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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
Modified  /trunk/madman/Rpacks/monocle/man/plot_genes_positive_cells.Rd
Added  /trunk/madman/Rpacks/monocle/man/plot_multiple_branches_heatmap.Rd
Added  /trunk/madman/Rpacks/monocle/man/plot_multiple_branches_pseudotime.Rd
Modified  /trunk/madman/Rpacks/monocle/man/plot_pseudotime_heatmap.Rd
Modified  /trunk/madman/Rpacks/monocle/man/reduceDimension.Rd
Modified  /trunk/madman/Rpacks/monocle/man/reducedDimK.Rd
Modified  /trunk/madman/Rpacks/monocle/man/relative2abs.Rd
Modified  /trunk/madman/Rpacks/monocle/man/responseMatrix.Rd
Modified  /trunk/madman/Rpacks/monocle/man/selectNegentropyGenes.Rd
Modified  /trunk/madman/Rpacks/monocle/man/setOrderingFilter.Rd
Modified  /trunk/madman/Rpacks/monocle/man/vstExprs.Rd
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/check_clustering_again-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/check_clustering_again-2.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/check_the_clustering_results-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/check_the_clustering_results-2.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/cluster_cells_semisup_clustering_no_impute-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/cluster_cells_semisup_clustering_no_impute-2.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/cluster_cells_semisup_clustering_with_impute-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/cluster_cells_semisup_pick_genes-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/cluster_cells_unsup_control_for_media-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/cluster_cells_unsup_gene_pick-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/cluster_cells_unsup_no_covariate-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/cluster_cells_unsup_no_covariate-2.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/cluster_cells_unsup_plot_by_cell_type-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/cluster_cells_unsup_plot_by_media-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/count_cells_semisup_pie-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/count_cells_unsup_readout-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/init_hsmm_facet_state-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/init_hsmm_jitter_state-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/init_treutlein-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/jitter_plot_diff_res-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/lognormal_plot-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/lung_beam_branched_heatmap-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/lung_beam_branched_pseudotime-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/order_cells_dp_feature-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/order_cells_pca_unsup-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/plot_diff_res_multi-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/plot_diff_res_pt-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/plot_diff_res_pt_heatmap-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/plot_markers_linear-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/plot_myog_jitter-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/plot_ordering_mst-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/plot_ordering_mst_by_state-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/plot_ordering_with_GM_state-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/plot_pc_variance-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/plot_rho_delta-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/semi_sup_ordering_genes_in_pseudotime-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/semi_sup_ordering_trajectory-1.png
Added  /trunk/madman/Rpacks/monocle/vignettes/figure/set_ordering_filter-1.png
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>
Revision: 130644
Author: v.obenchain
Date: 2017-06-23T17:55:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/ExperimentHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/ExperimentHubData/R/addResources.R
Modified  /trunk/madman/Rpacks/ExperimentHubData/man/ExperimentHubMetadata-class.Rd
Modified  /trunk/madman/Rpacks/ExperimentHubData/man/addResources.Rd
update addResources() and tidy man pages
Revision: 130643
Author: m.lawrence
Date: 2017-06-23T17:53:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggbio/DESCRIPTION
Modified  /trunk/madman/Rpacks/ggbio/R/plotGrandLinear.R
add pruning.mode="coarse"
Revision: 130642
Author: v.obenchain
Date: 2017-06-23T17:52:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/NAMESPACE
import dbGetQuery() from DBI
Revision: 130639
Author: l.gatto
Date: 2017-06-23T16:25:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/mzR/NEWS
Merge branch 'master' into devel

* master:
  update readme

From: Laurent <lg390@cam.ac.uk>
Revision: 130638
Author: l.gatto
Date: 2017-06-23T16:24:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/mzR/DESCRIPTION
Modified  /trunk/madman/Rpacks/mzR/NEWS
Modified  /trunk/madman/Rpacks/mzR/inst/unitTests/test_chromatograms.R
Modified  /trunk/madman/Rpacks/mzR/inst/unitTests/test_isolationWindow.R
Modified  /trunk/madman/Rpacks/mzR/inst/unitTests/test_pwiz.R
Modified  /trunk/madman/Rpacks/mzR/man/isolationWindow-methods.Rd
Modified  /trunk/madman/Rpacks/mzR/man/peaks.Rd
Merge branch 'master' into devel

