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This is a list of recent commits to the development branch of the Bioconductor Subversion repository.

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Revision: 130745
Author: f.seyednasrollah
Date: 2017-06-28T07:48:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/ROTS/DESCRIPTION
Bump version
Revision: 130744
Author: f.seyednasrollah
Date: 2017-06-28T07:46:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/ROTS/R/ROTS.R
Modified  /trunk/madman/Rpacks/ROTS/man/ROTS.Rd
Default parameters for B and K
Revision: 130743
Author: f.seyednasrollah
Date: 2017-06-28T07:25:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/ROTS/man/ROTS.Rd
Documentation update
Revision: 130741
Author: m.lawrence
Date: 2017-06-27T21:56:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/geom_alignment-method.R
avoid redundant aesthetics for the labels
Revision: 130738
Author: s.gogarten
Date: 2017-06-27T20:33:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/GENESIS/DESCRIPTION
version bump to 2.7.2
Revision: 130737
Author: m.riester
Date: 2017-06-27T20:30:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/R/setMappingBiasVcf.R
Modified  /trunk/madman/Rpacks/PureCN/inst/extdata/PureCN.R
Changed dnacopy output file from PureCN.R so that IGV accepts it.
Revision: 130736
Author: s.gogarten
Date: 2017-06-27T20:22:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/GENESIS/DESCRIPTION
Modified  /trunk/madman/Rpacks/GENESIS/R/assocTestMM.R
Added  /trunk/madman/Rpacks/GENESIS/inst/unitTests/test_assocTestMM.R
bug fix: Y chrom for assocTestMM with GenotypeData object
Revision: 130731
Author: j.collins
Date: 2017-06-27T18:45:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/LOBSTAHS/R/generateLOBdbase.R
Fixing missing bracket to close if statement
Revision: 130730
Author: j.collins
Date: 2017-06-27T18:45:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/LOBSTAHS/R/generateLOBdbase.R
Adds catch (and error message) for users supplying older-style input tables without an "Si" column
Revision: 130724
Author: j.collins
Date: 2017-06-27T17:37:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/LOBSTAHS/DESCRIPTION
Properly bump version to 1.3.1 for consistency with Bioconductor
Revision: 130723
Author: j.collins
Date: 2017-06-27T17:30:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/LOBSTAHS/vignettes/LOBSTAHS.Rmd
Fixed order in which xcms and CAMERA should be loaded
Revision: 130722
Author: j.collins
Date: 2017-06-27T17:28:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/LOBSTAHS/README.md
Fixed order in which xcms and CAMERA should be loaded
Revision: 130721
Author: j.collins
Date: 2017-06-27T17:28:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS.Rproj
Modified  /trunk/madman/Rpacks/LOBSTAHS/README.md
Modified  /trunk/madman/Rpacks/LOBSTAHS/vignettes/LOBSTAHS.Rmd
Minor updates to documentation to fix formatting
Revision: 130720
Author: j.collins
Date: 2017-06-27T17:28:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/LOBSTAHS/.gitignore
Small fix to .gitignore
Revision: 130719
Author: j.collins
Date: 2017-06-27T17:28:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/LOBSTAHS/vignettes/LOBSTAHS.Rmd
Update vignette to ensure users render vignette when installing from Github
Revision: 130718
Author: j.collins
Date: 2017-06-27T17:28:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/LOBSTAHS/README.md
Makes the figure a wee bit wider
Revision: 130717
Author: j.collins
Date: 2017-06-27T17:28:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/LOBSTAHS/README.md
Added  /trunk/madman/Rpacks/LOBSTAHS/vignettes/images/LOBSTAHS_TOC_Figure.png
Small change to the README (adds an image)
Revision: 130716
Author: j.collins
Date: 2017-06-27T17:28:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/LOBSTAHS/data/default.LOBdbase.RData
Rename parent object within default.LOBdbase.RData
Revision: 130713
Author: hpages
Date: 2017-06-27T17:05:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/AllelicImbalance/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/DEXSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/FourCSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenoGAM/DESCRIPTION
Modified  /trunk/madman/Rpacks/MinimumDistance/DESCRIPTION
Modified  /trunk/madman/Rpacks/REMP/DESCRIPTION
Modified  /trunk/madman/Rpacks/VanillaICE/DESCRIPTION
Modified  /trunk/madman/Rpacks/XBSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/bsseq/DESCRIPTION
Modified  /trunk/madman/Rpacks/coseq/DESCRIPTION
Modified  /trunk/madman/Rpacks/epigenomix/DESCRIPTION
Modified  /trunk/madman/Rpacks/erma/DESCRIPTION
Modified  /trunk/madman/Rpacks/genoset/DESCRIPTION
Modified  /trunk/madman/Rpacks/methyAnalysis/DESCRIPTION
Modified  /trunk/madman/Rpacks/methylPipe/DESCRIPTION
Modified  /trunk/madman/Rpacks/minfi/DESCRIPTION
Modified  /trunk/madman/Rpacks/roar/DESCRIPTION
Modified  /trunk/madman/Rpacks/soGGi/DESCRIPTION
Bump version of packages that define RangedSummarizedExperiment derivatives
(direct or indirect). Will help get rid of those class definitions that are
cached on the user machines and became stale after GenomicRangesORGRangesList
was renamed GenomicRanges_OR_GRangesList (on June 18, commit 130486).
Revision: 130712
Author: l.shepherd
Date: 2017-06-27T16:59:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocFileCache/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocFileCache/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocFileCache/R/sql.R
Modified  /trunk/madman/Rpacks/BiocFileCache/tests/testthat/test_BiocFileCache_class.R
Updates for new DBI/RSQLite

