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Revision: 98805
Author: r.nicolle
Date: 2015-01-28T12:51:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/CoRegNet/DESCRIPTION
Modified  /trunk/madman/Rpacks/CoRegNet/NEWS
Modified  /trunk/madman/Rpacks/CoRegNet/R/coRegnet.R
Modified  /trunk/madman/Rpacks/CoRegNet/R/display.R
Modified  /trunk/madman/Rpacks/CoRegNet/data/CIT_BLCA_Subgroup.RData
Modified  /trunk/madman/Rpacks/CoRegNet/man/HumanDataExamples.Rd
Modified  /trunk/madman/Rpacks/CoRegNet/man/hLICORN.Rd
Modified  /trunk/madman/Rpacks/CoRegNet/vignettes/CoRegNet.Rmd
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Commit information:

Commit id: dcb9bdd1979fc76b1b7ec7b6211a7d3ecc69d20f

    Merge branch 'master' of https://github.com/RemyNicolle/CoRegNet

    changed default hLICORN parameters, added missing man info.

Committed by: Remy Nicolle
Author Name: Remy Nicolle
Commit date: 2015-01-28 13:07:58 +0100
Author date: 2015-01-28 13:07:58 +0100

Commit id: 7da8869e2c5eacc150631bd49e5775fbb47c545b

    added safeguards to input in display function. Better default parameters in hLICORN. completed manual

Committed by: Rémy Nicolle
Author Name: Rémy Nicolle
Commit date: 2015-01-28 13:05:22 +0100
Author date: 2015-01-28 13:05:22 +0100
Revision: 98803
Author: e.bernard
Date: 2015-01-28T11:24:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/flipflop/DESCRIPTION
Modified  /trunk/madman/Rpacks/flipflop/R/flipflop.R
Modified  /trunk/madman/Rpacks/flipflop/inst/NEWS
Modified  /trunk/madman/Rpacks/flipflop/src/spams/prox/fista.h
the total num of mapped fragment
Revision: 98802
Author: d.rossell
Date: 2015-01-28T10:04:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/casper/R/calcDenovo.R
Modified  /trunk/madman/Rpacks/casper/R/pathCounts.R
Modified  /trunk/madman/Rpacks/casper/R/wrapDenovo.R
Fixed warnings
Revision: 98801
Author: j.malone
Date: 2015-01-28T09:28:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/AtlasRDF/DESCRIPTION
fix to version date
Revision: 98800
Author: hpages
Date: 2015-01-28T08:32:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/NAMESPACE
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGRanges.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/inst/unitTests/test_makeTxDbFromGRanges.R
more work on makeTxDbFromGRanges()
Revision: 98799
Author: r.castelo
Date: 2015-01-28T08:30:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantFiltering/R/autosomalRecessiveHomozygous.R
Modified  /trunk/madman/Rpacks/VariantFiltering/R/methods-VariantFilteringParam.R
Minor corrections when iterating through the VCF file.
Revision: 98798
Author: hpages
Date: 2015-01-28T08:21:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGRanges.R
more work on makeTxDbFromGRanges()
Revision: 98797
Author: g.yu
Date: 2015-01-28T07:37:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/clusterProfiler/NEWS
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 8d101cff4137e62daf08eb0629a13c5aa7ed1dd1

    update news

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-28 15:36:10 +0800
Author date: 2015-01-28 15:36:10 +0800
Revision: 98796
Author: g.yu
Date: 2015-01-28T07:30:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/clusterProfiler/vignettes/clusterProfiler.Rnw
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 6d40d860857187f8b972f2e57c5466c36680771b

    update vignettes

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-28 15:30:07 +0800
Author date: 2015-01-28 15:30:07 +0800
Revision: 98795
Author: g.yu
Date: 2015-01-28T07:11:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/clusterProfiler/DESCRIPTION
Modified  /trunk/madman/Rpacks/clusterProfiler/NAMESPACE
Modified  /trunk/madman/Rpacks/clusterProfiler/NEWS
Modified  /trunk/madman/Rpacks/clusterProfiler/R/enrichKEGG.R
Modified  /trunk/madman/Rpacks/clusterProfiler/R/utilities.R
Modified  /trunk/madman/Rpacks/clusterProfiler/inst/CITATION
Modified  /trunk/madman/Rpacks/clusterProfiler/man/buildKEGGmap.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/download.KEGG.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/enrichKEGG.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/vignettes/clusterProfiler.Rnw
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 4292c8f956c3c71b84a66097bbe15c4ab14b4d09

    online version of KEGG

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-28 15:10:50 +0800
Author date: 2015-01-28 15:10:50 +0800

Commit id: d24874fca8abaddcdc280567ff6de569f1a63be0

    update citation

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-28 11:58:44 +0800
Author date: 2015-01-28 11:58:44 +0800
Revision: 98794
Author: g.yu
Date: 2015-01-28T07:09:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOSE/DESCRIPTION
Modified  /trunk/madman/Rpacks/DOSE/NEWS
Modified  /trunk/madman/Rpacks/DOSE/R/utilities.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 4c5d6ec703961d0a53e6f574e1db7d23e2223797

    organismMapper

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-28 15:08:47 +0800
Author date: 2015-01-28 15:08:47 +0800
Revision: 98793
Author: hpages
Date: 2015-01-28T05:23:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGRanges.R
more work on makeTxDbFromGRanges()
Revision: 98792
Author: d.tenenbaum
Date: 2015-01-28T04:20:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocCheck/R/util.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 44492caec2a58831ef69cb922e919e917e113de9

    clean up diagnostics and bump version

Committed by: Dan Tenenbaum
Author Name: Dan Tenenbaum
Commit date: 2015-01-27 20:19:52 -0800
Author date: 2015-01-27 20:19:52 -0800
Revision: 98791
Author: t.girke
Date: 2015-01-28T04:12:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.R
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.pdf
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Commit information:

Commit id: caa5aa0ddfb1117536f10024c533cda5d5360a80

    vignette updates

Committed by: Thomas Girke
Author Name: Thomas Girke
Commit date: 2015-01-27 20:12:34 -0800
Author date: 2015-01-27 20:12:34 -0800
Revision: 98790
Author: j.paulson
Date: 2015-01-28T04:11:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/metagenomeSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/metagenomeSeq/NAMESPACE
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/allClasses.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/correlationTest.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/cumNorm.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/exportMat.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/filterData.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/fitDO.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/fitPA.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/plotCorr.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/plotFeature.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/plotGenus.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/plotMRheatmap.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/plotOTU.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/R/plotOrd.R
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/plotCorr.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/plotGenus.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/plotMRheatmap.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/man/plotOrd.Rd
Added  /trunk/madman/Rpacks/metagenomeSeq/man/returnAppropriateObj.Rd
Modified  /trunk/madman/Rpacks/metagenomeSeq/vignettes/metagenomeSeq.Rnw
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Commit information:

Commit id: bb56b8c79d287ca331714700f5249bb80965b9cb

    little cleanup of excess code

Committed by: nosson
Author Name: nosson
Commit date: 2015-01-27 23:11:35 -0500
Author date: 2015-01-27 23:11:35 -0500
Revision: 98789
Author: d.tenenbaum
Date: 2015-01-28T04:06:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/R/util.R
Commit made by the Bioconductor Git-SVN bridge.
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Commit information:

Commit id: 50b88ce1940e04dcadfa5cfc32246cc347d12eb4

    syntax fix....

Committed by: Dan Tenenbaum
Author Name: Dan Tenenbaum
Commit date: 2015-01-27 20:06:22 -0800
Author date: 2015-01-27 20:06:22 -0800
Revision: 98788
Author: d.tenenbaum
Date: 2015-01-28T04:03:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/R/util.R
Commit made by the Bioconductor Git-SVN bridge.
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Commit information:

Commit id: ff2ceed0ed1bf8bec1d98894f31f8b16ef98afe6

    syntax fix

Committed by: Dan Tenenbaum
Author Name: Dan Tenenbaum
Commit date: 2015-01-27 20:02:55 -0800
Author date: 2015-01-27 20:02:55 -0800
Revision: 98787
Author: g.yu
Date: 2015-01-28T03:59:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChIPseeker/NEWS
Modified  /trunk/madman/Rpacks/ChIPseeker/R/plotDistToTSS.R
Modified  /trunk/madman/Rpacks/ChIPseeker/man/plotDistToTSS-methods.Rd
Modified  /trunk/madman/Rpacks/ChIPseeker/vignettes/ChIPseeker.Rnw
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Commit information:

Commit id: ec78798fceb4b6555d9d133f9e8b5a5e8a67966e

    fixed in plotDistToTSS

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-28 11:59:08 +0800
Author date: 2015-01-28 11:59:08 +0800
Revision: 98786
Author: g.yu
Date: 2015-01-28T03:51:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOSemSim/NEWS
Modified  /trunk/madman/Rpacks/GOSemSim/inst/CITATION
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Commit information:

Commit id: 7d919ae65147f472ffc6c0398fba8594a6c94d0a

    doi in citation

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-28 11:51:03 +0800
Author date: 2015-01-28 11:51:03 +0800
Revision: 98785
Author: d.tenenbaum
Date: 2015-01-28T03:45:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/R/util.R
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Commit information:

Commit id: 73ff5a31d2dd42f196acb9214845e29ba787f833

    remove stray basename()

Committed by: Dan Tenenbaum
Author Name: Dan Tenenbaum
Commit date: 2015-01-27 19:45:25 -0800
Author date: 2015-01-27 19:45:25 -0800
Revision: 98784
Author: d.tenenbaum
Date: 2015-01-28T03:30:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/R/util.R
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Commit information:

Commit id: c24c10af59216fb0f8ffc3377999a4745077e400

    a possible fix

Committed by: Dan Tenenbaum
Author Name: Dan Tenenbaum
Commit date: 2015-01-27 19:30:41 -0800
Author date: 2015-01-27 19:30:41 -0800
Revision: 98783
Author: d.tenenbaum
Date: 2015-01-28T03:14:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/R/util.R
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Commit information:

Commit id: c9132be2e7fca3af8ea28dab1e98a92003037a62

    more diagnostics...

