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Revision: 93522
Author: p.shannon
Date: 2014-08-22T00:16:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/explorer.R
more polishing and elimination of dead code.
global initial.genes for some reason not seen in uiWidgets
Revision: 93520
Author: p.shannon
Date: 2014-08-21T23:31:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/explorer.R
works quite well, displaying pubmed abstract, and entrez gene pages for geneIDs A and B

emtpy.data.frame is now defined a little differently: as a 1-row table with empty strings in each column

starting cleanup
Revision: 93516
Author: v.obenchain
Date: 2014-08-21T23:03:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicAlignments/R/summarizeOverlaps-methods.R
Modified  /trunk/madman/Rpacks/GenomicAlignments/DESCRIPTION
fix strand-related warning in summarizeOverlaps()
Revision: 93515
Author: xi.wang
Date: 2014-08-21T21:31:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/SeqGSEA/DESCRIPTION
update version
Revision: 93514
Author: v.obenchain
Date: 2014-08-21T20:39:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/R/windows/zzz.R
Modified  /trunk/madman/Rpacks/BiocParallel/inst/unitTests/test_bpiterate.R
Modified  /trunk/madman/Rpacks/BiocParallel/man/bpiterate.Rd
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/R/unix/bpiterate.R
add 'REDUCE' to bpiterate() for collapsing results on-the-fly
Revision: 93513
Author: p.shannon
Date: 2014-08-21T19:13:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/explorer.R
gene A id now transmits successfully via its hidden div, and is retrieved by the gene A pubmed search
Revision: 93512
Author: p.shannon
Date: 2014-08-21T19:09:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/explorer.R
sneaking up on adding the A gene's id to a hidden div (those divs are actually not yet hidden)
Revision: 93511
Author: p.shannon
Date: 2014-08-21T19:04:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/RefNet/inst/apps/explorer.R
pubmed abstracts displayed.
next up:  save geneIDs into hiddenHtmlOutput divs, for retrieval by geneAURL & geneBURL functions
Revision: 93510
Author: a.frazee
Date: 2014-08-21T18:34:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/ballgown/.Rbuildignore
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 5d169928a11495e34c534c67bd00d21a975272ca
Commit message: deletes tablemaker from rbuildignore
Committed by: Alyssa Frazee
Author Name: Alyssa Frazee
Commit date: 2014-08-21 14:34:45 -0400
Author date: 2014-08-21 14:34:45 -0400

Revision: 93509
Author: a.frazee
Date: 2014-08-21T18:28:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/ballgown/vignettes/ballgown.Rmd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 1962203b4e6476d5c49d00ddb9a1278500322122
Commit message: updated tablemaker link in vignette
Committed by: Alyssa Frazee
Author Name: Alyssa Frazee
Commit date: 2014-08-21 14:28:45 -0400
Author date: 2014-08-21 14:28:45 -0400

