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Revision: 93751
Author: d.tenenbaum
Date: 2014-09-03T00:30:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/fastLiquidAssociation/vignettes/fastLiquidAssociation.Rnw
Modified  /trunk/madman/Rpacks/fastLiquidAssociation/DESCRIPTION
fix stopCluster typo
Revision: 93750
Author: g.becker
Date: 2014-09-02T22:42:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/gmapR/DESCRIPTION
version bump to deploy previous bugfix
Revision: 93749
Author: m.love
Date: 2014-09-02T21:07:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/R/rlogTransformation.R
Modified  /trunk/madman/Rpacks/DESeq2/NEWS
Modified  /trunk/madman/Rpacks/DESeq2/R/varianceStabilizingTransformation.R
Added  /trunk/madman/Rpacks/DESeq2/inst/unitTests/test_rlog.R
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
subsetting of genes for disp est for rlog fast=TRUE
Revision: 93748
Author: khansen
Date: 2014-09-02T21:00:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/minfi/R/preprocess.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 98ff6c4b236fa0020a4f12b0f4ddaa9349f5527f
Commit message: Merge branch 'master' of github.com:kasperdanielhansen/minfi
Committed by: Kasper Daniel Hansen
Author Name: Kasper Daniel Hansen
Commit date: 2014-09-02 17:00:38 -0400
Author date: 2014-09-02 17:00:38 -0400

Commit id: b63b41eaebace0cbcc7abc3cd35d7aeb10d2518f
Commit message: changed # to ##
Committed by: Kasper Daniel Hansen
Author Name: Kasper Daniel Hansen
Commit date: 2014-09-02 16:52:53 -0400
Author date: 2014-09-02 16:52:53 -0400

Revision: 93747
Author: m.love
Date: 2014-09-02T19:36:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/R/rlogTransformation.R
Modified  /trunk/madman/Rpacks/DESeq2/NEWS
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
speeding up rlog fast=TRUE
Revision: 93745
Author: h.corradabravo
Date: 2014-09-02T17:44:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/epivizr/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: ba1c55c046c89213dbcdd27e9041acfd4d794383
Commit message: version bump; add 'Mus.musculus' to 'Suggests'
Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-09-02 13:44:10 -0400
Author date: 2014-09-02 13:44:10 -0400

Revision: 93744
Author: g.yu
Date: 2014-09-02T17:11:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOSemSim/README.md
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 6d6afd107b2604e76648b9de1585f105e5031ec1
Commit message: update readme
Committed by: Guangchuang Yu
Author Name: Guangchuang Yu
Commit date: 2014-09-03 01:09:40 +0800
Author date: 2014-09-03 01:09:40 +0800

Revision: 93743
Author: g.yu
Date: 2014-09-02T17:03:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOSemSim/README.md
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 8c555c79a28d3c5f87b6e17ed09adb91ab1118b5
Commit message: update readme
Committed by: Guangchuang Yu
Author Name: Guangchuang Yu
Commit date: 2014-09-03 01:02:32 +0800
Author date: 2014-09-03 01:02:32 +0800

Revision: 93742
Author: g.yu
Date: 2014-09-02T17:01:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOSemSim/README.md
Modified  /trunk/madman/Rpacks/GOSemSim/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 958c2b4f2cec00a485866a8df1cb5017c22beb0e
Commit message: update readme
Committed by: Guangchuang Yu
Author Name: Guangchuang Yu
Commit date: 2014-09-03 01:00:24 +0800
Author date: 2014-09-03 01:00:24 +0800

Revision: 93741
Author: v.obenchain
Date: 2014-09-02T15:35:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/VCF-class.Rd
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-VCF-class.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/AllGenerics.R
add 'row.names' to info,VCF-method
Revision: 93740
Author: m.love
Date: 2014-09-02T15:30:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/man/results.Rd
Modified  /trunk/madman/Rpacks/DESeq2/R/results.R
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/R/core.R
only filter/replace when 3 or more replicates
Revision: 93739
Author: e.lowy
Date: 2014-09-02T15:28:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/CoverageView/R/cov.matrix.R
Modified  /trunk/madman/Rpacks/CoverageView/R/cov.bin.R
Modified  /trunk/madman/Rpacks/CoverageView/DESCRIPTION
Changes made to cov.bin.R, this version fixes a bug that affected
the behaviour of cov.matrix with CoverageBigWig files
Revision: 93738
Author: d.gatti
Date: 2014-09-02T12:47:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOQTL/R/hmm.intensity.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: bfb098675cc2d46a8bf5d1f6f3f044b26b56256c
Commit message: Fixed file name for output of initial cluster parameters.
Committed by: dmgatti
Author Name: dmgatti
Commit date: 2014-09-02 08:47:34 -0400
Author date: 2014-09-02 08:47:34 -0400

Revision: 93737
Author: l.pantano
Date: 2014-09-02T11:39:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGreport/DESCRIPTION
Modified  /trunk/madman/Rpacks/DEGreport/inst/NEWS
Modified  /trunk/madman/Rpacks/DEGreport/R/report.R
Modified  /trunk/madman/Rpacks/DEGreport/man/createReport.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: ad5ef3e879472a645cb8da45335efd0c470f4a9b
Commit message: add ncores to report creation and minor changes in style
Merge branch 'master' of https://github.com/lpantano/DEGreport

Conflicts:
    R/report.R
Committed by: Lorena Pantano
Author Name: Lorena Pantano
Commit date: 2014-09-02 07:38:58 -0400
Author date: 2014-09-02 07:38:58 -0400

Commit id: f51a4e5ed97a928e21c3652f9ca96e417a45c772
Commit message: clean up the code
Committed by: Lorena Pantano
Author Name: Lorena Pantano
Commit date: 2014-09-02 07:28:23 -0400
Author date: 2014-09-02 07:28:23 -0400

Revision: 93736
Author: d.strbenac
Date: 2014-09-02T06:00:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/R/edgeRselection.R
edgeRselection also returns numeric indices
Revision: 93735
Author: bolstad
Date: 2014-09-02T01:36:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/preprocessCore/inst/include/median.h
Modified  /trunk/madman/Rpacks/preprocessCore/src/median.c
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: a9de5d2adf89f0286057446d1c3f1dc00c8005c6
Commit message: Code documentation fixes
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-09-01 18:35:34 -0700
Author date: 2014-09-01 18:35:34 -0700

Revision: 93733
Author: d.strbenac
Date: 2014-09-02T01:27:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Test write permission
Revision: 93732
Author: bolstad
Date: 2014-09-02T01:18:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/preprocessCore/src/log_avg.c
Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commits.

Commit information:

Commit id: 96f45082e5980752c45629635d1f8c871f948ced
Commit message: fix missing SE computation
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-09-01 18:16:33 -0700
Author date: 2014-09-01 18:16:33 -0700

Commit id: acbbd2b19dca7c56e7c59a7eb54872b5dcac3849
Commit message: Code improvements
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-09-01 18:14:51 -0700
Author date: 2014-09-01 18:14:51 -0700

Commit id: f3dcbe6c5bc27d754f312a20c9537c5e34bf1344
Commit message: Add SE calculation using delta method approximation
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-09-01 18:14:02 -0700
Author date: 2014-09-01 18:14:02 -0700

Revision: 93731
Author: bolstad
Date: 2014-09-02T00:14:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/preprocessCore/inst/include/avg.h
Modified  /trunk/madman/Rpacks/preprocessCore/src/avg.c
Modified  /trunk/madman/Rpacks/preprocessCore/src/avg_log.c
Modified  /trunk/madman/Rpacks/preprocessCore/src/log_avg.c
Modified  /trunk/madman/Rpacks/preprocessCore/src/biweight.c
Commit made by the Bioconductor Git-SVN bridge.
Consists of 5 commits.