Committed by: Dan Tenenbaum
Author Name: Dan Tenenbaum
Commit date: 2015-01-27 19:14:17 -0800
Author date: 2015-01-27 19:14:17 -0800
Revision: 98782
Author: d.tenenbaum
Date: 2015-01-28T03:13:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/R/util.R
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Commit id: 2375bd8bb8a50d155284e2f87c3dce14ea22e7c3

    more diagnostics

Committed by: Dan Tenenbaum
Author Name: Dan Tenenbaum
Commit date: 2015-01-27 19:13:07 -0800
Author date: 2015-01-27 19:13:07 -0800
Revision: 98781
Author: d.tenenbaum
Date: 2015-01-28T02:59:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/R/util.R
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Commit information:

Commit id: bf0687e530b725291845836ad0c8f0535bde97b5

    diagnostics

Committed by: Dan Tenenbaum
Author Name: Dan Tenenbaum
Commit date: 2015-01-27 18:58:58 -0800
Author date: 2015-01-27 18:58:58 -0800
Revision: 98780
Author: m.jiang
Date: 2015-01-28T01:06:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/ncdfFlow/DESCRIPTION
Modified  /trunk/madman/Rpacks/ncdfFlow/R/ncdfIO.R
Modified  /trunk/madman/Rpacks/ncdfFlow/man/read.ncdfFlowSet.Rd
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Commit information:

Commit id: 0a211a8f4202c6affd28c1cc51124063a55cb8af

    Merge branch 'trunk'

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2015-01-27 17:05:14 -0800
Author date: 2015-01-27 17:05:14 -0800

Commit id: 770b231595d32fd2e826c1e05a615c92ec724874

    add mc.cores option to read.ncdfFlowSet for concurrent read FCS. #36

Committed by: mikejiang
Author Name: mikejiang
Commit date: 2015-01-27 17:04:08 -0800
Author date: 2015-01-27 16:39:56 -0800
Revision: 98779
Author: d.strbenac
Date: 2015-01-28T01:00:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/vignettes/ClassifyR.Rmd
Vignette contains comparison with other framework packages. A table of contents is also provided.
Revision: 98778
Author: m.lawrence
Date: 2015-01-28T01:00:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantTools/R/callVariants.R
revert to filtering by alt depth, instead of total depth (woops)
Revision: 98777
Author: m.carlson
Date: 2015-01-28T00:34:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocContributions/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocContributions/R/trackerCode.R
Breathes life into rebuildIssueTarball()
Revision: 98776
Author: d.tenenbaum
Date: 2015-01-28T00:10:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/NAMESPACE
Modified  /trunk/madman/Rpacks/AnnotationHub/R/hub.R
Support resources that live at FTP URLs.

Handle it if GET() returns an empty status code, which happens with FTP
URLs (see https://github.com/hadley/httr/issues/190).
Also handle it if the status code is 302, which just means there was a
redirect.

This still produces a lot of output from the FTP server.
Also if Rsamtools is not installed, downloading a dbSNP VCF resource
will cause an error, so some sort of dependency on Rsamtools needs to be declared.
Revision: 98775
Author: t.girke
Date: 2015-01-27T23:39:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/systemPipeR/DESCRIPTION
Modified  /trunk/madman/Rpacks/systemPipeR/R/utilities.R
Modified  /trunk/madman/Rpacks/systemPipeR/README
Modified  /trunk/madman/Rpacks/systemPipeR/vignettes/systemPipeR.Rnw
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Commit id: e29fd72c9ca15923e5b75ab68d3e8cbc673146ce

    vignette updates

Committed by: Thomas Girke
Author Name: Thomas Girke
Commit date: 2015-01-27 15:39:20 -0800
Author date: 2015-01-27 15:39:20 -0800
Revision: 98773
Author: m.carlson
Date: 2015-01-27T23:30:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocContributions/NAMESPACE
Added  /trunk/madman/Rpacks/BiocContributions/R/trackerCode.R
Adds some dabbling in some new functions for some utilities that should grow to become useful.
Revision: 98772
Author: s.arora
Date: 2015-01-27T22:53:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makedbSNPVCF.R
code update dbSNP vcf files

- change description map to accomodate "All.vcf.gz" file
- rdatapath should be same as sourceUrl, do not change to "rz"
Revision: 98769
Author: hpages
Date: 2015-01-27T20:50:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGRanges.R
Modified  /trunk/madman/Rpacks/GenomicFeatures/inst/unitTests/test_makeTxDbFromGRanges.R
more work on makeTxDbFromGRanges() (add support for exons and CDS with gene
parent)
Revision: 98768
Author: m.love
Date: 2015-01-27T20:35:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/R/AllClasses.R
adding an NA check to DESeqDataSet()
Revision: 98767
Author: m.carlson
Date: 2015-01-27T20:21:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/cleaver/DESCRIPTION
Modified  /trunk/madman/Rpacks/cleaver/vignettes/cleaver.Rnw
Calls the Uniprot.ws constructor
Revision: 98766
Author: l.pantano
Date: 2015-01-27T20:21:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGreport/.travis.yml
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Commit information:

Commit id: b97c67aff2180ce33df50ea402f065bba1cade37

    fix quote match

Committed by: Lorena
Author Name: Lorena
Commit date: 2015-01-27 15:21:49 -0500
Author date: 2015-01-27 15:21:49 -0500
Revision: 98765
Author: m.carlson
Date: 2015-01-27T20:21:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/UniProt.ws/DESCRIPTION
Modified  /trunk/madman/Rpacks/UniProt.ws/R/AllClasses.R
Adds default argument to constructor.
Revision: 98764
Author: l.pantano
Date: 2015-01-27T20:03:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGreport/.travis.yml
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Commit id: cf85a98cc8c683ca0a9fa87e5d7b621835760c04

    add installatino of dev branch

Committed by: Lorena
Author Name: Lorena
Commit date: 2015-01-27 15:03:46 -0500
Author date: 2015-01-27 15:03:46 -0500
Revision: 98763
Author: l.pantano
Date: 2015-01-27T19:51:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGreport/DESCRIPTION
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Commit information:

Commit id: 08b7200400458fe2a30e0d8f5236ea02b4d8b2d7

    up version

Committed by: Lorena
Author Name: Lorena
Commit date: 2015-01-27 14:50:44 -0500
Author date: 2015-01-27 14:50:44 -0500
Revision: 98762
Author: d.tenenbaum
Date: 2015-01-27T19:50:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/HTSeqGenie/DESCRIPTION
add RUnit to Suggests
Revision: 98761
Author: l.pantano
Date: 2015-01-27T19:49:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGreport/R/methods.R
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Commit information:

Commit id: e9d81bf24ef1f497cecae9db9d8143dd49d1f711

    fix mix string with variables

Committed by: Lorena
Author Name: Lorena
Commit date: 2015-01-27 14:49:11 -0500
Author date: 2015-01-27 14:49:11 -0500
Revision: 98760
Author: l.pantano
Date: 2015-01-27T19:47:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGreport/R/methods.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 4c857ea8e61cf581d7598b10b6a8ee109117c0f7

    fix type string

Committed by: Lorena
Author Name: Lorena
Commit date: 2015-01-27 14:47:11 -0500
Author date: 2015-01-27 14:47:11 -0500
Revision: 98759
Author: hpages
Date: 2015-01-27T19:32:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/inst/unitTests/test_makeTxDbFromGRanges.R
add more tests for makeTxDbFromGRanges()
Revision: 98758
Author: hpages
Date: 2015-01-27T19:12:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/inst/unitTests/test_makeTxDbFromGRanges.R
add unit tests for multiple-part transcript support in makeTxDbFromGRanges()
Revision: 98756
Author: d.rossell
Date: 2015-01-27T17:48:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/casper/DESCRIPTION
Fixed bug in modelPrior
Revision: 98754
Author: d.rossell
Date: 2015-01-27T17:48:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/casper/R/calcDenovo.R
Modified  /trunk/madman/Rpacks/casper/R/modelPrior.R
Modified  /trunk/madman/Rpacks/casper/data/hg19DB.RData
Modified  /trunk/madman/Rpacks/casper/src/seppel.cpp
Fixed bug in modelPrior
Revision: 98753
Author: r.castelo
Date: 2015-01-27T17:12:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantFiltering/R/AllClasses.R
Modified  /trunk/madman/Rpacks/VariantFiltering/R/annotationEngine.R
Modified  /trunk/madman/Rpacks/VariantFiltering/R/autosomalRecessiveHomozygous.R
Modified  /trunk/madman/Rpacks/VariantFiltering/R/methods-VariantFilteringParam.R
Modified  /trunk/madman/Rpacks/VariantFiltering/man/VariantFilteringParam-class.Rd
Refactored autosomalRecessiveHomozygous() to allow iterating through the VCF file in chunks using the TabixFile representation.
Revision: 98752
Author: r.stojnic
Date: 2015-01-27T17:09:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/ddgraph/DESCRIPTION
Modified  /trunk/madman/Rpacks/ddgraph/R/citest.R
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/meso_0.05.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/meso_0.1.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/meso_0.2.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/meso_sm_0.05.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/meso_sm_0.1.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/meso_sm_0.2.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/sm_0.05.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/sm_0.1.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/sm_0.2.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-meso_0.05.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-meso_0.1.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-meso_0.2.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-meso_sm_0.05.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-meso_sm_0.1.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-meso_sm_0.2.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-sm_0.05.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-sm_0.1.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-sm_0.2.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-vm_0.05.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-vm_0.1.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-vm_0.2.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-vm_sm_0.05.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-vm_sm_0.1.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/star-vm_sm_0.2.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/vm_0.05.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/vm_0.1.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/vm_0.2.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/vm_sm_0.05.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/vm_sm_0.1.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/gold_standard/vm_sm_0.2.txt
Modified  /trunk/madman/Rpacks/ddgraph/inst/tests/test_FurlongDataSet.R
Solve some interface breakages with bnlearn and switch to using mi-sh as the main testing parameter
Revision: 98750
Author: b.friedman
Date: 2015-01-27T15:01:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnalysisPageServer/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnalysisPageServer/R/test.R
Modified  /trunk/madman/Rpacks/AnalysisPageServer/inst/unitTests/test.memory.R
test.package accepts package name; test.check.memory correctly handles slight increase in memory usage during test
Revision: 98749
Author: g.yu
Date: 2015-01-27T13:27:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/ReactomePA/DESCRIPTION
Modified  /trunk/madman/Rpacks/ReactomePA/vignettes/ReactomePA.Rnw
Deleted  /trunk/madman/Rpacks/ReactomePA/vignettes/ReactomePA.pdf
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 0b78c22592c4d570e4fec220095b796412cb25d1

    update vignette

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-27 21:27:26 +0800
Author date: 2015-01-27 21:27:26 +0800
Revision: 98748
Author: g.yu
Date: 2015-01-27T13:22:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOSE/R/enrichMap.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: f65485f4a9bd10053a5463ce76b48a55af1d28c5

    fixed enrichMap

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-27 21:21:46 +0800
Author date: 2015-01-27 21:21:46 +0800
Revision: 98747
Author: g.yu
Date: 2015-01-27T12:43:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/clusterProfiler/README.md
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: c0b00b1fc4e0e2f0b1db2e58b4dc13b8a26a2b46