Revision: 93508
Author: a.frazee
Date: 2014-08-21T18:28:05+00:00
Paths:
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/lfd.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/Makefile.am
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/bits/graph_adaptor_extender.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/bfs.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/dfs.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/bits/array_map.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/nbhd.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/concepts/maps.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/density.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/graph_utils.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/Makefile.in
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/bits/debug_map.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/abundances.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/dens_odi.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/lfwin.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/GFaSeqGet.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/jensen_shannon.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/hits.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/solve.c
Modified  /trunk/madman/Rpacks/ballgown/README.md
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/scaffolds.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/matching_merge.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/strings.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/multireads.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/local.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/bits/alteration_notifier.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/concepts/ugraph.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/cmd.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/linalg.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/graph_optimize.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/config.h.in
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/ax_boost_system.m4
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/graph_adaptor.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/build-aux/missing
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/bundles.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/design.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/concepts/graph.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/ax_bam.m4
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/pcomp.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/build-aux/install-sh
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/preplot.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/README.cufflinks
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/minmax.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/scb_cons.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/simul.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/lfstr.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/ev_interp.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/wdiag.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/ar_funs.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/c_args.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/matching_merge.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/maps.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/bits/graph_extender.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/mutil.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/concepts/matrix_maps.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/m_eigen.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/band.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/adap.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/gff_utils.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/common.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/rounding.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/tokenize.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/GList.hh
Modified  /trunk/madman/Rpacks/ballgown/DESCRIPTION
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/genes.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/scaffold_graph.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/help.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/LICENSE
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/frend.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/clustering.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/bits/vector_map.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/negative_binomial_distribution.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/GBase.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/gff_utils.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/cufflinks.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/bits/traits.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/smart_graph.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/differential.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/locfit.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/assemble.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/scaffold_graph.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/concepts/bpugraph.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/genes.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/weight.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/GArgs.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/transitive_reduction.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/math.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/concepts/heap.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/fib_heap.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/AUTHORS
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/build-aux/config.sub
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/README.md
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/vari.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/makecmd.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/m_chol.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/dist.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/bin_heap.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/GBase.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/build-aux/ar-lib
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Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/readfile.c
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Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/GVec.hh
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Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/ax_check_eigen.m4
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/arith.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/ev_trian.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/scb.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/tokenize.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/bucket_heap.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/codons.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/replicates.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/ev_main.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/c_plot.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/bits/path_dump.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/Makefile.am
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/GFastaIndex.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/concepts/graph_components.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/biascorrection.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/math.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/multireads.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/Makefile.in
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/sampling.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/jensen_shannon.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/GFaSeqGet.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/build-aux/config.guess
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/filters.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/GStr.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/graph_optimize.cpp
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/locfit/ev_kdtre.c
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/lemon/bits/utility.h
Deleted  /trunk/madman/Rpacks/ballgown/tablemaker/tablemaker-2.1.1/src/clustering.h
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 28bcc66cdc08c612e4d638ad39ac9f36953d1c5c
Commit message: moves tablemaker to its own repo
Committed by: Alyssa Frazee
Author Name: Alyssa Frazee
Commit date: 2014-08-21 14:27:29 -0400
Author date: 2014-08-21 14:27:29 -0400

Revision: 93507
Author: t.hardcastle
Date: 2014-08-21T13:21:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/riboSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/riboSeq/R/plotCodons.R
v. 0.99.14; fix to stop codon labelling.
Revision: 93504
Author: j.gadin
Date: 2014-08-21T08:55:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/barplot-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/ASEset-accessors.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commits.

Commit information:

Commit id: 4d21ae9acb67c56882ac488ae9f35cd4576fc680
Commit message: bump
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-21 10:54:47 +0200
Author date: 2014-08-21 10:54:47 +0200

Commit id: 060ba8de389cd58dbd1ff1a9f56a505dbb115756
Commit message: one sample in the correct way
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-21 10:49:47 +0200
Author date: 2014-08-21 10:49:47 +0200

Commit id: 848a6271a42c9b376c25ea606c93f058536a9cd1
Commit message: one sample works
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-20 20:27:14 +0200
Author date: 2014-08-20 20:27:14 +0200