Commit information:

Commit id: b812698e02d70c0719b6647c5472fc4275f95c7a
Commit message: Code doc cleanup
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-09-01 17:11:40 -0700
Author date: 2014-09-01 17:11:40 -0700

Commit id: 6c3417eceb5ddc9ce244d8c11803b45a8a6b7500
Commit message: updating code documentation
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-09-01 16:31:02 -0700
Author date: 2014-09-01 16:31:02 -0700

Commit id: 4a0e383118bcc56b09806100f5bc33af16ccac7c
Commit message: clean up code doc
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-09-01 16:24:18 -0700
Author date: 2014-09-01 16:24:18 -0700

Commit id: e34ce7c7cb25d2d91ab50514f0f2e836beef4c27
Commit message: improve code documentation
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-09-01 16:12:11 -0700
Author date: 2014-09-01 16:12:11 -0700

Commit id: aa818e1a0922968e85d43c530a8938470c34f300
Commit message: code doc cleanup
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-09-01 09:24:49 -0700
Author date: 2014-09-01 09:24:49 -0700

Revision: 93730
Author: t.morris
Date: 2014-09-01T17:26:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChAMP/R/champ.MVP.R
Modified  /trunk/madman/Rpacks/ChAMP/man/ChAMP-package.Rd
Modified  /trunk/madman/Rpacks/ChAMP/DESCRIPTION
Updated champ.MVP to correct error with groups
Revision: 93729
Author: j.gadin
Date: 2014-09-01T13:44:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-glocationplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-lbarplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/binom.test-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/chisq.test-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/data/ASEset.rdata
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/ASEset-class.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/getAlleleCounts2.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/binom.test.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/initialize-ASEset.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/initialize-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-barplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/chisq.test.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/barplot-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/GvizTrack-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-class.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-locationplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/getAlleleCounts.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/locationplot-methods.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 09899a5026bdfc4b2c7fd169b40089f50c5e28f0
Commit message: fix and bump
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-09-01 15:43:45 +0200
Author date: 2014-09-01 15:43:45 +0200

Commit id: cc85d3f62dc32ef907ce627e0d6da32f872c87fa
Commit message: dropped count matrix named  non-stranded
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-09-01 13:24:34 +0200
Author date: 2014-09-01 13:24:34 +0200

Revision: 93728
Author: fhahne
Date: 2014-09-01T09:49:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/Gviz/man/DataTrack-class.Rd
Modified  /trunk/madman/Rpacks/Gviz/DESCRIPTION
Modified  /trunk/madman/Rpacks/Gviz/NAMESPACE
Adding a missing export for the CustomTrack constructor
Revision: 93727
Author: h.hettling
Date: 2014-09-01T08:50:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiGGR/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: c089b8dbbf9f3b5af425ddff8a7965a3867637e2
Commit message: Changed package description, bumped version number
Committed by: hettling
Author Name: hettling
Commit date: 2014-09-01 10:50:03 +0200
Author date: 2014-09-01 10:50:03 +0200

Revision: 93726
Author: h.hettling
Date: 2014-09-01T08:44:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiGGR/DESCRIPTION
setting up git-svn bridge
Revision: 93724
Author: bolstad
Date: 2014-09-01T01:47:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/preprocessCore/src/biweight.h
Modified  /trunk/madman/Rpacks/preprocessCore/inst/include/preprocessCore_summarization_stubs.c
Modified  /trunk/madman/Rpacks/preprocessCore/inst/include/median.h
Modified  /trunk/madman/Rpacks/preprocessCore/inst/include/median_log.h
Modified  /trunk/madman/Rpacks/preprocessCore/inst/include/log_median.h
Modified  /trunk/madman/Rpacks/preprocessCore/src/log_avg.c
Modified  /trunk/madman/Rpacks/preprocessCore/inst/include/preprocessCore_summarization_stubs.h
Modified  /trunk/madman/Rpacks/preprocessCore/inst/include/biweight.h
Modified  /trunk/madman/Rpacks/preprocessCore/src/log_avg.h
Modified  /trunk/madman/Rpacks/preprocessCore/inst/include/log_avg.h
Modified  /trunk/madman/Rpacks/preprocessCore/src/median.c
Modified  /trunk/madman/Rpacks/preprocessCore/src/median_log.c
Modified  /trunk/madman/Rpacks/preprocessCore/src/log_median.c
Modified  /trunk/madman/Rpacks/preprocessCore/src/median.h
Modified  /trunk/madman/Rpacks/preprocessCore/src/biweight.c
Modified  /trunk/madman/Rpacks/preprocessCore/src/median_log.h
Modified  /trunk/madman/Rpacks/preprocessCore/src/log_median.h
Commit made by the Bioconductor Git-SVN bridge.
Consists of 8 commits.

Commit information:

Commit id: 5945c9202e735242649e1194f6e8315a5836f1ff
Commit message: changes to the external library c code interface
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-08-31 18:45:49 -0700
Author date: 2014-08-31 18:45:49 -0700

Commit id: 612f85fd6681f4cbab1d4f27e3669e35a68adf4b
Commit message: changes to size_t for median_log
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-08-31 18:32:29 -0700
Author date: 2014-08-31 18:32:29 -0700

Commit id: 0dccf18748a6c98dd1acbe8db34b77cca5fe53f5
Commit message: median changes for size_t
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-08-31 18:17:20 -0700
Author date: 2014-08-31 18:17:20 -0700

Commit id: e65b4f64dfa7940685ca21f28b56e4ee5300bb1e
Commit message: log_median changes for size_t
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-08-31 18:08:11 -0700
Author date: 2014-08-31 18:08:11 -0700

Commit id: b9984cf077c87cf39e02f1f488fe80a6ff43c91d
Commit message: fix mismatch between header and implementation
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-08-31 17:56:54 -0700
Author date: 2014-08-31 17:56:54 -0700

Commit id: 5a486521d978d49e95418286e1b348e66eb97395
Commit message: log_avg size_t changes
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-08-31 17:52:57 -0700
Author date: 2014-08-31 17:52:57 -0700

Commit id: 2675ccbfb8c1062c18426dd3e2cc2eba20eb9412
Commit message: biweight changes to update to size_t where appropriate
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-08-31 17:42:51 -0700
Author date: 2014-08-31 17:42:51 -0700

Commit id: 6a058f67ace9f88e78834e84932b71747c78abe6
Commit message: size_t rlated changes
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-08-31 17:08:05 -0700
Author date: 2014-08-31 17:08:05 -0700

Revision: 93723
Author: bolstad
Date: 2014-08-31T23:03:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/preprocessCore/inst/include/avg.h
Modified  /trunk/madman/Rpacks/preprocessCore/inst/include/avg_log.h
Modified  /trunk/madman/Rpacks/preprocessCore/src/avg_log.c
Modified  /trunk/madman/Rpacks/preprocessCore/src/avg_log.h
Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commits.