    update readme

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-27 20:43:19 +0800
Author date: 2015-01-27 20:43:19 +0800
Revision: 98746
Author: g.yu
Date: 2015-01-27T12:39:23+00:00
Paths:
Added  /trunk/madman/Rpacks/clusterProfiler/.gitignore
Modified  /trunk/madman/Rpacks/clusterProfiler/DESCRIPTION
Modified  /trunk/madman/Rpacks/clusterProfiler/NAMESPACE
Modified  /trunk/madman/Rpacks/clusterProfiler/NEWS
Modified  /trunk/madman/Rpacks/clusterProfiler/R/enrichGO.R
Modified  /trunk/madman/Rpacks/clusterProfiler/R/enrichKEGG.R
Modified  /trunk/madman/Rpacks/clusterProfiler/R/gseAnalyzer.R
Modified  /trunk/madman/Rpacks/clusterProfiler/R/utilities.R
Modified  /trunk/madman/Rpacks/clusterProfiler/man/DataSet.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/Gff2GeneTable.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/buildGOmap.Rd
Added  /trunk/madman/Rpacks/clusterProfiler/man/buildKEGGmap.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/clusterProfiler-package.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/cnetplot.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/compareCluster.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/compareClusterResult-class.Rd
Added  /trunk/madman/Rpacks/clusterProfiler/man/download.KEGG.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/enrichGO.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/enrichKEGG.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/enrichMap.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/getGOLevel.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/getGeneSet.BP.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/getGeneSet.CC.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/getGeneSet.GO.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/getGeneSet.KEGG.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/getGeneSet.MF.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/groupGO.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/groupGOResult-class.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/gseGO.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/gseKEGG.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/gseaplot.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/plot-methods.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/plotting.clusterProfile.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/man/viewKEGG.Rd
Modified  /trunk/madman/Rpacks/clusterProfiler/vignettes/clusterProfiler.Rnw
Deleted  /trunk/madman/Rpacks/clusterProfiler/vignettes/clusterProfiler.pdf
Added  /trunk/madman/Rpacks/clusterProfiler/vignettes/figures
Added  /trunk/madman/Rpacks/clusterProfiler/vignettes/figures/hsa04110_pathview.png
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: e9b4dd97a79e20d42a97a030997ab9d2f7ad33e0

    use.KEGG.db parameter in enrichKEGG

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-27 20:38:54 +0800
Author date: 2015-01-27 20:38:54 +0800

Commit id: 8c464da52b5838400d048054210a21c5540647b6

    update vignette

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-27 17:55:21 +0800
Author date: 2015-01-27 17:55:21 +0800
Revision: 98745
Author: g.yu
Date: 2015-01-27T12:36:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOSE/DESCRIPTION
Modified  /trunk/madman/Rpacks/DOSE/NEWS
Modified  /trunk/madman/Rpacks/DOSE/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/DOSE/R/enrich.internal.R
Modified  /trunk/madman/Rpacks/DOSE/R/enrichMap.R
Modified  /trunk/madman/Rpacks/DOSE/man/ALLEXTID.DO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/ALLEXTID.DOLite.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/ALLEXTID.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/EXTID2TERMID.DO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/EXTID2TERMID.DOLite.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/EXTID2TERMID.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERM2NAME.DO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERM2NAME.DOLite.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERM2NAME.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERMID2EXTID.DO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERMID2EXTID.DOLite.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERMID2EXTID.Rd
Modified  /trunk/madman/Rpacks/DOSE/vignettes/DOSE.Rnw
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: b34e111d3e6e954ffa56bca62dc9db04968892bb

    use.KEGG.db

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-27 20:36:11 +0800
Author date: 2015-01-27 20:36:11 +0800
Revision: 98744
Author: g.yu
Date: 2015-01-27T11:44:28+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: 0e35f16cce5cbc6638fe2158578ef83e93298785

    update README.md

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-27 19:44:08 +0800
Author date: 2015-01-27 19:44:08 +0800
Revision: 98743
Author: g.klambauer
Date: 2015-01-27T10:47:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/dexus/DESCRIPTION
forgot to update description file
Revision: 98742
Author: g.klambauer
Date: 2015-01-27T10:46:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/dexus/R/dexus.R
Solved problem for single gene supervised mode
Revision: 98740
Author: g.yu
Date: 2015-01-27T08:44:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOSE/DESCRIPTION
Modified  /trunk/madman/Rpacks/DOSE/NEWS
Modified  /trunk/madman/Rpacks/DOSE/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/DOSE/R/enrich.internal.R
Modified  /trunk/madman/Rpacks/DOSE/man/ALLEXTID.DO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/ALLEXTID.DOLite.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/ALLEXTID.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/EXTID2TERMID.DO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/EXTID2TERMID.DOLite.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/EXTID2TERMID.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERM2NAME.DO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERM2NAME.DOLite.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERM2NAME.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERMID2EXTID.DO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERMID2EXTID.DOLite.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERMID2EXTID.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/enrich.internal.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 2ef43b5d78223f72c5c80a7aa6c63cb100a004b7