  - remove src_sqlite, to remove auto-disconnect message
  - dbSendQuery/dbFetch produced warnings, updated to appropriate statements
  - cleaned whitespace

From: Lori Shepherd <shepherl@gmail.com>
Revision: 130708
Author: a.oles
Date: 2017-06-27T15:36:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocStyle/R/html_fragment.R
Added  /trunk/madman/Rpacks/BiocStyle/inst/resources/fragment.html
version 2.5.4
- 'html_fragment': add mathjax and toc

From: aoles <andrzej.oles@gmail.com>
Revision: 130701
Author: c.panse
Date: 2017-06-27T08:04:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/cosmiq/DESCRIPTION
Modified  /trunk/madman/Rpacks/cosmiq/vignettes/poster.Rnw
added poster ID
Revision: 130700
Author: m.lawrence
Date: 2017-06-26T23:14:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/extractList.R
as.factor2() handles NULL case
Revision: 130699
Author: m.lawrence
Date: 2017-06-26T23:13:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationDbi/R/methods-geneCentricDbs.R
allow for empty keys vector
Revision: 130695
Author: a.rodriguez-martinez
Date: 2017-06-26T22:17:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/MetaboSignal/DESCRIPTION
Modified  /trunk/madman/Rpacks/MetaboSignal/R/MS_keggNetwork.R
1.7.6
Revision: 130692
Author: v.obenchain
Date: 2017-06-26T19:58:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/inst/unitTests/test_recipe.R
remove hard coded biocVersion in unit tests
Revision: 130691
Author: mtmorgan
Date: 2017-06-26T19:47:17+00:00
Paths:
Added  /trunk/madman/Rpacks/grasp2db/README
add README about version control / annotation package
Revision: 130690
Author: mtmorgan
Date: 2017-06-26T19:46:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/grasp2db/R/db_create.R
tweak -- no need to require an imported package
Revision: 130688
Author: hpages
Date: 2017-06-26T17:06:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/S4Vectors/R/List-class.R
small edit
Revision: 130687
Author: mtmorgan
Date: 2017-06-26T16:51:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/grasp2db/DESCRIPTION
Modified  /trunk/madman/Rpacks/grasp2db/NAMESPACE
Modified  /trunk/madman/Rpacks/grasp2db/R/zzz.R
update to use dbplyr

