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Revision: 98840
Author: hpages
Date: 2015-01-29T07:56:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGRanges.R
more work on makeTxDbFromGRanges()
Revision: 98839
Author: t.pedersen
Date: 2015-01-29T07:40:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/mzID/DESCRIPTION
Modified  /trunk/madman/Rpacks/mzID/NAMESPACE
Modified  /trunk/madman/Rpacks/mzID/R/mzID.R
Modified  /trunk/madman/Rpacks/mzID/R/mzIDCollection.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: f8b15163c410ce08c6ca211a2684cc2888e64c7e

    Merge pull request #28 from sgibb/master

    export S4 classes mzID and mzIDCollection; closes #26
Committed by: Thomas Lin Pedersen
Author Name: Thomas Lin Pedersen
Commit date: 2015-01-29 08:40:12 +0100
Author date: 2015-01-29 08:40:12 +0100

Commit id: 891958928d822c2a8ad878daaf671b36696ea5be

    export S4 classes mzID and mzIDCollection; closes #26

Committed by: Sebastian Gibb
Author Name: Sebastian Gibb
Commit date: 2015-01-27 20:23:08 +0100
Author date: 2015-01-27 20:21:05 +0100
Revision: 98838
Author: hpages
Date: 2015-01-29T05:51:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGRanges.R
more work on makeTxDbFromGRanges()
Revision: 98836
Author: v.obenchain
Date: 2015-01-29T03:08:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/coordinate-mapping-methods.R
bug fixes in mapToTranscripts()
- shifting ranges on neg strand
- confirm all elements of GRangesList same strand
Revision: 98835
Author: x.zheng
Date: 2015-01-29T01:47:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/gdsfmt/DESCRIPTION
Modified  /trunk/madman/Rpacks/gdsfmt/NEWS
Modified  /trunk/madman/Rpacks/gdsfmt/R/gdsfmt-main.r
Modified  /trunk/madman/Rpacks/gdsfmt/README.md
Modified  /trunk/madman/Rpacks/gdsfmt/inst/include/CoreDEF.h
Modified  /trunk/madman/Rpacks/gdsfmt/inst/include/R_GDS.h
Modified  /trunk/madman/Rpacks/gdsfmt/src/CoreArray/dBase.cpp
Modified  /trunk/madman/Rpacks/gdsfmt/src/CoreArray/dBase.h
Modified  /trunk/madman/Rpacks/gdsfmt/src/CoreArray/dFile.cpp
Modified  /trunk/madman/Rpacks/gdsfmt/src/CoreArray/dFile.h
Modified  /trunk/madman/Rpacks/gdsfmt/src/CoreArray/dStream.cpp
Modified  /trunk/madman/Rpacks/gdsfmt/src/CoreArray/dStream.h
Modified  /trunk/madman/Rpacks/gdsfmt/src/R_CoreArray.cpp
Modified  /trunk/madman/Rpacks/gdsfmt/src/gdsfmt.cpp
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 22d649dcf277c11bce42c4256307f52edb354bf0

    v1.3.4: fixes the issue #6

    * fixes https://github.com/zhengxwen/gdsfmt/issues/6

Committed by: Xiuwen Zheng
Author Name: Xiuwen Zheng
Commit date: 2015-01-28 17:46:01 -0800
Author date: 2015-01-28 17:46:01 -0800
Revision: 98834
Author: g.yu
Date: 2015-01-29T01:43:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/R/tree.R
Modified  /trunk/madman/Rpacks/ggtree/R/treeIO.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 478d0ac7fd08f1b7b0ed3f1e55a48e4f2f14a67a

    remove scaling cladogram branch

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-01-29 09:42:53 +0800
Author date: 2015-01-29 09:42:53 +0800
Revision: 98833
Author: hpages
Date: 2015-01-29T01:33:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicFeatures/R/makeTxDbFromGRanges.R
more work on makeTxDbFromGRanges()
Revision: 98832
Author: m.carlson
Date: 2015-01-29T01:24:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/R/trackerCode.R
Checks in comments that show how to solve the harder part of what I am doing.
Revision: 98831
Author: d.strbenac
Date: 2015-01-29T01:00:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/vignettes/ClassifyR.Rmd
Changed vignette engine to a newer engine.
Revision: 98830
Author: m.jiang
Date: 2015-01-29T01:00:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowClust/R/flowClust.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 2db2c3baa052ab12360ca92cf0dbb490bab927c4

    Fix logic in test of randomStart for warning.

