspose.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqVCF.Header.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqVCF.SampID.Rd
Modified  /trunk/madman/Rpacks/SeqArray/man/seqVCF2GDS.Rd
Modified  /trunk/madman/Rpacks/SeqArray/src/ConvVCF2GDS.cpp
Modified  /trunk/madman/Rpacks/SeqArray/src/Methods.cpp
Modified  /trunk/madman/Rpacks/SeqArray/vignettes/SeqArrayTutorial.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: da4533d62b104116a7d0dcec93bf1bb74c2d1480

    a new function "seqExport"

Revision: 106744
Author: s.arora
Date: 2015-07-24T21:29:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/AnnotationHubMetadata-class.R
code update

- sometimes genome can be 'NA_character_' which is more than 12 characters
thus, have updated the if(condiction) to to test for a genome to have more
than 15 characters.
Revision: 106743
Author: c.determan
Date: 2015-07-24T20:08:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/OmicsMarkeR/.travis.yml
Modified  /trunk/madman/Rpacks/OmicsMarkeR/OmicsMarkeR.Rproj
Commit made by the Bioconductor Git-SVN bridge.

Commit id: e2ed6ff4caf4971f469139c379217ae43daf9de4

    install assertive.base package


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