Commit information:

Commit id: ce26f1d519ca5e35d47fd1d8cfd5eae6fb8a5a10
Commit message: fix missed size_t typo
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-08-31 16:02:25 -0700
Author date: 2014-08-31 16:02:25 -0700

Commit id: 1bf9bb8a913d0bd7a2ae760afc84c5c223591602
Commit message: change the linking interfaces to match changes to code
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-08-31 15:58:09 -0700
Author date: 2014-08-31 15:58:09 -0700

Commit id: 832752c8a9b4dc0c2eb846db7240487fd36b6ceb
Commit message: change, where appropriate, to size_t
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-08-31 15:50:19 -0700
Author date: 2014-08-31 15:50:19 -0700

Revision: 93722
Author: bolstad
Date: 2014-08-31T22:39:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/preprocessCore/src/avg.c
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 68e28d767511fa63455f278bd8d962563ed4f096
Commit message: fix some code documentation
Committed by: Ben Bolstad
Author Name: Ben Bolstad
Commit date: 2014-08-31 15:38:50 -0700
Author date: 2014-08-31 15:38:50 -0700

Revision: 93721
Author: bolstad
Date: 2014-08-31T22:31:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/preprocessCore/src/avg.c
Modified  /trunk/madman/Rpacks/preprocessCore/src/avg.h
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: e2d415b18736ff2179381b5005bbe9efc9810155
Commit message: change, where appropriate, to size_t arguments in c code
Committed by: R building
Author Name: R building
Commit date: 2014-08-31 15:25:49 -0700
Author date: 2014-08-31 15:25:49 -0700

Revision: 93717
Author: j.gadin
Date: 2014-08-31T13:33:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/reads.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/getDefaultMapBiasExpMean.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-glocationplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/barplot-lattice-support.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-lbarplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/binom.test-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/chisq.test-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/ASEset-class.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/AllelicImbalance-package.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/getAlleleCounts2.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/getAreaFromGeneNames.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/GRvariants.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/binom.test.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/initialize-ASEset.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/initialize-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/coverageMatrixListFromGAL.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-barplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/chisq.test.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/implodeList.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-gviztrack.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/barplot-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-class.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/GvizTrack-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/scanForHeterozygotes.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-locationplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/getSnpIdFromLocation.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/getAlleleCounts.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/locationplot-methods.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 88e3a2b320d7a3d0d98aa5fb7e5e601671baeeff
Commit message: removed alien characters
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-31 15:32:49 +0200
Author date: 2014-08-31 15:32:49 +0200

Revision: 93716
Author: j.gadin
Date: 2014-08-30T13:22:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/barplot-methods.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: aedb1e380836e603b9f53495c2b540e6c861d1f4
Commit message: x11 fix
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-30 15:21:13 +0200
Author date: 2014-08-30 15:21:13 +0200

Revision: 93714
Author: g.feng
Date: 2014-08-30T09:03:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneAnswers/R/zzz.R
Added  /trunk/madman/Rpacks/GeneAnswers/R/getREACTOMEPATHTerms.R
Modified  /trunk/madman/Rpacks/GeneAnswers/R/groupReport.R
the latest getREACTOMEPATHTherm.R
Revision: 93713
Author: g.feng
Date: 2014-08-30T09:02:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneAnswers/DESCRIPTION
new team members
Revision: 93712
Author: r.castelo
Date: 2014-08-30T08:37:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/R/commonFunctions.R
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
elt.Hits to elt.hits
Revision: 93711
Author: a.stilp
Date: 2014-08-29T23:39:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/GWASTools/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/GWASTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/GWASTools/R/ncdfImputedDosage.R
removed older .probToDosage function definition in ncdfImputedDosage
Revision: 93710
Author: d.tenenbaum
Date: 2014-08-29T22:30:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/KEGGREST/man/keggConv.Rd
Modified  /trunk/madman/Rpacks/KEGGREST/DESCRIPTION
shorten example output
Revision: 93709
Author: v.obenchain
Date: 2014-08-29T22:19:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/R/bplapply-methods.R
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/man/register.Rd
fix recursion problem for BPPARAM as list
Revision: 93707
Author: d.tenenbaum
Date: 2014-08-29T22:01:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/fastLiquidAssociation/vignettes/fastLiquidAssociation.Rnw
Modified  /trunk/madman/Rpacks/fastLiquidAssociation/DESCRIPTION
Modified  /trunk/madman/Rpacks/fastLiquidAssociation/man/fastboots.GLA-methods.Rd
Be sure and stop clusters that are started. This is necessary on windows.
Revision: 93706
Author: jmacdon
Date: 2014-08-29T21:44:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/affycoretools/R/foldFilt.R
Modified  /trunk/madman/Rpacks/affycoretools/man/geneSetPage.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/vennSelect2.Rd
Modified  /trunk/madman/Rpacks/affycoretools/R/hyperGtable.R
Modified  /trunk/madman/Rpacks/affycoretools/R/vennSelect.R
Modified  /trunk/madman/Rpacks/affycoretools/man/dataAndHeatmapPage.Rd
Modified  /trunk/madman/Rpacks/affycoretools/R/affycoretools.R
Modified  /trunk/madman/Rpacks/affycoretools/man/makeImages.Rd
Modified  /trunk/madman/Rpacks/affycoretools/DESCRIPTION
Modified  /trunk/madman/Rpacks/affycoretools/man/makeVenn.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/outputRomer.Rd
Modified  /trunk/madman/Rpacks/affycoretools/R/probes2table.R
Modified  /trunk/madman/Rpacks/affycoretools/R/limma2annaffy.R
Modified  /trunk/madman/Rpacks/affycoretools/R/geneSetTables.R
Modified  /trunk/madman/Rpacks/affycoretools/man/fixHeaderAndGo.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/runRomer.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/gsHeatmap.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/makeGoGeneTable.Rd
Modified  /trunk/madman/Rpacks/affycoretools/man/makeGoTable.Rd
Modified  /trunk/madman/Rpacks/affycoretools/R/biomartfuns.R
Added  /trunk/madman/Rpacks/affycoretools/vignettes/RefactoredAffycoretools.Rnw
Modified  /trunk/madman/Rpacks/affycoretools/R/reportingTools.R
Modified  /trunk/madman/Rpacks/affycoretools/vignettes/affycoretools.Rnw
Modified  /trunk/madman/Rpacks/affycoretools/NAMESPACE
Refactoring to use ReportingTools instead of annaffy. Added vignette to explain differences.
Revision: 93704
Author: l.pantano
Date: 2014-08-29T21:14:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGreport/R/methods.R
Modified  /trunk/madman/Rpacks/DEGreport/R/report.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 433f3d25293deb31bbb44523ab00e6bbf26e8f0a
Commit message: add genes as row.names and add parallel option to report creation
Committed by: Lorena
Author Name: Lorena
Commit date: 2014-08-29 17:16:12 -0400
Author date: 2014-08-29 17:16:12 -0400

Revision: 93703
Author: r.castelo
Date: 2014-08-29T21:08:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/R/commonFunctions.R
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
Replace argument eltHits by elt.Hits in the call to mapCoords()
Revision: 93702
Author: d.tenenbaum
Date: 2014-08-29T20:30:45+00:00
Paths:
Added  /trunk/madman/Rpacks/rSFFreader/src/Makevars.win
add Makevars.win
Revision: 93701
Author: d.tenenbaum
Date: 2014-08-29T20:28:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/rSFFreader/src/SFF-io.c
Deleted  /trunk/madman/Rpacks/rSFFreader/.BBSoptions
Modified  /trunk/madman/Rpacks/rSFFreader/DESCRIPTION
Changed an include to be OS-conditional so package now compiles/installs
on windows. However, it does not build or check because the vignette
and example allocate too much memory (on win32 there is a 3GB limit).
Revision: 93699
Author: s.neumann
Date: 2014-08-29T19:38:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/CAMERA/man/annotateDiffreport.Rd
fixed manpage
Revision: 93696
Author: m.lawrence
Date: 2014-08-29T17:04:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/findOverlaps-methods.R
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
fix findOverlaps,IRanges for select="last" (seems never to have been implemented)
Revision: 93692
Author: l.gatto
Date: 2014-08-29T15:47:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/NEWS
Modified  /trunk/madman/Rpacks/MSnbase/man/MIAPE-class.Rd
Modified  /trunk/madman/Rpacks/MSnbase/R/map.R
Modified  /trunk/madman/Rpacks/MSnbase/DESCRIPTION
Merge branch 'master' into local-hedgehog
Revision: 93690
Author: mtmorgan
Date: 2014-08-29T14:00:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/explorase/DESCRIPTION
Modified  /trunk/madman/Rpacks/explorase/R/io.R
avoid deprecated / defunct .path.package
Revision: 93689
Author: j.gadin
Date: 2014-08-29T13:54:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/reads.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/getDefaultMapBiasExpMean.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-glocationplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/barplot-lattice-support.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/import-bam.Rd
Deleted  /trunk/madman/Rpacks/AllelicImbalance/tests/testthat/cigar-utility.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/ASEset-class.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/NAMESPACE
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/getAreaFromGeneNames.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/GRvariants.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/binom.test.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/coverageMatrixListFromGAL.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/barplot-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-gviztrack.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/GvizTrack-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/getSnpIdFromLocation.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/getAlleleCounts.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/locationplot-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/cigar-utilities.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-lbarplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/import-bcf.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/binom.test-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/chisq.test-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions-annotation.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/annotation-wrappers.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/getAlleleCounts2.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/AllelicImbalance-package.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/initialize-ASEset.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/initialize-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/implodeList.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-barplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/chisq.test.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/scanForHeterozygotes.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-class.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-locationplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/tests/testthat/test_cigar_utility.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 207508e4694069a4456d823b76dc1a760e717ef9
Commit message: format by formatR
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-29 15:53:43 +0200
Author date: 2014-08-29 15:53:43 +0200