    Bug in test of randomStart to warn about use of prior with non-zero randomStart
Committed by: Greg Finak
Author Name: Greg Finak
Commit date: 2015-01-28 16:59:59 -0800
Author date: 2015-01-28 16:59:59 -0800
Revision: 98829
Author: m.carlson
Date: 2015-01-29T00:36:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocContributions/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocContributions/R/trackerCode.R
More changes to make filterIssues more useful and meaningful
Revision: 98828
Author: k.horan
Date: 2015-01-29T00:13:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/eiR/R/core.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 8a73b3ad9b242c991140b0ccb65b592358e8adc4

    disable debug

Committed by: khoran
Author Name: khoran
Commit date: 2015-01-28 16:13:07 -0800
Author date: 2015-01-28 16:13:07 -0800
Revision: 98827
Author: k.horan
Date: 2015-01-29T00:12:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChemmineR/R/compound_db.R
Modified  /trunk/madman/Rpacks/ChemmineR/inst/schema/compounds.RPostgreSQL
Modified  /trunk/madman/Rpacks/ChemmineR/man/setPriorities.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 0609ae350c00d7786cb1295a64da06632006b38b

    Merge remote branch 'origin/master'

Committed by: khoran
Author Name: khoran
Commit date: 2015-01-28 16:11:08 -0800
Author date: 2015-01-28 16:11:08 -0800

Commit id: 661e87d7de72b0116d0b71b0d013a8144e730321

    make setPrioroties use a cluster if passed

Committed by: khoran
Author Name: khoran
Commit date: 2015-01-28 16:10:14 -0800
Author date: 2015-01-28 16:10:14 -0800
Revision: 98826
Author: k.horan
Date: 2015-01-29T00:09:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/eiR/R/core.R
Modified  /trunk/madman/Rpacks/eiR/R/db.R
Modified  /trunk/madman/Rpacks/eiR/inst/schema/data.RPostgreSQL
Modified  /trunk/madman/Rpacks/eiR/inst/unitTests/test_main.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 11 commits.

Commit information:

Commit id: 77b8e83c26d9f2989d82ff52b6117bd78fff840b

    performance improvements

Committed by: khoran
Author Name: khoran
Commit date: 2015-01-28 16:07:43 -0800
Author date: 2015-01-28 16:07:43 -0800

Commit id: fcf1712bc71e3e64958a04773a7bbcd4b63a1d62

    Merge branch 'desc_query_improv'

Committed by: khoran
Author Name: khoran
Commit date: 2014-12-15 09:09:07 -0800
Author date: 2014-12-15 09:09:07 -0800

Commit id: 9ceda7b7504ba6df765784b1e1053887148cc17e

    Merge remote branch 'origin/master'

Committed by: khoran
Author Name: khoran
Commit date: 2014-12-15 09:08:33 -0800
Author date: 2014-12-15 09:08:33 -0800

Commit id: a724aee14158c9bc55ec19268a0e3c0e1880cf45

    bug fix, added embedding check function

Committed by: khoran
Author Name: khoran
Commit date: 2014-12-15 09:07:33 -0800
Author date: 2014-12-15 09:07:33 -0800

Commit id: 878cb3aec1016fc62e97a1a1c484e214cd1206bf

    Merge remote branch 'origin/master'

Committed by: khoran
Author Name: khoran
Commit date: 2014-10-06 09:58:29 -0700
Author date: 2014-10-06 09:58:29 -0700

Commit id: 2bd77bde0b33ec1c8474de6d64417f00c79839c3

    improve the descriptor query and make the cache system actually work

Committed by: khoran
Author Name: khoran
Commit date: 2014-10-06 09:56:29 -0700
Author date: 2014-10-06 09:56:29 -0700

Commit id: 7e212ec3b2e6a47a7e9688fbd68b68173678f05e

    Merge remote branch 'origin/master'

Committed by: khoran
Author Name: khoran
Commit date: 2014-08-27 09:19:37 -0700
Author date: 2014-08-27 09:19:37 -0700

Commit id: 2c429d9ccebf1aab59a6f2c9e1391b00af27df46

    some improvements made for updating database

Committed by: khoran
Author Name: khoran
Commit date: 2014-08-27 09:07:29 -0700
Author date: 2014-08-27 09:07:29 -0700

Commit id: bb132d8f2fc223208cbdc27a021bb0971c1275ee

    change writeMatrix to refresh its db connection on each query

Committed by: khoran
Author Name: khoran
Commit date: 2014-05-12 10:41:07 -0700
Author date: 2014-05-12 10:41:07 -0700

Commit id: 48ed83b06df0247fbb15dd63f9bec7b2067427d1

    change how writeMatrix grabs data

Committed by: khoran
Author Name: khoran
Commit date: 2014-05-07 10:22:54 -0700
Author date: 2014-05-07 10:22:54 -0700

Commit id: 3b3d4120ad7dfaf2eef94b43a4ff3fa396692534

    fix for finding un-embedded descriptor quickly

Committed by: khoran
Author Name: khoran
Commit date: 2014-05-06 09:52:17 -0700
Author date: 2014-05-06 09:52:17 -0700
Revision: 98823
Author: s.arora
Date: 2015-01-28T23:36:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEncodeDCC.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makedbSNPVCF.R
Enocde recipe update