- use dbplyr::src_dbi() rather than src_sql()
- additional minor tweaks
Revision: 130686
Author: mtmorgan
Date: 2017-06-26T16:47:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/grasp2db/man/grasp2db-package.Rd
Modified  /trunk/madman/Rpacks/grasp2db/vignettes/grasp2db.Rmd
further minor changes
Revision: 130685
Author: m.riester
Date: 2017-06-26T16:37:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/R/findBestNormal.R
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Modified  /trunk/madman/Rpacks/PureCN/vignettes/Quick.Rnw
Bugfix: coverage in findBestNormal pooling not correct (average.coverage was); had probably no effect since log-ratios are re-calibrated anyways.
Revision: 130684
Author: mtmorgan
Date: 2017-06-26T16:28:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocParallel/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocParallel/NAMESPACE
oops, don't need a dynamic library
Revision: 130679
Author: hpages
Date: 2017-06-26T15:20:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/IRanges/R/CompressedList-class.R
Modified  /trunk/madman/Rpacks/IRanges/inst/unitTests/test_DataFrameList.R
Modified  /trunk/madman/Rpacks/S4Vectors/DESCRIPTION
Modified  /trunk/madman/Rpacks/S4Vectors/R/List-class.R
Modified  /trunk/madman/Rpacks/S4Vectors/inst/unitTests/test_List-class.R
A couple of (long-time due) tweaks and fixes to "unlist" method for List objects
so that it behaves consistently with "unlist" method for CompressedList objects.
Revision: 130677
Author: mtmorgan
Date: 2017-06-26T14:23:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/grasp2db/R/doanti.R
Modified  /trunk/madman/Rpacks/grasp2db/vignettes/BiocGRASP2.Rmd
minor cleanup
Revision: 130673
Author: m.love
Date: 2017-06-26T13:04:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/vignettes/DESeq2.Rmd
sort by p
Revision: 130671
Author: c.ruiz-arenas
Date: 2017-06-26T12:51:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/MultiDataSet/DESCRIPTION
Modified  /trunk/madman/Rpacks/MultiDataSet/NAMESPACE
Deleted  /trunk/madman/Rpacks/MultiDataSet/R/0_AllClasses.R
Deleted  /trunk/madman/Rpacks/MultiDataSet/R/1_AllGenerics.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/1_MethylationSet-ClassGenerics.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/1_MultiDataSet-ClassGenerics.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/2_ResultSet-ClassGenerics.R
Modified  /trunk/madman/Rpacks/MultiDataSet/R/MultiDataSet-add_methy.R
Modified  /trunk/madman/Rpacks/MultiDataSet/R/MultiDataSet-as_list.R
Modified  /trunk/madman/Rpacks/MultiDataSet/R/MultiDataSet-constructor.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/MultiDataSet-ncol.R
Deleted  /trunk/madman/Rpacks/MultiDataSet/R/MultiDataSet-ncols.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/MultiDataSet-nrow.R
Deleted  /trunk/madman/Rpacks/MultiDataSet/R/MultiDataSet-nrows.R
Modified  /trunk/madman/Rpacks/MultiDataSet/R/MultiDataSet.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/ResultSet-fData.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/ResultSet-getAssociation.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/ResultSet-length.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/ResultSet-names.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/ResultSet-opt.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/ResultSet-plot.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/ResultSet-show.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/ResultSet-varLabels.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/create_resultset.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/lambdaClayton.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/qq_plot.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/rset.R