Revision: 93503
Author: l.varemo
Date: 2014-08-21T07:02:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/piano/R/writeFilesForKiwi.R
Modified  /trunk/madman/Rpacks/piano/DESCRIPTION
Fixed bug in writeFilesForKiwi so that duplicate gene-names are now allowed to be used
Revision: 93500
Author: v.obenchain
Date: 2014-08-20T21:36:06+00:00
Paths:
Added  /trunk/madman/Rpacks/BiocParallel/vignettes/IntroductionToBiocParallel.Rnw
Deleted  /trunk/madman/Rpacks/BiocParallel/vignettes/Overview.Rnw
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
update vignette introduction and rename file
Revision: 93498
Author: b.fischer
Date: 2014-08-20T20:37:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/rhdf5/CHANGES
Added  /trunk/madman/Rpacks/rhdf5/src/H5P.h
Added  /trunk/madman/Rpacks/rhdf5/man/H5P.Rd
Modified  /trunk/madman/Rpacks/rhdf5/NAMESPACE
Added  /trunk/madman/Rpacks/rhdf5/R/H5P.R
Modified  /trunk/madman/Rpacks/rhdf5/R/h5checktype.R
Modified  /trunk/madman/Rpacks/rhdf5/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/rhdf5/src/H5constants.c
Modified  /trunk/madman/Rpacks/rhdf5/src/wrap.c
Modified  /trunk/madman/Rpacks/rhdf5/DESCRIPTION
Added  /trunk/madman/Rpacks/rhdf5/src/H5P.c
Added support for the HDF5 property list H5P and added low level functions H5Pcreate, H5Pcopy, H5Pget_class, H5Pclose, H5Pclose_class
Revision: 93497
Author: mtmorgan
Date: 2014-08-20T19:29:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/SummarizedExperiment-class.R
missed arg on [rc]bind-method
Revision: 93496
Author: mtmorgan
Date: 2014-08-20T19:26:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/NEWS
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/SummarizedExperiment-class.R
[cr]bind,SummarizedExperiment-methods respect derived classes
Revision: 93495
Author: d.tenenbaum
Date: 2014-08-20T18:36:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneticsPed/DESCRIPTION
Modified  /trunk/madman/Rpacks/GeneticsPed/NAMESPACE
move gdata to Imports: and import in NAMESPACE
Revision: 93494
Author: h.klein
Date: 2014-08-20T17:33:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/epigenomix/R/normalizeChIP.R
Modified normilzeChIP(x, method="scaleMedianRegion"), so that it works for large samples sizes

Revision: 93493
Author: j.gadin
Date: 2014-08-20T16:50:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/NAMESPACE
Deleted  /trunk/madman/Rpacks/AllelicImbalance/tmp
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/AllGenerics.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 317bc409414ae63db658d4d1d14232ac82d95610
Commit message: a move from depends to imports
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-20 18:35:26 +0200
Author date: 2014-08-20 18:35:26 +0200

Revision: 93492
Author: k.horan
Date: 2014-08-20T16:11:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChemmineR/inst/CITATION
Modified  /trunk/madman/Rpacks/ChemmineR/R/sim.R
Modified  /trunk/madman/Rpacks/ChemmineR/R/compound_db.R
Modified  /trunk/madman/Rpacks/ChemmineR/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 927f4f6a2d1d115a0b9d45cf74f01e1afff83a07
Commit message: fixed bug in selectInBatches, fixed CITATION file
Committed by: khoran
Author Name: khoran
Commit date: 2014-08-20 09:11:01 -0700
Author date: 2014-08-20 09:11:01 -0700

Revision: 93490
Author: m.schroeder
Date: 2014-08-20T13:19:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/survcomp/DESCRIPTION
Modified  /trunk/madman/Rpacks/survcomp/man/km.coxph.plot.Rd
Modified  /trunk/madman/Rpacks/survcomp/R/concordance.index.R
Modified  /trunk/madman/Rpacks/survcomp/R/km.coxph.plot.R
Modified  /trunk/madman/Rpacks/survcomp/man/survcomp-package.Rd
Modified  /trunk/madman/Rpacks/survcomp/vignettes/survcomp.Rnw
Minor bug fixes and new contact details. Version bump to 1.15.1.
Revision: 93489
Author: j.gadin
Date: 2014-08-20T12:47:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/NAMESPACE
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-glocationplot.Rd
Added  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-lbarplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/auxillary-functions.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/initialize-ASEset.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset.Rd
Added  /trunk/madman/Rpacks/AllelicImbalance/man/coverageMatrixListFromGAL.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/barplot-methods.R
Added  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-Gviz-tracks.Rd
Added  /trunk/madman/Rpacks/AllelicImbalance/man/barplot-lattice.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/GvizTrack-methods.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/man/ASEset-locationplot.Rd
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/AllGenerics.R
Modified  /trunk/madman/Rpacks/AllelicImbalance/R/locationplot-methods.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 4 commits.