Commit id: 7b324c6641fffe777cf7e218cad9212b5784ebae
Commit message: format by formatR
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-29 15:53:12 +0200
Author date: 2014-08-29 15:53:12 +0200

Revision: 93688
Author: j.gadin
Date: 2014-08-29T12:44:34+00:00
Paths:
Deleted  /trunk/madman/Rpacks/AllelicImbalance/inst/unitTests/test_funRealCigarPos.R
Added  /trunk/madman/Rpacks/AllelicImbalance/tests/testthat
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
Added  /trunk/madman/Rpacks/AllelicImbalance/tests/test-all.R
Added  /trunk/madman/Rpacks/AllelicImbalance/tests/testthat/cigar-utility.R
Deleted  /trunk/madman/Rpacks/AllelicImbalance/tests/runTests.R
Added  /trunk/madman/Rpacks/AllelicImbalance/tests/testthat/test_cigar_utility.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 5ad8590b506b4b4b88503d5c1b1374183e62b998
Commit message: changed to testthat
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-29 14:43:35 +0200
Author date: 2014-08-29 14:43:35 +0200

Revision: 93687
Author: l.gatto
Date: 2014-08-29T06:56:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/MLInterfaces/DESCRIPTION
Modified  /trunk/madman/Rpacks/MLInterfaces/NEWS
Modified  /trunk/madman/Rpacks/MLInterfaces/man/confuTab.Rd
Merge branch 'master' into remotes/hedgehog
Revision: 93686
Author: t.peters
Date: 2014-08-29T03:33:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/DMRcate/man/dmrcate.Rd
Modified  /trunk/madman/Rpacks/DMRcate/R/dmrcate.R
Modified  /trunk/madman/Rpacks/DMRcate/man/cpg.annotate.Rd
Modified  /trunk/madman/Rpacks/DMRcate/LICENSE
Modified  /trunk/madman/Rpacks/DMRcate/DESCRIPTION
Modified  /trunk/madman/Rpacks/DMRcate/man/DMRcate-package.Rd
Deleted  /trunk/madman/Rpacks/DMRcate/NEWS
Modified  /trunk/madman/Rpacks/DMRcate/vignettes/DMRcate.Rnw
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: b123c8097e5e05dadad01ada32de6da61bdbd4a2
Commit message: DMRcate_1.1.6
Committed by: timpeters82
Author Name: timpeters82
Commit date: 2014-08-29 13:33:38 +1000
Author date: 2014-08-29 13:33:38 +1000

Revision: 93685
Author: m.lawrence
Date: 2014-08-29T03:18:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/R/subsetting-internals.R
add replaceROWS,NULL from Peter Hickey
Revision: 93684
Author: j.gadin
Date: 2014-08-28T22:52:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: d4d89a6aac0f38ad06d429e21826e312fd5b9bfe
Commit message: replaced list with env hash
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-29 00:52:05 +0200
Author date: 2014-08-29 00:52:05 +0200

Revision: 93683
Author: m.lawrence
Date: 2014-08-28T22:32:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
Modified  /trunk/madman/Rpacks/S4Vectors/R/subsetting-internals.R
add replaceROWS,matrix
Revision: 93682
Author: d.tenenbaum
Date: 2014-08-28T21:55:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocCheck/R/checks.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: c554334027b48361753211c8595fe9becc573945
Commit message: Try harder to remove whitespace from biocViews before checking them for validity.
Committed by: Dan Tenenbaum
Author Name: Dan Tenenbaum
Commit date: 2014-08-28 14:55:15 -0700
Author date: 2014-08-28 14:55:15 -0700

Revision: 93681
Author: v.obenchain
Date: 2014-08-28T19:33:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/man/register.Rd
modify 'register' man page example to use PSOCK instead of MPI
Revision: 93680
Author: h.jaffee
Date: 2014-08-28T19:15:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/bumphunter/data/TT.rda
Modified  /trunk/madman/Rpacks/bumphunter/man/TT.Rd
Modified  /trunk/madman/Rpacks/bumphunter/R/known_transcripts.R
Modified  /trunk/madman/Rpacks/bumphunter/man/annotateNearest.Rd
Modified  /trunk/madman/Rpacks/bumphunter/NAMESPACE
Modified  /trunk/madman/Rpacks/bumphunter/R/matchGenes.R
Modified  /trunk/madman/Rpacks/bumphunter/R/nearestgene.R
Modified  /trunk/madman/Rpacks/bumphunter/DESCRIPTION
Improvements to known_transcripts, now exported, and data/TT, now a
list containing the txdb and org packageDescriptions used to make it.
matchGenes now accepts, and passes to the internal nearestgene(), the
arguments 'coding_only' and 'reference'.

Revision: 93679
Author: j.fortin
Date: 2014-08-28T18:10:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/shinyMethyl/README.md
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: f480a793b1db14e80264955863876af2188e8b3c
Commit message: Added paper link
Committed by: Jean-Philippe Fortin
Author Name: Jean-Philippe Fortin
Commit date: 2014-08-28 14:10:02 -0400
Author date: 2014-08-28 14:10:02 -0400

Revision: 93678
Author: j.gadin
Date: 2014-08-28T17:26:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/NAMESPACE
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions.R
Added  /trunk/madman/Rpacks/AllelicImbalance/man/implodeList.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/barplot-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/GvizTrack-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/locationplot-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/AllelicImbalance-package.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 417247bc9a8740c12a638354f657b45bedd0b3fb
Commit message: new implode function
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-28 19:25:40 +0200
Author date: 2014-08-28 19:25:40 +0200

Commit id: c4543e9b5bc92b217bfdb58a6ccd929bea842647
Commit message: in the process of adapting type='count' to glocationplot
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-28 15:14:01 +0200
Author date: 2014-08-28 15:14:01 +0200

Revision: 93676
Author: p.lijnzaad
Date: 2014-08-28T15:26:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/dyebias/DESCRIPTION
version bump on prev commit
Revision: 93675
Author: p.lijnzaad
Date: 2014-08-28T15:26:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/dyebias/inst/CITATION
fixed syntax (used to work, but newer R`s are prolly pickier.)
Revision: 93674
Author: s.neumann
Date: 2014-08-28T12:15:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/mzR/inst/unitTests/runit.cdf.R
Modified  /trunk/madman/Rpacks/mzR/NEWS
Modified  /trunk/madman/Rpacks/mzR/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 779d3a0d7777fcc518eb56d275cb90ad3c34ef95
Commit message: Remove superflouus library call in unitTests, should fix R CMD check on windows
Committed by: Steffen Neumann
Author Name: Steffen Neumann
Commit date: 2014-08-28 14:15:07 +0200
Author date: 2014-08-28 14:15:07 +0200

Revision: 93673
Author: j.gadin
Date: 2014-08-28T11:43:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: e8e60f1546a7799580cd5b44dc3f2efa76dea123
Commit message: change of variable name
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-28 13:43:12 +0200
Author date: 2014-08-28 13:43:12 +0200