    add ... parameter in enrich.internal

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-27 16:43:48 +0800
Author date: 2015-01-27 16:43:48 +0800
Revision: 98739
Author: hpages
Date: 2015-01-27T08:11:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGRanges.R
more work on makeTxDbFromGRanges() (add support for multiple-part transcripts)
Revision: 98738
Author: f.comoglio
Date: 2015-01-27T07:58:07+00:00
Paths:
Added  /trunk/madman/Rpacks/wavClusteR/.Rapp.history
Modified  /trunk/madman/Rpacks/wavClusteR/R/FDRbyRSF.R
Modified  /trunk/madman/Rpacks/wavClusteR/R/annotateClusters.R
Modified  /trunk/madman/Rpacks/wavClusteR/R/export.R
Modified  /trunk/madman/Rpacks/wavClusteR/R/filterClusters.R
Modified  /trunk/madman/Rpacks/wavClusteR/R/fitMixtureModel.R
Modified  /trunk/madman/Rpacks/wavClusteR/R/getAllSub.R
Modified  /trunk/madman/Rpacks/wavClusteR/R/getClusters.R
Modified  /trunk/madman/Rpacks/wavClusteR/R/getExpInterval.R
Modified  /trunk/madman/Rpacks/wavClusteR/R/getHighConfSub.R
Modified  /trunk/madman/Rpacks/wavClusteR/R/getMeta.R
Modified  /trunk/madman/Rpacks/wavClusteR/man/filterClusters.Rd
Modified  /trunk/madman/Rpacks/wavClusteR/man/wavClusteR-package.Rd
Modified  /trunk/madman/Rpacks/wavClusteR/vignettes/Rplots.pdf
Modified  /trunk/madman/Rpacks/wavClusteR/vignettes/wavCluster_vignette.pdf
Added  /trunk/madman/Rpacks/wavClusteR/vignettes/wavCluster_vignette.tex
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 5fc9bacc69a0828d6d1c686d0c5381aae315d110

    Moved to Roxygen2 documentation

Committed by: FC
Author Name: FC
Commit date: 2015-01-27 08:57:52 +0100
Author date: 2015-01-27 08:57:52 +0100
Revision: 98737
Author: g.yu
Date: 2015-01-27T07:49:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOSE/DESCRIPTION
Modified  /trunk/madman/Rpacks/DOSE/NAMESPACE
Modified  /trunk/madman/Rpacks/DOSE/NEWS
Modified  /trunk/madman/Rpacks/DOSE/R/DOSE-package.R
Modified  /trunk/madman/Rpacks/DOSE/R/enrich.internal.R
Modified  /trunk/madman/Rpacks/DOSE/R/enrichDO.R
Modified  /trunk/madman/Rpacks/DOSE/R/enrichMap.R
Modified  /trunk/madman/Rpacks/DOSE/man/ALLEXTID.DO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/ALLEXTID.DOLite.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/ALLEXTID.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/DOSE-package.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/DataSet.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/EXTID2NAME.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/EXTID2TERMID.DO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/EXTID2TERMID.DOLite.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/EXTID2TERMID.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERM2NAME.DO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERM2NAME.DOLite.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERM2NAME.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERMID2EXTID.DO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERMID2EXTID.DOLite.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/TERMID2EXTID.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/barplot.enrichResult.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/cnetplot-methods.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/cnetplot.internal.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/computeIC.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/doSim.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/enrich.internal.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/enrichDO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/enrichMap.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/enrichResult-class.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/fortify.enrichResult.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/fortify.gseaResult.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/gene2DO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/geneSim.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/getALLEG.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/getGeneSet.DO.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/getGeneSet.DOLite.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/getGeneSet.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/gseAnalyzer.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/gsea.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/gseaResult-class.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/gseaplot.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/list2graph.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/netplot.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/plot-methods.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/rebuildAnnoData.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/scaleNodeColor.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/setReadable.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/setting.graph.attributes.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/show-methods.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/simplot.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/summary-methods.Rd
Modified  /trunk/madman/Rpacks/DOSE/man/theme_dose.Rd
Modified  /trunk/madman/Rpacks/DOSE/vignettes/DOSE.Rnw
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: ae20f476388d5e9db723d13b7ac79a407a448ecb

    test

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-27 15:48:52 +0800
Author date: 2015-01-27 15:48:52 +0800