Commit information:

Commit id: 551c61847b53756e7291f69e6e35cb88498af669
Commit message: and the bump
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-20 14:47:00 +0200
Author date: 2014-08-20 14:47:00 +0200

Commit id: f6c5e00b7f0fea73fdf4d8da32b85b672f7eaff0
Commit message: R CMD check ok
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-20 14:45:00 +0200
Author date: 2014-08-20 14:45:00 +0200

Commit id: 7be7d3bea298d3d38274f6b47c4e7268db09fc0c
Commit message: updated docs
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-20 13:43:43 +0200
Author date: 2014-08-20 13:43:43 +0200

Commit id: c8cfe1005a5f1202d89184fc1562929fbf29c616
Commit message: fixed counts option bug for trellis plots
Committed by: Jesper R. Gådin
Author Name: Jesper R. Gådin
Commit date: 2014-08-19 16:46:29 +0200
Author date: 2014-08-19 16:46:29 +0200

Revision: 93488
Author: m.schroeder
Date: 2014-08-20T11:42:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/genefu/DESCRIPTION
Updated R dependency >=2.10 for compressed data folder.
Revision: 93487
Author: m.schroeder
Date: 2014-08-20T11:32:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/genefu/R/gene70.R
Modified  /trunk/madman/Rpacks/genefu/vignettes/genefu.Rnw
Added  /trunk/madman/Rpacks/genefu/inst/extdata/filipits2011_sig_endopredict.csv
Modified  /trunk/madman/Rpacks/genefu/R/intrinsic.cluster.predict.R
Modified  /trunk/madman/Rpacks/genefu/man/genefu-package.Rd
Modified  /trunk/madman/Rpacks/genefu/DESCRIPTION
Updated contact details and version number. Fixed minor bugs.
Revision: 93486
Author: a.reyes
Date: 2014-08-20T09:16:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEXSeq/vignettes/DEXSeq.Rnw
Modified  /trunk/madman/Rpacks/DEXSeq/DESCRIPTION
added dispersion estimation changes from DESeq2
Revision: 93484
Author: h.corradabravo
Date: 2014-08-20T05:26:50+00:00
Paths:
Added  /trunk/madman/Rpacks/epivizr/vignettes/Makefile
Modified  /trunk/madman/Rpacks/epivizr/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 032007b96f0436964bbc73171489cb43a3e1968f
Commit message: style the vignette
Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-08-20 01:16:16 -0400
Author date: 2014-08-20 01:16:16 -0400

Revision: 93482
Author: h.corradabravo
Date: 2014-08-20T03:24:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/epivizr/R/EpivizDeviceMgr-class.R
Modified  /trunk/madman/Rpacks/epivizr/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 21cae7eafb586ca090a9acb0b76f8b114f9ec724
Commit message: fix limit on slideshow; regenerate vignette
Committed by: hcorrada
Author Name: hcorrada
Commit date: 2014-08-19 23:23:42 -0400
Author date: 2014-08-19 23:23:42 -0400