* master:
  specify full name as pattern for get the small TMT Erwinia subset
  make sure use only 1 TMT raw file
  bump gh devel version

From: Laurent <lg390@cam.ac.uk>
Revision: 130637
Author: a.oles
Date: 2017-06-23T15:50:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocStyle/DESCRIPTION
Added  /trunk/madman/Rpacks/BiocStyle/R/html_fragment.R
version 2.5.3
- 'html_fragment' draft for generating workflow pages for the BioC website

From: aoles <andrzej.oles@gmail.com>
Revision: 130635
Author: f.albrecht
Date: 2017-06-23T15:48:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/DeepBlueR/R/liftover.R
deepblue_liftover confused source and target
Revision: 130632
Author: j.rodriguez
Date: 2017-06-23T14:08:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/MIGSA/DESCRIPTION
Modified  /trunk/madman/Rpacks/MIGSA/NEWS
Modified  /trunk/madman/Rpacks/MIGSA/R/Genesets-loadGo.R
Bug fix on loadGo function
Revision: 130631
Author: a.delabriere
Date: 2017-06-23T11:41:40+00:00
Paths:
Added  /trunk/madman/Rpacks/proFIA/man/impute.FIA-proFIAset-method.Rd
Added the missing doc impute.FIA-proFIAset-method.Rd
Revision: 130628
Author: v.obenchain
Date: 2017-06-23T05:10:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-locateVariants.R
fix bug in locateVariants(..., AllVariants()); code to fetch IntronVariants()
was incorrectly fetching IntergenicVariants()
Revision: 130626
Author: l.goldstein
Date: 2017-06-22T22:34:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/SGSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/SGSeq/R/plots.R
changed functions plotFeatures and plotVariants so top-right panel is reserved for user-defined plots
Revision: 130624
Author: d.vantwisk
Date: 2017-06-22T21:03:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/Organism.dplyr/DESCRIPTION
Version bump.
Revision: 130623
Author: d.vantwisk
Date: 2017-06-22T20:58:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/Organism.dplyr/R/src.R
Fixed bug with .getSeqinfo()