Added  /trunk/madman/Rpacks/MultiDataSet/R/volcano_plot.R
Added  /trunk/madman/Rpacks/MultiDataSet/data
Added  /trunk/madman/Rpacks/MultiDataSet/data/rset.rda
Added  /trunk/madman/Rpacks/MultiDataSet/inst/scripts
Added  /trunk/madman/Rpacks/MultiDataSet/inst/scripts/create_rset.R
Modified  /trunk/madman/Rpacks/MultiDataSet/man/MethylationSet-class.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/MultiDataSet-class.Rd
Added  /trunk/madman/Rpacks/MultiDataSet/man/ResultSet-class.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/add_eset.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/add_genexp.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/add_methy.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/add_rnaseq-methods.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/add_rse.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/add_se.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/add_snps.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/add_table.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/commonIds.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/commonSamples.Rd
Added  /trunk/madman/Rpacks/MultiDataSet/man/getAssociation-methods.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/getMs-methods.Rd
Added  /trunk/madman/Rpacks/MultiDataSet/man/lambdaClayton.Rd
Added  /trunk/madman/Rpacks/MultiDataSet/man/opt-methods.Rd
Added  /trunk/madman/Rpacks/MultiDataSet/man/qq_plot.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/rowRangesElements.Rd
Added  /trunk/madman/Rpacks/MultiDataSet/man/rset.Rd
Added  /trunk/madman/Rpacks/MultiDataSet/man/volcano_plot.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/w_iclusterplus.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/man/w_mcia.Rd
Modified  /trunk/madman/Rpacks/MultiDataSet/tests/testthat/test_05checkMultiDataSet.R
New version
Add ResultSet to MultiDataSet
Revision: 130667
Author: s.xu
Date: 2017-06-26T06:15:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/PGA/DESCRIPTION
Modified  /trunk/madman/Rpacks/PGA/NEWS
Modified  /trunk/madman/Rpacks/PGA/R/dbCreator.R
Fix minor bug
Revision: 130665
Author: a.gutierrez-sacristan
Date: 2017-06-25T16:35:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/psygenet2r/DESCRIPTION
Modified  /trunk/madman/Rpacks/psygenet2r/NAMESPACE
Modified  /trunk/madman/Rpacks/psygenet2r/R/psygenet2r.R
Update NAMESPACE.
Revision: 130663
Author: c.trapnell
Date: 2017-06-24T22:37:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/monocle/DESCRIPTION
Modified  /trunk/madman/Rpacks/monocle/NAMESPACE
Modified  /trunk/madman/Rpacks/monocle/R/plotting.R
Deleted  /trunk/madman/Rpacks/monocle/R/untitled.R
Modified  /trunk/madman/Rpacks/monocle/man/plot_genes_jitter.Rd
Modified  /trunk/madman/Rpacks/monocle/man/plot_multiple_branches_heatmap.Rd
Modified  /trunk/madman/Rpacks/monocle/man/plot_multiple_branches_pseudotime.Rd
Deleted  /trunk/madman/Rpacks/monocle/vignettes/monocle-vignette-knitr.Rnw
Added  /trunk/madman/Rpacks/monocle/vignettes/monocle-vignette.Rnw
Merge branch 'master' into devel