Commit id: e77c8e3edaf6a6182ce7190c73a23dcbe9d285ac

    update vignette

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-27 15:33:07 +0800
Author date: 2015-01-27 15:33:07 +0800
Revision: 98736
Author: a.lun
Date: 2015-01-27T07:44:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/csaw/DESCRIPTION
Modified  /trunk/madman/Rpacks/csaw/R/basefun.R
Modified  /trunk/madman/Rpacks/csaw/R/combineTests.R
Modified  /trunk/madman/Rpacks/csaw/R/getBestTest.R
Modified  /trunk/madman/Rpacks/csaw/R/profileSites.R
Modified  /trunk/madman/Rpacks/csaw/R/regionCounts.R
Modified  /trunk/madman/Rpacks/csaw/R/scaledAverage.R
Modified  /trunk/madman/Rpacks/csaw/R/windowCounts.R
Modified  /trunk/madman/Rpacks/csaw/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/csaw/inst/doc/csawUserGuide.pdf
Modified  /trunk/madman/Rpacks/csaw/inst/tests/test-best.R
Modified  /trunk/madman/Rpacks/csaw/inst/tests/test-best.Rout.save
Modified  /trunk/madman/Rpacks/csaw/inst/tests/test-chip.R
Modified  /trunk/madman/Rpacks/csaw/inst/tests/test-chip.Rout.save
Modified  /trunk/madman/Rpacks/csaw/man/combineTests.Rd
Modified  /trunk/madman/Rpacks/csaw/man/getBestTest.Rd
Modified  /trunk/madman/Rpacks/csaw/man/getWidths.Rd
Modified  /trunk/madman/Rpacks/csaw/man/mergeWindows.Rd
Modified  /trunk/madman/Rpacks/csaw/man/profileSites.Rd
Modified  /trunk/madman/Rpacks/csaw/man/regionCounts.Rd
Modified  /trunk/madman/Rpacks/csaw/man/windowCounts.Rd
Modified  /trunk/madman/Rpacks/csaw/src/csaw.h
Modified  /trunk/madman/Rpacks/csaw/src/get_cluster_stats.cpp
Modified  /trunk/madman/Rpacks/csaw/src/init.cpp
Modified  /trunk/madman/Rpacks/csaw/tests/test-basic.R
Modified  /trunk/madman/Rpacks/csaw/tests/test-basic.Rout.save
Modified variable ext interface, cleaned up getBestTest and combineTest code. Updated UG.
Revision: 98735
Author: g.yu
Date: 2015-01-27T07:43:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/GOSemSim/DESCRIPTION
Modified  /trunk/madman/Rpacks/GOSemSim/NAMESPACE
Modified  /trunk/madman/Rpacks/GOSemSim/inst/CITATION
Modified  /trunk/madman/Rpacks/GOSemSim/man/GOSemSim-package.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/IC.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/clusterSim.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/combineScores.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/geneSim.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/getDb.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/getSupported_Org.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/goSim.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/infoContentMethod.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/loadGOMap.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/loadICdata.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/mclusterSim.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/mgeneSim.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/mgoSim.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/termSim.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/man/wangMethod.Rd
Modified  /trunk/madman/Rpacks/GOSemSim/vignettes/GOSemSim.Rnw
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 0afec5a414bf5973c392cf2a58fc9f849073066b

    update man

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-27 15:43:18 +0800
Author date: 2015-01-27 15:43:18 +0800
Revision: 98734
Author: d.strbenac
Date: 2015-01-27T07:00:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/R/ROCplot.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/utilities.R
Modified  /trunk/madman/Rpacks/ClassifyR/vignettes/ClassifyR.Rmd
binValues returns final version of return variable and ROCplot's old code for cut function result removed.
Revision: 98733
Author: hpages
Date: 2015-01-27T06:13:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/NAMESPACE
Modified  /trunk/madman/Rpacks/IRanges/R/AtomicList-impl.R
Modified  /trunk/madman/Rpacks/IRanges/man/AtomicList-class.Rd
300x speedup or more when doing unique() on a CompressedRleList object
Revision: 98731
Author: j.fortin
Date: 2015-01-27T02:02:29+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: 6ef541959e63516891dc73015304c9be182be5b3

    Update README.md

Committed by: Jean-Philippe Fortin
Author Name: Jean-Philippe Fortin
Commit date: 2015-01-26 21:02:24 -0500
Author date: 2015-01-26 21:02:24 -0500
Revision: 98730
Author: j.fortin
Date: 2015-01-27T02:01:39+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: e4b320d9027604813041cfe7b86b674e1e8e4201

    Updated citation

Committed by: Jean-Philippe Fortin
Author Name: Jean-Philippe Fortin
Commit date: 2015-01-26 21:01:33 -0500
Author date: 2015-01-26 21:01:33 -0500
Revision: 98729
Author: s.arora
Date: 2015-01-27T01:33:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHubResource-class.R
code update

add client code for dbSNp VCF files
Revision: 98727
Author: m.carlson
Date: 2015-01-27T00:15:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/unitTests/test_AnnotationHubMetadata.R
Adds back some more core unit tests.
Revision: 98726
Author: m.carlson
Date: 2015-01-27T00:04:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/unitTests/test_AnnotationHubMetadata.R
Repairs some of the more core unit tests.
Revision: 98724
Author: d.tenenbaum
Date: 2015-01-26T23:31:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/HilbertVisGUI/DESCRIPTION
Modified  /trunk/madman/Rpacks/HilbertVisGUI/R/loadLib.R
make error handling code aware of mac.binary.mavericks package type
Revision: 98722
Author: d.tenenbaum
Date: 2015-01-26T23:12:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOQTL/DESCRIPTION
Modified  /trunk/madman/Rpacks/DOQTL/NAMESPACE
Import S4Vectors so that metadata<- function is found.
Revision: 98720
Author: s.arora
Date: 2015-01-26T22:31:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makedbSNPVCF.R
dbSNP VCF code update

- make recipe compatible for ".tbi" files
- add description for "All_papu" files 
Revision: 98719
Author: s.neumann
Date: 2015-01-26T22:22:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/xcms/DESCRIPTION
Modified  /trunk/madman/Rpacks/xcms/NAMESPACE
Added  /trunk/madman/Rpacks/xcms/R/plotQC.R
Modified  /trunk/madman/Rpacks/xcms/inst/NEWS
Added  /trunk/madman/Rpacks/xcms/man/plotQC.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 27fd70787ea8d174f7de8daeffb43472e03580e9

    introduced plotQC

Committed by: Steffen Neumann
Author Name: Steffen Neumann
Commit date: 2015-01-26 21:35:03 +0100
Author date: 2015-01-26 21:35:03 +0100
Revision: 98718
Author: d.tenenbaum
Date: 2015-01-26T21:39:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocCheck/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocCheck/R/util.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 1048339d389c8457309ac73ad4a17e3c5de2b3e9