Revision: 93669
Author: a.gobbi
Date: 2014-08-28T08:56:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiRewire/DESCRIPTION
fixed versioning number
Revision: 93668
Author: s.neumann
Date: 2014-08-28T07:53:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rdisop/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: b8bf58c2eae12ee49bf0fa5f76ef9808008f5fee
Commit message: Update description with URLs
Committed by: sneumann
Author Name: sneumann
Commit date: 2014-08-28 09:53:32 +0200
Author date: 2014-08-28 09:53:32 +0200

Revision: 93667
Author: s.neumann
Date: 2014-08-28T07:52:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/CAMERA/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: dd703304fcf2f0fdfbf0e75ada9a13d3eb3407aa
Commit message: Update description with URLs
Committed by: sneumann
Author Name: sneumann
Commit date: 2014-08-28 09:52:52 +0200
Author date: 2014-08-28 09:52:52 +0200

Revision: 93666
Author: s.neumann
Date: 2014-08-28T07:52:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/xcms/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 56cb79844f3d4224bc2985209eedd060e13dec73
Commit message: Update description with URLs
Committed by: sneumann
Author Name: sneumann
Commit date: 2014-08-28 09:52:10 +0200
Author date: 2014-08-28 09:52:10 +0200

Revision: 93665
Author: s.neumann
Date: 2014-08-28T07:51:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/mzR/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 5d97262c7a9530ef599c6190bed07e3c7fe36a7e
Commit message: Update description with URLs
Committed by: sneumann
Author Name: sneumann
Commit date: 2014-08-28 09:51:23 +0200
Author date: 2014-08-28 09:51:23 +0200

Revision: 93664
Author: xiaojing.wang
Date: 2014-08-28T05:21:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/customProDB/NEWS
Modified  /trunk/madman/Rpacks/customProDB/R/OutputNovelJun.R
Modified  /trunk/madman/Rpacks/customProDB/DESCRIPTION
fixed a bug
Revision: 93663
Author: g.yu
Date: 2014-08-28T03:38:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/clusterProfiler/NEWS
Modified  /trunk/madman/Rpacks/clusterProfiler/R/utilities.R
Modified  /trunk/madman/Rpacks/clusterProfiler/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 673d867d19ddfd4fd8f11de0136a7eae49de07b3
Commit message: add keepGOlevel, keepGOterm, excludeGOlevel, excludeGOterm, not exported yet <2014-08-28, Thu>
Committed by: Guangchuang Yu
Author Name: Guangchuang Yu
Commit date: 2014-08-28 11:37:57 +0800
Author date: 2014-08-28 11:37:57 +0800

Revision: 93661
Author: c.fletez-brant
Date: 2014-08-28T02:12:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowClean/vignettes/flowClean.Rnw
Modified  /trunk/madman/Rpacks/flowClean/R/flowClean.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commits.

Commit information:

Commit id: 62b22c2449ad16c8266beb415cef51f6dbb6cdc4
Commit message: Merge branch 'master' of github.com:cafletezbrant/flowClean
Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-08-27 19:09:59 -0700
Author date: 2014-08-27 19:09:59 -0700

Commit id: b974edfcc47a6ad03c93028c1e203d03c90433cc
Commit message: Revert "fixed erroneous vignette discussion"
This reverts commit 4661d4ca77eeef2a20cfe285df79554456c004e8.
Committed by: kipper
Author Name: kipper
Commit date: 2014-08-27 22:11:04 -0400
Author date: 2014-08-27 22:11:04 -0400

Commit id: 093f2a948cf86644c780c5d8c333d52405bd538b
Commit message: testing
Committed by: kipper
Author Name: kipper
Commit date: 2014-08-27 22:06:31 -0400
Author date: 2014-08-27 22:06:31 -0400

Revision: 93659
Author: c.fletez-brant
Date: 2014-08-28T01:41:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowClean/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 3bcbe5021b64f12d59e9c33b18a6e712a47db6ec
Commit message: Merge branch 'master' of github.com:cafletezbrant/flowClean
Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-08-27 18:39:13 -0700
Author date: 2014-08-27 18:39:13 -0700

Commit id: 5db3d72e906c955f8597cce9084e40eff804860a
Commit message: vignette error
Committed by: kipper
Author Name: kipper
Commit date: 2014-08-27 21:41:13 -0400
Author date: 2014-08-27 21:41:13 -0400

Revision: 93658
Author: c.fletez-brant
Date: 2014-08-28T01:40:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowClean/vignettes/flowClean.Rnw
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 618fe74fcf9e38c0b6b63eb068c094e0f557b9af
Commit message: Merge branch 'master' of github.com:cafletezbrant/flowClean
Committed by: Bioconductor Git-SVN Bridge
Author Name: Bioconductor Git-SVN Bridge
Commit date: 2014-08-27 18:38:21 -0700
Author date: 2014-08-27 18:38:21 -0700

Commit id: 4661d4ca77eeef2a20cfe285df79554456c004e8
Commit message: fixed erroneous vignette discussion
Committed by: kipper
Author Name: kipper
Commit date: 2014-08-27 21:40:06 -0400
Author date: 2014-08-27 21:40:06 -0400

Revision: 93657
Author: r.castelo
Date: 2014-08-27T23:38:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/qpgraph/DESCRIPTION
Modified  /trunk/madman/Rpacks/qpgraph/R/qpgraph.R
Modified  /trunk/madman/Rpacks/qpgraph/man/qpPlotNetwork.Rd
Fixed bug in qpAnyGraph().
Revision: 93656
Author: d.tenenbaum
Date: 2014-08-27T22:54:09+00:00
Paths:
Deleted  /trunk/madman/Rpacks/flowMerge/.BBSoptions
delete empty .BBSoptions file
Revision: 93655
Author: v.obenchain
Date: 2014-08-27T22:11:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/inst/unitTests/test_VCF-class.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-VCF-class.R
propagate changes made to rbind/cbind for SummarizedExperment to VCF
Revision: 93654
Author: v.obenchain
Date: 2014-08-27T22:02:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/SummarizedExperiment-class.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/mapCoords-methods.Rd
remove unused lapply in .rbind.SummarizeExperiment()
Revision: 93653
Author: j.gadin
Date: 2014-08-27T21:58:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-lbarplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/barplot-methods.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 9d014ab11aa0224a09d764161799ac0aaa27919b
Commit message: small dev
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-27 23:58:04 +0200
Author date: 2014-08-27 23:58:04 +0200