Revision: 93480
Author: l.zhu
Date: 2014-08-19T22:20:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
Modified  /trunk/madman/Rpacks/CRISPRseek/tests/runTests.R
disable unit test
Revision: 93479
Author: l.zhu
Date: 2014-08-19T22:19:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
Modified  /trunk/madman/Rpacks/CRISPRseek/R/offTargetAnalysis.R
Modified  /trunk/madman/Rpacks/CRISPRseek/R/filterOffTarget.R
Modified  /trunk/madman/Rpacks/CRISPRseek/tests/runTests.R
Updated TranscriptDb to TxDb
Revision: 93478
Author: r.castelo
Date: 2014-08-19T22:10:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/NAMESPACE
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
Added import method VariantAnnotation::samples() to NAMESPACE.
Revision: 93477
Author: q.sheng
Date: 2014-08-19T20:00:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/DupChecker/DESCRIPTION
Modified  /trunk/madman/Rpacks/DupChecker/vignettes/DupChecker.Rnw
Modified  /trunk/madman/Rpacks/DupChecker/NEWS
Modified  /trunk/madman/Rpacks/DupChecker/R/DupChecker.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: f036faccb2d3134a54ee92d07efe208adbe95ebf
Commit message:
Committed by: shengqh
Author Name: shengqh
Commit date: 2014-08-19 15:00:46 -0500
Author date: 2014-08-19 15:00:46 -0500

Revision: 93476
Author: v.obenchain
Date: 2014-08-19T20:00:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/ensemblVEP/README
Modified  /trunk/madman/Rpacks/ensemblVEP/DESCRIPTION
mention .profile in README
Revision: 93475
Author: d.tenenbaum
Date: 2014-08-19T18:47:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/FGNet/DESCRIPTION
Added whitespace at start of biocViews continuation line
Revision: 93473
Author: d.gatti
Date: 2014-08-19T17:59:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOQTL/man/sdp.plot.Rd
Modified  /trunk/madman/Rpacks/DOQTL/man/assoc.plot.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: e9a24b5ed7f4a6c13c17b497a15ba09998d4d3d6
Commit message: Fixed doc errors
Committed by: dmgatti
Author Name: dmgatti
Commit date: 2014-08-19 13:59:30 -0400
Author date: 2014-08-19 13:59:30 -0400

Revision: 93470
Author: d.gatti
Date: 2014-08-19T17:42:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOQTL/R/assoc.map.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 1931ae74204786bc6c9c1dbe7f4bec17648262f1
Commit message: Set sdp.plot x-axis to not plot when making an assoc.plot.
Committed by: dmgatti
Author Name: dmgatti
Commit date: 2014-08-19 13:41:47 -0400
Author date: 2014-08-19 13:41:47 -0400

Revision: 93469
Author: v.obenchain
Date: 2014-08-19T17:03:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/man/bpiterate.Rd
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
clarify wording in bpiterate man page examples
Revision: 93468
Author: a.oles
Date: 2014-08-19T14:20:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocStyle/R/markdown.R
version 1.3.9
correct rendering of the Html style in R Studio when markdown v1 is used
Revision: 93466
Author: b.fischer
Date: 2014-08-19T09:19:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/rhdf5/man/h5write.Rd
Modified  /trunk/madman/Rpacks/rhdf5/CHANGES
Modified  /trunk/madman/Rpacks/rhdf5/NAMESPACE
Modified  /trunk/madman/Rpacks/rhdf5/inst/NEWS.Rd
Added  /trunk/madman/Rpacks/rhdf5/R/h5readAttributes.R
Modified  /trunk/madman/Rpacks/rhdf5/DESCRIPTION
New function h5readAttributes implemented that reads all HDF5 attributes of one object.
Revision: 93465
Author: g.klambauer
Date: 2014-08-19T08:48:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/cn.mops/R/normalizeChromosomes.R
Modified  /trunk/madman/Rpacks/cn.mops/DESCRIPTION
Modified  /trunk/madman/Rpacks/cn.mops/R/makeRobustCNVR.R
Modified  /trunk/madman/Rpacks/cn.mops/man/normalizeChromosomes.Rd
update in Rd files
Revision: 93464
Author: s.arora
Date: 2014-08-18T23:41:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/GenomeInfoDb/DESCRIPTION
video update