- chnage RdatacLass to GRangesResource
- add code to remove warnings that user sees in the vcf code.
Revision: 98822
Author: s.arora
Date: 2015-01-28T22:52:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/NAMESPACE
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeEncodeDCC.R
Encode DCC recipe update

- remove leftover browser() calls
- remove leftover namespace export - EncodeImportPreparer
- Change RDataClass to "EncodeDCC"
- add function for recipe to return GRanges
Revision: 98821
Author: m.carlson
Date: 2015-01-28T22:34:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocContributions/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocContributions/R/trackerCode.R
More safety and utility for getFilteredIDsAndFileNames
Revision: 98820
Author: a.frazee
Date: 2015-01-28T22:24:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/polyester/README.md
Modified  /trunk/madman/Rpacks/polyester/vignettes/polyester.Rmd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: dd485af4cd75b7c8a3ca96aa8d9e1ad5f4206cfa

    add read ID info to readme/vignette

Committed by: Alyssa Frazee
Author Name: Alyssa Frazee
Commit date: 2015-01-28 17:24:05 -0500
Author date: 2015-01-28 17:24:05 -0500
Revision: 98819
Author: m.carlson
Date: 2015-01-28T22:14:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/R/trackerCode.R
change year argument to 'date' for getFilteredIDsAndFileNames
Revision: 98818
Author: m.carlson
Date: 2015-01-28T22:12:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocContributions/R/trackerCode.R
Enhancements and rename for MySQL accessor
Revision: 98817
Author: a.frazee
Date: 2015-01-28T22:10:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/polyester/R/generate_fragments.R
Modified  /trunk/madman/Rpacks/polyester/R/get_reads.R
Modified  /trunk/madman/Rpacks/polyester/R/sgseq.R
Modified  /trunk/madman/Rpacks/polyester/man/generate_fragments.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 1c30e8b6a0e7f0b51422b6f2c0d0b9b21f93d33c

    clarify get_reads w/ comments

Committed by: Alyssa Frazee
Author Name: Alyssa Frazee
Commit date: 2015-01-28 17:10:00 -0500
Author date: 2015-01-28 17:10:00 -0500

Commit id: e2f1bb97a20485fe7d834e0933230e5bea98f360

    update read position annotation

Committed by: Alyssa Frazee
Author Name: Alyssa Frazee
Commit date: 2015-01-28 17:09:34 -0500
Author date: 2015-01-28 17:09:34 -0500
Revision: 98816
Author: m.carlson
Date: 2015-01-28T21:35:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocContributions/R/trackerCode.R
Changes the argument name for rebuildIssueTarball so that it's less confusing.
Revision: 98815
Author: m.carlson
Date: 2015-01-28T21:16:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocContributions/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocContributions/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocContributions/R/trackerCode.R
Adds function to allow you to remove unwanted tracker issues.
Revision: 98814
Author: s.arora
Date: 2015-01-28T21:03:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/NAMESPACE
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/EncodeImportPreparer-class.R
Added  /trunk/madman/Rpacks/AnnotationHubData/R/makeEncodeDCC.R
Deleted  /trunk/madman/Rpacks/AnnotationHubData/man/EncodeBaseURL.Rd
Encode DCC recipe update

- add new file which contains R code for new recipe
- comment out all code from Paul (will be deleted later)
- modify NAMESPACE and DESCRIPTION files accordingl
- delete man page for url link
Revision: 98811
Author: a.frazee
Date: 2015-01-28T20:15:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/polyester/R/generate_fragments.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 8b3a6cce6e2482b1a0f31360ddbf8b39f00423b1

    add fragment start pos to fragment labels

Committed by: Alyssa Frazee
Author Name: Alyssa Frazee
Commit date: 2015-01-28 15:14:49 -0500
Author date: 2015-01-28 15:14:49 -0500
Revision: 98810
Author: d.tenenbaum
Date: 2015-01-28T20:14:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/inSilicoDb/DESCRIPTION
add missing comma in Authors@R
Revision: 98809
Author: m.carlson
Date: 2015-01-28T19:36:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/updateResources.R
Adds some checks to the function
Revision: 98808
Author: m.carlson
Date: 2015-01-28T19:35:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/updateResources.R
Adds helper function that removes a record from the database.

This is not exported and it's potentially dangerous.  We should be careful with it.
Revision: 98807
Author: d.rossell
Date: 2015-01-28T18:27:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/casper/DESCRIPTION
Modified  /trunk/madman/Rpacks/casper/NAMESPACE
Modified  /trunk/madman/Rpacks/casper/R/wrapDenovo.R
Modified  /trunk/madman/Rpacks/casper/src/seppel.cpp
Fixed bugs
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
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

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
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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
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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 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 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
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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
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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 information:

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 information:

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
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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

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