Revision: 93652
Author: b.fischer
Date: 2014-08-27T21:27:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/rhdf5/CHANGES
Modified  /trunk/madman/Rpacks/rhdf5/src/H5P.h
Modified  /trunk/madman/Rpacks/rhdf5/man/H5P_LINK_CREATE.Rd
Modified  /trunk/madman/Rpacks/rhdf5/NAMESPACE
Modified  /trunk/madman/Rpacks/rhdf5/R/H5P.R
Modified  /trunk/madman/Rpacks/rhdf5/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/rhdf5/src/wrap.c
Modified  /trunk/madman/Rpacks/rhdf5/DESCRIPTION
Modified  /trunk/madman/Rpacks/rhdf5/man/H5P_DATASET_CREATE.Rd
Modified  /trunk/madman/Rpacks/rhdf5/src/H5P.c
Added low level functions H5Pget_char_encoding, H5Pget_create_intermediate_group, H5Pget_layout, H5Pget_chunk, H5Pfill_value_defined, H5Pget_fill_time, H5Pget_alloc_time.
Revision: 93651
Author: m.carlson
Date: 2014-08-27T21:26:05+00:00
Paths:
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/otuSites.Rd
Added  /trunk/madman/Rpacks/methylPipe/inst/extdata/gec.IMR90.Rdata
Added  /trunk/madman/Rpacks/MBASED/man/logLikelihoodCalculator2s.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/troubleshootLinkers.Rd
Added  /trunk/madman/Rpacks/erccdashboard/R/maSignal.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/crossOverCheck.Rd
Added  /trunk/madman/Rpacks/MBASED/man/maxLogLikelihoodCalculator1s.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/replicateReads.Rd
Added  /trunk/madman/Rpacks/MBASED/R/MBASEDBetaBinomialFunctions.R
Added  /trunk/madman/Rpacks/methylPipe/inst/extdata/IMR90_chr20_CG_10k.gz
Added  /trunk/madman/Rpacks/erccdashboard/man/MET.CTL.countDat.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/NEWS
Added  /trunk/madman/Rpacks/erccdashboard/man/UHRR.HBRR.countDat.Rd
Added  /trunk/madman/Rpacks/MBASED/man/generatingBetaBinomialCounts.Rd
Added  /trunk/madman/Rpacks/erccdashboard/R/geneExprTest.R
Added  /trunk/madman/Rpacks/MBASED/man/FreemanTukeyFunctions.Rd
Added  /trunk/madman/Rpacks/methylPipe/man/getCpos.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/GRanges2ucsc.R
Added  /trunk/madman/Rpacks/compEpiTools/man/TSS.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/GRcoverageInbins.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/splitSeqsToFiles.Rd
Added  /trunk/madman/Rpacks/methylPipe/R/BSdata-methods.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/pairUpAlignments.Rd
Added  /trunk/madman/Rpacks/compEpiTools/man/GRangesInPromoters-methods.Rd
Added  /trunk/madman/Rpacks/erccdashboard/R/loadExpMeas.R
Added  /trunk/madman/Rpacks/compEpiTools/NEWS
Added  /trunk/madman/Rpacks/MBASED/man/runMBASED.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/GRmidpoint.R
Added  /trunk/madman/Rpacks/compEpiTools/R/featuresLength.R
Added  /trunk/madman/Rpacks/compEpiTools/inst/extdata/Pol2.bam
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/tests/tests
Added  /trunk/madman/Rpacks/MBASED/vignettes/MBASED.Rnw
Added  /trunk/madman/Rpacks/compEpiTools/man/makeGtfFromDb.Rd
Added  /trunk/madman/Rpacks/compEpiTools/man/GRannotateSimple.Rd
Added  /trunk/madman/Rpacks/methylPipe/src/binning.c
Added  /trunk/madman/Rpacks/compEpiTools/R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/findPrimers.Rd
Added  /trunk/madman/Rpacks/methylPipe/src/binning.h
Added  /trunk/madman/Rpacks/MBASED/inst/NEWS
Added  /trunk/madman/Rpacks/compEpiTools/vignettes
Added  /trunk/madman/Rpacks/erccdashboard/man/UHRR.HBRR.arrayDat.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/extdata/FLX_sample_run/RunData/3.TCA.454Reads.fna.gz
Added  /trunk/madman/Rpacks/compEpiTools/inst/extdata/H3K4me1.bam.bai
Added  /trunk/madman/Rpacks/compEpiTools/man
Added  /trunk/madman/Rpacks/compEpiTools/inst/extdata/H3K4me3.bam.bai
Added  /trunk/madman/Rpacks/methylPipe/man/BSdata-class.Rd
Added  /trunk/madman/Rpacks/erccdashboard/R/estLODR.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/blatListedSet.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/extdata/FLX_sample_run/RunData
Added  /trunk/madman/Rpacks/MBASED/man/testNumericDiff.Rd
Added  /trunk/madman/Rpacks/erccdashboard/DESCRIPTION
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/pslToRangedObject.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/removeReadsWithNs.Rd
Added  /trunk/madman/Rpacks/erccdashboard/R/loadERCCInfo.R
Added  /trunk/madman/Rpacks/compEpiTools/man/GRcoverageSummit-methods.Rd
Added  /trunk/madman/Rpacks/compEpiTools/man/GRcoverage-methods.Rd
Added  /trunk/madman/Rpacks/methylPipe/R
Added  /trunk/madman/Rpacks/compEpiTools/R/distanceFromTSS.R
Added  /trunk/madman/Rpacks/methylPipe/inst/extdata/GR_chr20.Rdata
Added  /trunk/madman/Rpacks/compEpiTools/R/heatmapData.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/clusterSites.Rd
Added  /trunk/madman/Rpacks/erccdashboard/man/SEQC.Example.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/heatmapPlot.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst
Added  /trunk/madman/Rpacks/methylPipe/R/BSdataSet-methods.R
Added  /trunk/madman/Rpacks/compEpiTools/man/plotStallingIndex.Rd
Added  /trunk/madman/Rpacks/erccdashboard/R/saveERCCPlots.R
Added  /trunk/madman/Rpacks/MBASED/inst/unitTests/test_miscellaneous_helper_functions.R
Added  /trunk/madman/Rpacks/compEpiTools/R/ucsc2GRanges.R
Added  /trunk/madman/Rpacks/compEpiTools/man/countOverlapsInBins-methods.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/read.blast8.Rd
Added  /trunk/madman/Rpacks/methylPipe/R/GElist-methods.R
Added  /trunk/madman/Rpacks/methylPipe/man/splitChrs.Rd
Added  /trunk/madman/Rpacks/MBASED/inst/unitTests/test_FT_functions.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/NAMESPACE
Added  /trunk/madman/Rpacks/methylPipe/NAMESPACE
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/pslCols.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor
Added  /trunk/madman/Rpacks/erccdashboard/man/UHRR.HBRR.totalReads.Rd
Added  /trunk/madman/Rpacks/erccdashboard/man/saveERCCPlots.Rd
Added  /trunk/madman/Rpacks/methylPipe/man/profileDNAmetBin.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/stallingIndex.R
Added  /trunk/madman/Rpacks/MBASED/man/maxLogLikelihoodCalculator2s.Rd
Added  /trunk/madman/Rpacks/compEpiTools/man/unionMaxScore-methods.Rd
Added  /trunk/madman/Rpacks/compEpiTools/inst
Added  /trunk/madman/Rpacks/MBASED/man/MBASEDVectorizedPropDiffTest.Rd
Added  /trunk/madman/Rpacks/compEpiTools/inst/extdata/H3K4me1.bam
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/tests
Added  /trunk/madman/Rpacks/hiReadsProcessor/DESCRIPTION
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/seqProps.Rd
Added  /trunk/madman/Rpacks/MBASED/man/estimateMAF1s.Rd
Added  /trunk/madman/Rpacks/erccdashboard/R/multiplot.R
Added  /trunk/madman/Rpacks/MBASED/man/getPFinal.Rd
Added  /trunk/madman/Rpacks/methylPipe/man/process.hmc.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/findLTRs.Rd
Added  /trunk/madman/Rpacks/methylPipe/inst/extdata/DMRs.Rdata
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/extdata
Added  /trunk/madman/Rpacks/MBASED/NAMESPACE
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/pairwiseAlignSeqs.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/psl.Rd
Added  /trunk/madman/Rpacks/erccdashboard/data
Added  /trunk/madman/Rpacks/MBASED/man/runMBASED1s.Rd