- add video for GenomeInfoDb
Revision: 93463
Author: d.tenenbaum
Date: 2014-08-18T22:13:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/IPPD/DESCRIPTION
Modified  /trunk/madman/Rpacks/IPPD/R/internals.R
fix data set name
Revision: 93460
Author: b.afsari
Date: 2014-08-18T21:59:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSReg/R/internalFuncs.R
Updating internalFuncs.R. A minor bug was fixed.
Revision: 93459
Author: d.tenenbaum
Date: 2014-08-18T21:48:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneticsPed/man/TDT.Rd
made geneFlowT example contingent on presence of gdata package.
if this example should always work, gdata should be moved to Depends/Imports.
Revision: 93457
Author: b.afsari
Date: 2014-08-18T20:33:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSReg/NAMESPACE
Modified  /trunk/madman/Rpacks/GSReg/DESCRIPTION
Modified  /trunk/madman/Rpacks/GSReg/vignettes/GSReg.Rnw
removing Sweave.sty
Revision: 93456
Author: b.afsari
Date: 2014-08-18T20:20:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSReg/man/GSReg_GeneSets_VReg..Rd
Replacing VReg by EVA.
Revision: 93455
Author: d.tenenbaum
Date: 2014-08-18T20:19:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/cn.mops/DESCRIPTION
Modified  /trunk/madman/Rpacks/cn.mops/NAMESPACE
Modified  /trunk/madman/Rpacks/cn.mops/R/getReadCountsFromBAM.R
fix imports (seqlengths and sortSeqlevels come from GenomeInfoDb)
Revision: 93454
Author: b.afsari
Date: 2014-08-18T20:11:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSReg/R/exportedFuncs.R
Replacing "VReg" by "EVA."
Revision: 93453
Author: b.afsari
Date: 2014-08-18T20:07:30+00:00
Paths:
Deleted  /trunk/madman/Rpacks/GSReg/vignettes/Sweave.sty
Removing Sweave.sty
Revision: 93452
Author: d.clayton
Date: 2014-08-18T19:51:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/snpStats/src/Makevars.win
Try again to replace indentation in Makevars.win
Revision: 93450
Author: d.tenenbaum
Date: 2014-08-18T19:05:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneticsPed/DESCRIPTION
add gdata to Suggests since it is in VignetteDepends, bump version
Revision: 93448
Author: d.gatti
Date: 2014-08-18T18:12:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOQTL/R/scanone.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: b55bddaa242999207b11b3f0b3a6447013a3fc7e
Commit message: Fixed bug in which the sex column was not being found correctly.
Committed by: dmgatti
Author Name: dmgatti
Commit date: 2014-08-18 14:12:30 -0400
Author date: 2014-08-18 14:12:30 -0400

Revision: 93445
Author: d.gatti
Date: 2014-08-18T16:55:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/DOQTL/R/gene.plot.R
Modified  /trunk/madman/Rpacks/DOQTL/man/sdp.plot.Rd
Modified  /trunk/madman/Rpacks/DOQTL/man/assoc.plot.Rd
Modified  /trunk/madman/Rpacks/DOQTL/R/assoc.map.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 503ccfe706c69514a2c4e87271a9b34205bbf58e
Commit message: Added SDP plot to assoc plot.
Committed by: dmgatti
Author Name: dmgatti
Commit date: 2014-08-18 12:54:21 -0400
Author date: 2014-08-18 12:54:21 -0400

Revision: 93443
Author: a.frazee
Date: 2014-08-18T16:47:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/ballgown/NAMESPACE
Modified  /trunk/madman/Rpacks/ballgown/NEWS
Modified  /trunk/madman/Rpacks/ballgown/DESCRIPTION
Added  /trunk/madman/Rpacks/ballgown/man/exprfilter.Rd
Added  /trunk/madman/Rpacks/ballgown/R/exprfilter.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commits.