    Use purl only where appropriate

Committed by: Dan Tenenbaum
Author Name: Dan Tenenbaum
Commit date: 2015-01-26 13:39:06 -0800
Author date: 2015-01-26 13:39:06 -0800
Revision: 98717
Author: v.obenchain
Date: 2015-01-26T21:22:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/man/bpiterate.Rd
add exception to bpiterate man page
Revision: 98715
Author: j.fortin
Date: 2015-01-26T20:59:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/shinyMethyl/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 571612d889438ac95357cea04899a3bb7a0e03ac

    Update CITATION

Committed by: Jean-Philippe Fortin
Author Name: Jean-Philippe Fortin
Commit date: 2015-01-26 15:59:10 -0500
Author date: 2015-01-26 15:59:10 -0500
Revision: 98714
Author: j.fortin
Date: 2015-01-26T20:58:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/shinyMethyl/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: bc24b00a5de3969cb87522d3778c56c97084f6ec

    Updated citation

Committed by: Jean-Philippe Fortin
Author Name: Jean-Philippe Fortin
Commit date: 2015-01-26 15:58:52 -0500
Author date: 2015-01-26 15:58:52 -0500
Revision: 98713
Author: p.shannon
Date: 2015-01-26T20:54:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/PSICQUIC/DESCRIPTION
Modified  /trunk/madman/Rpacks/PSICQUIC/inst/unitTests/test_PSICQUIC.R
on dan's advice, explicity library statements now in test_PSICQUIC.R
Revision: 98712
Author: k.horan
Date: 2015-01-26T20:41:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChemmineR/R/draw_sdf.r
Added  /trunk/madman/Rpacks/ChemmineR/man/draw_sdf.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 8 commits.

Commit information:

Commit id: 89c0f28689ab26fb67138c63ff3c6b7cd9d893f1

    Merge pull request #27 from johnasharifi/master

    added draw_sdf help file
Committed by: kevin
Author Name: kevin
Commit date: 2015-01-26 12:40:51 -0800
Author date: 2015-01-26 12:40:51 -0800

Commit id: acc701ba13cc9bebe8dade16dd4b3b6f7dfeb95b

    Update draw_sdf.Rd

Committed by: johnasharifi
Author Name: johnasharifi
Commit date: 2015-01-18 21:43:27 -0800
Author date: 2015-01-18 21:43:27 -0800

Commit id: a4cad615b3fd54ac4440c105f91b2c6e4d34e567

    Update draw_sdf.Rd

    Corrected R coding standard violations.
Committed by: johnasharifi
Author Name: johnasharifi
Commit date: 2015-01-18 21:42:40 -0800
Author date: 2015-01-18 21:42:40 -0800

Commit id: 2584c62cb44cd54cb3c1cc9aaf074433a97f505a

    Update draw_sdf.r

    Incorporated changes from github to local file, uploading local file
Committed by: johnasharifi
Author Name: johnasharifi
Commit date: 2015-01-18 21:32:47 -0800
Author date: 2015-01-18 21:32:47 -0800

Commit id: a161aea0ddd0ae351c8f1d5d5e2870951af15a26

    Update draw_sdf.r

    Added option to draw background whitespace, addressed issue with multiple plots being printed rather than returned, removed reference to local folder './.html/'
Committed by: johnasharifi
Author Name: johnasharifi
Commit date: 2015-01-18 21:28:07 -0800
Author date: 2015-01-18 21:28:07 -0800

Commit id: 80e217d301397a6031021fb26faa800cf842d204

    Create draw_sdf.Rd

    Added help file for draw_sdf.r
Committed by: johnasharifi
Author Name: johnasharifi
Commit date: 2014-12-21 22:30:35 -0800
Author date: 2014-12-21 22:30:35 -0800

Commit id: 184ddd780bc6a1828a7d92dd0ea35edd1e384e6e

    Update draw_sdf.r

    Delegated requires to subfunction which requires them
Committed by: johnasharifi
Author Name: johnasharifi
Commit date: 2014-12-21 21:51:55 -0800
Author date: 2014-12-21 21:51:55 -0800

Commit id: cc66ea9c46de61c0992f728c94dce3c3adcb8642

    Update draw_sdf.r

    Removed references to ./.html/test.jpg, filepath probably not present on non-dev machines. Also standardized library import styles.
Committed by: johnasharifi
Author Name: johnasharifi
Commit date: 2014-12-21 21:32:45 -0800
Author date: 2014-12-21 21:32:45 -0800
Revision: 98710
Author: j.fortin
Date: 2015-01-26T20:36:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/shinyMethyl/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 7c5b89c6d97b3ecfb4bf9a1322c3440913968491

    Fixed typo

Committed by: jfortin
Author Name: jfortin
Commit date: 2015-01-26 15:36:06 -0500
Author date: 2015-01-26 15:36:06 -0500
Revision: 98707
Author: raffaele.calogero
Date: 2015-01-26T19:39:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/chimera/DESCRIPTION
Modified  /trunk/madman/Rpacks/chimera/src/StarParser.cpp
Fixing a bug in STAR data import

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