Added  /trunk/madman/Rpacks/erccdashboard/man
Added  /trunk/madman/Rpacks/erccdashboard/R/runDashboard.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/findVector.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/extractSeqs.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/findIntegrations.Rd
Added  /trunk/madman/Rpacks/compEpiTools/vignettes/compEpiTools.rnw
Added  /trunk/madman/Rpacks/erccdashboard/man/dynRangePlot.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/vignettes/Tutorial.Rmd
Added  /trunk/madman/Rpacks/erccdashboard/R/normalizeDat.R
Added  /trunk/madman/Rpacks/erccdashboard/man/estLODR.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/overlapOfGRanges.R
Added  /trunk/madman/Rpacks/erccdashboard
Added  /trunk/madman/Rpacks/compEpiTools/inst/extdata
Added  /trunk/madman/Rpacks/erccdashboard/R/dynRangePlot.R
Added  /trunk/madman/Rpacks/methylPipe/man/plotMeth.Rd
Added  /trunk/madman/Rpacks/compEpiTools/man/overlapOfGRanges-methods.Rd
Added  /trunk/madman/Rpacks/compEpiTools/man/compEpiTools-package.Rd
Added  /trunk/madman/Rpacks/erccdashboard/man/annotLODR.Rd
Added  /trunk/madman/Rpacks/methylPipe/DESCRIPTION
Added  /trunk/madman/Rpacks/methylPipe/inst/extdata/uncov_GR.Rdata
Added  /trunk/madman/Rpacks/compEpiTools/man/heatmapData.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/trimSeqs.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/extdata/FLX_sample_run/RunData/1.TCA.454Reads.fna
Added  /trunk/madman/Rpacks/methylPipe/src
Added  /trunk/madman/Rpacks/compEpiTools/man/findLncRNA.Rd
Added  /trunk/madman/Rpacks/methylPipe/inst/extdata/test_methcall/methylPipe_ex.sam
Added  /trunk/madman/Rpacks/compEpiTools/man/GRbaseCoverage-methods.Rd
Added  /trunk/madman/Rpacks/methylPipe/man/BSdataSet-class.Rd
Added  /trunk/madman/Rpacks/compEpiTools/man/palette2d.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/primerIDAlignSeqs.Rd
Added  /trunk/madman/Rpacks/MBASED/man/MBASEDMetaAnalysis.Rd
Added  /trunk/madman/Rpacks/erccdashboard/man/geneExprTest.Rd
Added  /trunk/madman/Rpacks/erccdashboard/R/prepERCCDat.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/findBarcodes.Rd
Added  /trunk/madman/Rpacks/erccdashboard/R/initDat.R
Added  /trunk/madman/Rpacks/erccdashboard/R
Added  /trunk/madman/Rpacks/methylPipe/inst/extdata/gec.H1.Rdata
Added  /trunk/madman/Rpacks/MBASED/man/runMBASED2s1aseID.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/tests/tests/test_coreFeatures.R
Added  /trunk/madman/Rpacks/MBASED/man/betaParametrizationConverters.Rd
Added  /trunk/madman/Rpacks/erccdashboard/man/est_r_m.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/GRbaseCoverage.R
Added  /trunk/madman/Rpacks/erccdashboard/man/ERCCDef.Rd
Added  /trunk/madman/Rpacks/compEpiTools/DESCRIPTION
Added  /trunk/madman/Rpacks/compEpiTools/man/stallingIndex.Rd
Added  /trunk/madman/Rpacks/methylPipe/man/findPMDs.Rd
Added  /trunk/madman/Rpacks/MBASED/R/MBASEDStatsHelperFunctions1s.R
Added  /trunk/madman/Rpacks/MBASED/R/MBASEDUnitTestsFunctions.R
Added  /trunk/madman/Rpacks/MBASED/man/shiftAndAttenuateProportions.Rd
Added  /trunk/madman/Rpacks/methylPipe/exec
Added  /trunk/madman/Rpacks/erccdashboard/R/erccROC.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/extdata/FLX_sample_run/RunData/2.TCA.454Reads.fna
Added  /trunk/madman/Rpacks/methylPipe/man/meth.call.Rd
Added  /trunk/madman/Rpacks/erccdashboard/man/MET.CTL.totalReads.Rd
Added  /trunk/madman/Rpacks/erccdashboard/R/est_r_m.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/chunkize.Rd
Added  /trunk/madman/Rpacks/erccdashboard/NAMESPACE
Added  /trunk/madman/Rpacks/hiReadsProcessor/data/psl.RData
Added  /trunk/madman/Rpacks/MBASED/tests/runTests.R
Added  /trunk/madman/Rpacks/methylPipe/man/mapBSdata2GRanges.Rd
Added  /trunk/madman/Rpacks/erccdashboard/vignettes/erccdashboard.Rnw
Added  /trunk/madman/Rpacks/methylPipe/inst/extdata
Added  /trunk/madman/Rpacks/MBASED/R/MBASEDPackageStatement.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/getIntegrationSites.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/findLncRNA.R
Added  /trunk/madman/Rpacks/MBASED/tests
Added  /trunk/madman/Rpacks/compEpiTools/inst/extdata/H3K4me3GR.Rda
Added  /trunk/madman/Rpacks/hiReadsProcessor/.Rinstignore
Added  /trunk/madman/Rpacks/erccdashboard/R/getDesignMat.R
Added  /trunk/madman/Rpacks/compEpiTools/R/GRenrichment.R
Added  /trunk/madman/Rpacks/MBASED/man/MBASED.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/addListNameToReads.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/GRangesInPromoters.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/read.psl.Rd
Added  /trunk/madman/Rpacks/MBASED/man
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/extdata/FLX_sample_run/RunData/3.TCA.454Reads.fna
Added  /trunk/madman/Rpacks/MBASED/inst/unitTests/test_MBASED_2s_method.R
Added  /trunk/madman/Rpacks/MBASED/inst
Added  /trunk/madman/Rpacks/methylPipe/man/extractBinGRanges.Rd
Added  /trunk/madman/Rpacks/erccdashboard/R/testDEArray.R
Added  /trunk/madman/Rpacks/methylPipe/vignettes/methylPipe.rnw
Added  /trunk/madman/Rpacks/MBASED/man/estimateMAF2s.Rd
Added  /trunk/madman/Rpacks/methylPipe/inst/extdata/test_methcall
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/annotateSites.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/plotStallingIndex.R
Added  /trunk/madman/Rpacks/methylPipe/man/BSprepare.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/extractFeature.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/write.psl.Rd
Added  /trunk/madman/Rpacks/methylPipe/exec/methinfo.pl
Added  /trunk/madman/Rpacks/methylPipe/R/GEcollection-methods.R
Added  /trunk/madman/Rpacks/compEpiTools/R/GRannotateSimple.R
Added  /trunk/madman/Rpacks/methylPipe/man
Added  /trunk/madman/Rpacks/erccdashboard/man/multiplot.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/read.SeqFolder.Rd
Added  /trunk/madman/Rpacks/compEpiTools/inst/extdata/Pol2GR.Rda
Added  /trunk/madman/Rpacks/MBASED/man/runMBASED2s.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/GRsetwidth.R
Added  /trunk/madman/Rpacks/erccdashboard/data/ERCC.RData
Added  /trunk/madman/Rpacks/hiReadsProcessor/data/FLX_seqProps.RData
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/extdata/FLX_sample_run/Vectors/MLV-vector.fa
Added  /trunk/madman/Rpacks/methylPipe/inst/extdata/H1_chr20_CG_10k.gz.tbi
Added  /trunk/madman/Rpacks/compEpiTools/man/matchEnhancers.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/GRannotate.R
Added  /trunk/madman/Rpacks/methylPipe
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Added  /trunk/madman/Rpacks/compEpiTools/man/GRenrichment-methods.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/extdata/FLX_sample_run/RunData/1.TCA.454Reads.fna.gz
Added  /trunk/madman/Rpacks/compEpiTools/R/countOverlapsInBins.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/read.seqsFromSector.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/data
Added  /trunk/madman/Rpacks/methylPipe/man/consolidateDMRs.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/extdata/FLX_sample_run/Vectors
Added  /trunk/madman/Rpacks/erccdashboard/man/initDat.Rd
Modified  /trunk/madman/Rpacks/bioc_3.0.manifest