Commit information:

Commit id: 0a8e73bbde56499a583528a023ecc4e59b7265d3
Commit message: version bump + NEWS update
Committed by: Alyssa Frazee
Author Name: Alyssa Frazee
Commit date: 2014-08-18 12:47:25 -0400
Author date: 2014-08-18 12:47:25 -0400

Commit id: b6a1f431b080f3065836d9422276a0da7b1f1f76
Commit message: adds exprfilter function
Committed by: Alyssa Frazee
Author Name: Alyssa Frazee
Commit date: 2014-08-18 12:46:18 -0400
Author date: 2014-08-18 12:46:18 -0400

Revision: 93442
Author: g.feng
Date: 2014-08-18T16:46:42+00:00
Paths:
Deleted  /trunk/madman/Rpacks/GeneAnswers/R/getREACTOMEPATHTerms.R
remove one function
Revision: 93441
Author: k.horan
Date: 2014-08-18T16:34:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/eiR/DESCRIPTION
Modified  /trunk/madman/Rpacks/eiR/src/f2c.h
Modified  /trunk/madman/Rpacks/eiR/README
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 02435debae0f8d833398c5fdd0c7a04810a49452
Commit message: revert -pedantic chagne and added a note about it in README. also fixed CITATIONS again
Committed by: khoran
Author Name: khoran
Commit date: 2014-08-18 09:34:39 -0700
Author date: 2014-08-18 09:34:39 -0700

Revision: 93440
Author: k.horan
Date: 2014-08-18T16:30:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/fmcsR/DESCRIPTION
Modified  /trunk/madman/Rpacks/fmcsR/inst/CITATION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: b987c5a4201ca72347d12a8c189fe8cce0754c7d
Commit message: added missing library call in CITATIONS file
Committed by: khoran
Author Name: khoran
Commit date: 2014-08-18 09:30:16 -0700
Author date: 2014-08-18 09:30:16 -0700

Revision: 93439
Author: g.feng
Date: 2014-08-18T14:59:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/GeneAnswers/R/zzz.R
Modified  /branches/RELEASE_2_14/madman/Rpacks/GeneAnswers/DESCRIPTION
add new udpates
Revision: 93438
Author: j.ou
Date: 2014-08-18T14:32:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/trackViewer/DESCRIPTION
Modified  /trunk/madman/Rpacks/trackViewer/vignettes/trackViewer.Rnw
update vignettes
Revision: 93436
Author: r.romoli
Date: 2014-08-18T11:13:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/flagme/DESCRIPTION
Modified  /trunk/madman/Rpacks/flagme/R/addXCMSPeaks.R
debug addXCMSPeaks.R
Revision: 93435
Author: smyth
Date: 2014-08-18T09:40:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/limma/man/topSplice.Rd
Modified  /trunk/madman/Rpacks/limma/DESCRIPTION
Modified  /trunk/madman/Rpacks/limma/inst/doc/changelog.txt
Modified  /trunk/madman/Rpacks/limma/man/diffSplice.Rd
Modified  /trunk/madman/Rpacks/limma/R/diffSplice.R
Modified  /trunk/madman/Rpacks/limma/inst/doc/usersguide.pdf
18 Aug 2014: limma 3.21.13

- Speed improvement for the calculation of Simes adjusted p-values by
  diffSplice().

- argument 'level' for diffSplice() renamed to 'test', with possible
  values "simes", "F" or "t".
Revision: 93434
Author: g.yu
Date: 2014-08-18T09:24:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/R/tagMatrix.R
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: f657f0afd503feec1af01d3b02a22a1af66f84f3
Commit message: update tagMatrix
Committed by: Guangchuang Yu
Author Name: Guangchuang Yu
Commit date: 2014-08-18 17:24:35 +0800
Author date: 2014-08-18 17:24:35 +0800