* master:
  version bump
  vignette file name changed
  update the documentation
  really remove untitled.R this time!!
  remove untitled.R; add missing documentation
  edited abstract (English was wrong and awkward
  added Andrew & Jose's violin plot

From: Cole Trapnell <coletrap@uw.edu>
Revision: 130660
Author: l.gatto
Date: 2017-06-24T20:54:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/tests/testthat.R
fix conflict
Revision: 130659
Author: m.teng
Date: 2017-06-24T19:13:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/gcapc/DESCRIPTION
Modified  /trunk/madman/Rpacks/gcapc/R/gcapcPeaks.r
overflow bug fixed
Revision: 130656
Author: t.silva
Date: 2017-06-24T18:57:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/download_prepare.Rmd
update pkg
Revision: 130654
Author: m.riester
Date: 2017-06-24T17:49:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Minor corrections and clarifications in vignette.
Revision: 130653
Author: p.angerer
Date: 2017-06-24T16:47:33+00:00
Paths:
Modified  /trunk/madman/Rpacks/destiny/DESCRIPTION
Modified  /trunk/madman/Rpacks/destiny/R/diffusionmap.r
Cope with small k
Revision: 130652
Author: m.riester
Date: 2017-06-24T16:07:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/NEWS
Modified  /trunk/madman/Rpacks/PureCN/R/PureCN-internal.R
Modified  /trunk/madman/Rpacks/PureCN/R/plotAbs.R
Modified  /trunk/madman/Rpacks/PureCN/R/predictSomatic.R
Modified  /trunk/madman/Rpacks/PureCN/R/runAbsoluteCN.R
Modified  /trunk/madman/Rpacks/PureCN/inst/extdata/Coverage.R
Modified  /trunk/madman/Rpacks/PureCN/inst/extdata/PureCN.R
Modified  /trunk/madman/Rpacks/PureCN/man/predictSomatic.Rd
Modified  /trunk/madman/Rpacks/PureCN/man/runAbsoluteCN.Rd
Modified  /trunk/madman/Rpacks/PureCN/vignettes/Quick.Rnw
Started the long needed reworking of the log-ratio calibration. Initial tweek seem to fix a few more samples than it breaks, needs more testing in panels; removed log-ratio outliers in histogram; make debugging easier in PureCN.R
Revision: 130650
Author: t.xu
Date: 2017-06-24T10:15:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/CancerSubtypes/DESCRIPTION
Modified  /trunk/madman/Rpacks/CancerSubtypes/R/DataProcess.R
Modified  /trunk/madman/Rpacks/CancerSubtypes/README.md
fix a bug for data.normalization()
Revision: 130649
Author: v.obenchain
Date: 2017-06-23T19:39:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/Category/DESCRIPTION
Modified  /trunk/madman/Rpacks/Category/NAMESPACE
import dbGetQuery() from DBI instead of RSQLite
Revision: 130645
Author: c.trapnell
Date: 2017-06-23T18:38:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/monocle/NAMESPACE
Modified  /trunk/madman/Rpacks/monocle/R/clustering.R
Modified  /trunk/madman/Rpacks/monocle/R/plotting.R
Added  /trunk/madman/Rpacks/monocle/R/untitled.R
Modified  /trunk/madman/Rpacks/monocle/man/BEAM.Rd
Deleted  /trunk/madman/Rpacks/monocle/man/SubSet_cds.Rd
Modified  /trunk/madman/Rpacks/monocle/man/detectGenes.Rd
Modified  /trunk/madman/Rpacks/monocle/man/fitModel.Rd
Modified  /trunk/madman/Rpacks/monocle/man/get_classic_muscle_markers.Rd
Modified  /trunk/madman/Rpacks/monocle/man/load_HSMM.Rd
Modified  /trunk/madman/Rpacks/monocle/man/load_HSMM_markers.Rd
Modified  /trunk/madman/Rpacks/monocle/man/load_lung.Rd
Modified  /trunk/madman/Rpacks/monocle/man/markerDiffTable.Rd
Modified  /trunk/madman/Rpacks/monocle/man/newCellTypeHierarchy.Rd
Modified  /trunk/madman/Rpacks/monocle/man/plot_cell_trajectory.Rd
Modified  /trunk/madman/Rpacks/monocle/man/plot_clusters.Rd
Added  /trunk/madman/Rpacks/monocle/man/plot_complex_cell_trajectory.Rd
Modified  /trunk/madman/Rpacks/monocle/man/plot_genes_branched_heatmap.Rd
Modified  /trunk/madman/Rpacks/monocle/man/plot_genes_branched_pseudotime.Rd
Modified  /trunk/madman/Rpacks/monocle/man/plot_genes_in_pseudotime.Rd
Modified  /trunk/madman/Rpacks/monocle/man/plot_genes_jitter.Rd
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Added  /trunk/madman/Rpacks/monocle/vignettes/figure/show_mRNA_totals-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/monocle-vignette-knitr-concordance.tex
Modified  /trunk/madman/Rpacks/monocle/vignettes/monocle-vignette-knitr.Rnw
Added  /trunk/madman/Rpacks/monocle/vignettes/monocle-vignette-knitr.bbl
Added  /trunk/madman/Rpacks/monocle/vignettes/monocle-vignette-knitr.log
Added  /trunk/madman/Rpacks/monocle/vignettes/monocle-vignette-knitr.pdf
Added  /trunk/madman/Rpacks/monocle/vignettes/monocle-vignette-knitr.synctex.gz
Added  /trunk/madman/Rpacks/monocle/vignettes/monocle-vignette-knitr.tex
Added  /trunk/madman/Rpacks/monocle/vignettes/monocle-vignette-knitr.toc
Merge branch 'master' into devel

* master:
  add citation to Census/Monocle 2 in abstract
  add hidden set.seed
  add detectCore back
  add the multiple branch plot in; facilitate the vignettee building

From: Cole Trapnell <coletrap@uw.edu>

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