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/write.listedDNAStringSet.Rd
Added  /trunk/madman/Rpacks/MBASED/man/MBASEDMetaAnalysisGetMeansAndSEs.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/findAndRemoveVector.Rd
Added  /trunk/madman/Rpacks/compEpiTools/man/enhancers.Rd
Added  /trunk/madman/Rpacks/MBASED/R/MBASEDStatsHelperFunctions2s.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/isuSites.Rd
Added  /trunk/madman/Rpacks/compEpiTools/man/GR2fasta-methods.Rd
Added  /trunk/madman/Rpacks/compEpiTools/NAMESPACE
Added  /trunk/madman/Rpacks/MBASED/inst/unitTests
Added  /trunk/madman/Rpacks/erccdashboard/man/runDashboard.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/vignettes/hiReadsProcessor_object.png
Added  /trunk/madman/Rpacks/erccdashboard/man/ERCC.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/R
Added  /trunk/madman/Rpacks/compEpiTools/man/GRanges2ucsc-methods.Rd
Added  /trunk/madman/Rpacks/methylPipe/man/chiCombP.Rd
Added  /trunk/madman/Rpacks/erccdashboard/R/annotLODR.R
Added  /trunk/madman/Rpacks/compEpiTools/R/makeGtfFromDb.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/vignettes
Added  /trunk/madman/Rpacks/methylPipe/vignettes
Added  /trunk/madman/Rpacks/compEpiTools/man/simplifyGOterms.Rd
Added  /trunk/madman/Rpacks/methylPipe/NEWS
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/dereplicateReads.Rd
Added  /trunk/madman/Rpacks/erccdashboard/NEWS
Added  /trunk/madman/Rpacks/compEpiTools/R/GRcoverageSummit.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/addFeature.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/extdata/FLX_sample_run
Added  /trunk/madman/Rpacks/methylPipe/inst/extdata/IMR90_chr20_CG_10k.gz.tbi
Added  /trunk/madman/Rpacks/MBASED/R/MBASEDStatsMainFunctionsExport.R
Added  /trunk/madman/Rpacks/compEpiTools/R/unionMaxScore.R
Added  /trunk/madman/Rpacks/methylPipe/man/methylPipe-package.Rd
Added  /trunk/madman/Rpacks/compEpiTools/man/heatmapPlot.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/getPromoterClass.R
Added  /trunk/madman/Rpacks/compEpiTools/R/simplifyGOterms.R
Added  /trunk/madman/Rpacks/methylPipe/src/R_init_methylPipe.c
Added  /trunk/madman/Rpacks/MBASED/man/logLikelihoodCalculator1s.Rd
Added  /trunk/madman/Rpacks/methylPipe/R/Allfunctions.R
Added  /trunk/madman/Rpacks/methylPipe/man/GElist-class.Rd
Added  /trunk/madman/Rpacks/MBASED/R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/sampleSummary.Rd
Added  /trunk/madman/Rpacks/compEpiTools/man/topGOres.Rd
Added  /trunk/madman/Rpacks/erccdashboard/man/maSignal.Rd
Added  /trunk/madman/Rpacks/compEpiTools/inst/extdata/H3K4me1GR.Rda
Added  /trunk/madman/Rpacks/compEpiTools/man/GRannotate-methods.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/R/hiReadsProcessor.R
Added  /trunk/madman/Rpacks/compEpiTools/inst/extdata/H3K4me3.bam
Added  /trunk/madman/Rpacks/compEpiTools/R/palette2d.R
Added  /trunk/madman/Rpacks/erccdashboard/data/datalist
Added  /trunk/madman/Rpacks/MBASED/vignettes
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/splitByBarcode.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/findLinkers.Rd
Added  /trunk/madman/Rpacks/MBASED/R/MBASEDStatsMainFunctions1s.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/getSectorsForSamples.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/blatSeqs.Rd
Added  /trunk/madman/Rpacks/erccdashboard/R/printLODRres.R
Added  /trunk/madman/Rpacks/erccdashboard/data/SEQC.Example.RData
Added  /trunk/madman/Rpacks/erccdashboard/R/plotAdjust.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/vpairwiseAlignSeqs.Rd
Added  /trunk/madman/Rpacks/erccdashboard/man/ERCCMix1and2.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/getSonicAbund.Rd
Added  /trunk/madman/Rpacks/MBASED/man/runMBASED1s1aseID.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/doRCtest.Rd
Added  /trunk/madman/Rpacks/methylPipe/man/mCsmoothing.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/GR2fasta.R
Added  /trunk/madman/Rpacks/compEpiTools/R/TSS.R
Added  /trunk/madman/Rpacks/compEpiTools/man/getPromoterClass-methods.Rd
Added  /trunk/madman/Rpacks/MBASED
Added  /trunk/madman/Rpacks/methylPipe/man/getCposDensity.Rd
Added  /trunk/madman/Rpacks/compEpiTools/man/distanceFromTSS-methods.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/read.sampleInfo.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/extdata/FLX_sample_run/sampleInfo.xls
Added  /trunk/madman/Rpacks/compEpiTools/man/GRmidpoint-methods.Rd
Added  /trunk/madman/Rpacks/methylPipe/man/GEcollection-class.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/hiReadsProcessor.Rd
Added  /trunk/madman/Rpacks/MBASED/DESCRIPTION
Added  /trunk/madman/Rpacks/MBASED/man/testQuantiles.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/topGOres.R
Added  /trunk/madman/Rpacks/compEpiTools/man/GRsetwidth.Rd
Added  /trunk/madman/Rpacks/compEpiTools/man/ucsc2GRanges.Rd
Added  /trunk/madman/Rpacks/compEpiTools/R/enhancers.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/extdata/FLX_sample_run/RunData/2.TCA.454Reads.fna.gz
Added  /trunk/madman/Rpacks/MBASED/inst/unitTests/test_betabinomial_functions.R
Added  /trunk/madman/Rpacks/methylPipe/inst
Added  /trunk/madman/Rpacks/methylPipe/inst/extdata/H1_chr20_CG_10k.gz
Added  /trunk/madman/Rpacks/erccdashboard/inst
Added  /trunk/madman/Rpacks/compEpiTools/R/matchEnhancers.R
Added  /trunk/madman/Rpacks/compEpiTools/R/GRcoverage.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/findAndTrimSeq.Rd
Added  /trunk/madman/Rpacks/methylPipe/R/AllClasses.R
Added  /trunk/madman/Rpacks/MBASED/inst/unitTests/test_MBASED_1s_method.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/read.BAMasPSL.Rd
Added  /trunk/madman/Rpacks/erccdashboard/inst/CITATION
Added  /trunk/madman/Rpacks/methylPipe/man/tabixdata2GR.Rd
Added  /trunk/madman/Rpacks/MBASED/man/getSimulationPvalue.Rd
Added  /trunk/madman/Rpacks/MBASED/man/MBASEDVectorizedMetaprop.Rd
Added  /trunk/madman/Rpacks/erccdashboard/R/dashboardFile.R
Added  /trunk/madman/Rpacks/compEpiTools
Added  /trunk/madman/Rpacks/methylPipe/R/zzz.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/vignettes/hiReadsProcessor_workflow.png
Added  /trunk/madman/Rpacks/erccdashboard/man/erccROC.Rd
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/tests/runTests.R
Added  /trunk/madman/Rpacks/hiReadsProcessor/inst/extdata/FLX_sample_run/Vectors/HIV1.fa
Added  /trunk/madman/Rpacks/erccdashboard/R/testDECount.R
Added  /trunk/madman/Rpacks/methylPipe/revisionNotes.R
Added  /trunk/madman/Rpacks/compEpiTools/inst/extdata/Pol2.bam.bai
Added  /trunk/madman/Rpacks/hiReadsProcessor/man
Added  /trunk/madman/Rpacks/erccdashboard/vignettes
Added  /trunk/madman/Rpacks/hiReadsProcessor/man/startgfServer.Rd
Added  /trunk/madman/Rpacks/MBASED/R/MBASEDStatsMainFunctions2s.R
Add compEpiTools/ erccdashboard/ hiReadsProcessor/ MBASED/ methylPipe/ to the repos.

Source Code & Build Reports »

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

Software packages are built and checked nightly. Build reports:

 

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Bioconductor packages under development:


Developer Resources:

Fred Hutchinson Cancer Research Center