Revision: 93433
Author: g.yu
Date: 2014-08-18T08:57:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChIPseeker/NAMESPACE
Modified  /trunk/madman/Rpacks/ChIPseeker/NEWS
Modified  /trunk/madman/Rpacks/ChIPseeker/vignettes/ChIPseeker.Rnw
Modified  /trunk/madman/Rpacks/ChIPseeker/DESCRIPTION
Deleted  /trunk/madman/Rpacks/ChIPseeker/R/plotChrCov.R
Added  /trunk/madman/Rpacks/ChIPseeker/man/covplot.Rd
Added  /trunk/madman/Rpacks/ChIPseeker/R/covplot.R
Modified  /trunk/madman/Rpacks/ChIPseeker/man/ChIPseeker-package.Rd
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: 300728d971e2d087b2eb04e2a147a05ebf5bcb80
Commit message: deprecated plotChrCov to new function covplot
Committed by: Guangchuang Yu
Author Name: Guangchuang Yu
Commit date: 2014-08-18 16:57:13 +0800
Author date: 2014-08-18 16:57:13 +0800

Revision: 93432
Author: m.iterson
Date: 2014-08-18T06:21:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/TurboNorm/NAMESPACE
Modified  /trunk/madman/Rpacks/TurboNorm/DESCRIPTION
fixed bug in NAMESPACE
Revision: 93430
Author: d.tenenbaum
Date: 2014-08-17T19:31:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/data/biocViewsVocab.rda
Modified  /trunk/madman/Rpacks/biocViews/inst/extdata/biocViewsVocab.sqlite
update rda and sqlite
Revision: 93429
Author: d.clayton
Date: 2014-08-17T15:33:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/snpStats/DESCRIPTION
Modified  /trunk/madman/Rpacks/snpStats/man/snpStats-package.Rd
Modified  /trunk/madman/Rpacks/snpStats/src/Makevars.win
Change blanks to tab in indented line in Makevars.win
Revision: 93427
Author: t.pedersen
Date: 2014-08-17T12:28:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/mzID/NEWS
Modified  /trunk/madman/Rpacks/mzID/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: ddc3dfe80d404287581eeb1258af929a52a7f9f0
Commit message: Version bump
Committed by: Thomas Dybdal Pedersen
Author Name: Thomas Dybdal Pedersen
Commit date: 2014-08-17 14:28:23 +0200
Author date: 2014-08-17 14:28:23 +0200

Revision: 93425
Author: smyth
Date: 2014-08-17T03:50:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/edgeR/man/estimateDisp.Rd
Modified  /trunk/madman/Rpacks/edgeR/src/init.cpp
Modified  /trunk/madman/Rpacks/edgeR/R/estimateDisp.R
Modified  /trunk/madman/Rpacks/edgeR/R/readDGE.R
Modified  /trunk/madman/Rpacks/edgeR/inst/doc/edgeRUsersGuide.pdf
Modified  /trunk/madman/Rpacks/edgeR/DESCRIPTION
edgeR 3.7.14.
- update to User's Guide section on pseudo-counts.
- estimateDisp has a new argument min.row.sum
Revision: 93424
Author: l.pantano
Date: 2014-08-16T13:24:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGreport/DESCRIPTION
Added  /trunk/madman/Rpacks/DEGreport/data/geneInfo.rda
Modified  /trunk/madman/Rpacks/DEGreport/vignettes/DEGreport.Rnw
Deleted  /trunk/madman/Rpacks/DEGreport/vignettes/DEGreportHTML.Rmd
Modified  /trunk/madman/Rpacks/DEGreport/inst/NEWS
Added  /trunk/madman/Rpacks/DEGreport/man/geneInfo.Rd
Added  /trunk/madman/Rpacks/DEGreport/R/geneInfo.R
Modified  /trunk/madman/Rpacks/DEGreport/data/datalist
Commit made by the Bioconductor Git-SVN bridge.
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Commit information:

Commit id: c1d0ee8552bd40bb668e08ad81dbd7940ca7ced9
Commit message: remove biomart from vignettes due to unknown build issues in bioC checking.
Committed by: Lorena Pantano
Author Name: Lorena Pantano
Commit date: 2014-08-16 09:24:14 -0400
Author date: 2014-08-16 09:24:14 -0400


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