Changed .getSeqinfo() so that the arguments passed to Seqinfo() now specifically
reference the column names instead of the column numbers.
Revision: 130621
Author: m.love
Date: 2017-06-22T19:42:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/R/plots.R
make intgroup level names shorter in plotPCA and plotCounts
Revision: 130620
Author: mtmorgan
Date: 2017-06-22T19:42:40+00:00
Paths:
Added  /trunk/madman/Rpacks/RTNsurvival
Added  /trunk/madman/Rpacks/RTNsurvival/DESCRIPTION
Added  /trunk/madman/Rpacks/RTNsurvival/NAMESPACE
Added  /trunk/madman/Rpacks/RTNsurvival/R
Added  /trunk/madman/Rpacks/RTNsurvival/R/AllChecks.R
Added  /trunk/madman/Rpacks/RTNsurvival/R/AllClasses.R
Added  /trunk/madman/Rpacks/RTNsurvival/R/AllGenerics.R
Added  /trunk/madman/Rpacks/RTNsurvival/R/AllMethods.R
Added  /trunk/madman/Rpacks/RTNsurvival/R/AllSupplements.R
Added  /trunk/madman/Rpacks/RTNsurvival/data
Added  /trunk/madman/Rpacks/RTNsurvival/data/datalist
Added  /trunk/madman/Rpacks/RTNsurvival/data/survival.data.RData
Added  /trunk/madman/Rpacks/RTNsurvival/inst
Added  /trunk/madman/Rpacks/RTNsurvival/inst/CITATION
Added  /trunk/madman/Rpacks/RTNsurvival/inst/NEWS.Rd
Added  /trunk/madman/Rpacks/RTNsurvival/inst/unitTests
Added  /trunk/madman/Rpacks/RTNsurvival/inst/unitTests/test.R
Added  /trunk/madman/Rpacks/RTNsurvival/man
Added  /trunk/madman/Rpacks/RTNsurvival/man/RTNsurvival-package.Rd
Added  /trunk/madman/Rpacks/RTNsurvival/man/TNS-class.Rd
Added  /trunk/madman/Rpacks/RTNsurvival/man/TNS.data.Rd
Added  /trunk/madman/Rpacks/RTNsurvival/man/tnsCox-methods.Rd
Added  /trunk/madman/Rpacks/RTNsurvival/man/tnsGSEA2-methods.Rd
Added  /trunk/madman/Rpacks/RTNsurvival/man/tnsGet-methods.Rd
Added  /trunk/madman/Rpacks/RTNsurvival/man/tnsKM-methods.Rd
Added  /trunk/madman/Rpacks/RTNsurvival/man/tnsPlotGSEA2.Rd
Added  /trunk/madman/Rpacks/RTNsurvival/man/tnsPreprocess-methods.Rd
Added  /trunk/madman/Rpacks/RTNsurvival/tests
Added  /trunk/madman/Rpacks/RTNsurvival/tests/runTests.R
Added  /trunk/madman/Rpacks/RTNsurvival/vignettes
Added  /trunk/madman/Rpacks/RTNsurvival/vignettes/RTNsurvival.Rmd
Added  /trunk/madman/Rpacks/RTNsurvival/vignettes/bibliography.bib
Added  /trunk/madman/Rpacks/RTNsurvival/vignettes/figures
Added  /trunk/madman/Rpacks/RTNsurvival/vignettes/figures/FOXM1survplot.png
Added  /trunk/madman/Rpacks/RTNsurvival/vignettes/figures/MB-5115_FOXM1.png
Added  /trunk/madman/Rpacks/RTNsurvival/vignettes/figures/coxplot.png
Added  /trunk/madman/Rpacks/RTNsurvival/vignettes/figures/dES_heatmap.png
Added  /trunk/madman/Rpacks/Scale4C
Added  /trunk/madman/Rpacks/Scale4C/DESCRIPTION
Added  /trunk/madman/Rpacks/Scale4C/NAMESPACE
Added  /trunk/madman/Rpacks/Scale4C/R
Added  /trunk/madman/Rpacks/Scale4C/R/AllClasses.r
Added  /trunk/madman/Rpacks/Scale4C/R/AllGenerics.r
Added  /trunk/madman/Rpacks/Scale4C/R/calculateFingerprintMap.r
Added  /trunk/madman/Rpacks/Scale4C/R/calculateScaleSpace.r
Added  /trunk/madman/Rpacks/Scale4C/R/findSingularities.r
Added  /trunk/madman/Rpacks/Scale4C/R/importBasic4CseqData.r
Added  /trunk/madman/Rpacks/Scale4C/R/methods-Scale4C.r
Added  /trunk/madman/Rpacks/Scale4C/R/outputScaleSpaceTree.r
Added  /trunk/madman/Rpacks/Scale4C/R/plotInflectionPoints.r
Added  /trunk/madman/Rpacks/Scale4C/R/plotTesselation.r
Added  /trunk/madman/Rpacks/Scale4C/R/plotTraceback.r
Added  /trunk/madman/Rpacks/Scale4C/R/traceContour.r
Added  /trunk/madman/Rpacks/Scale4C/data
Added  /trunk/madman/Rpacks/Scale4C/data/liverData.RData
Added  /trunk/madman/Rpacks/Scale4C/data/liverDataVP.RData
Added  /trunk/madman/Rpacks/Scale4C/inst
Added  /trunk/madman/Rpacks/Scale4C/inst/NEWS
Added  /trunk/madman/Rpacks/Scale4C/inst/extdata
Added  /trunk/madman/Rpacks/Scale4C/inst/extdata/liverData.csv
Added  /trunk/madman/Rpacks/Scale4C/inst/extdata/vp.txt
Added  /trunk/madman/Rpacks/Scale4C/man
Added  /trunk/madman/Rpacks/Scale4C/man/Scale4C-class.Rd
Added  /trunk/madman/Rpacks/Scale4C/man/Scale4C.Rd
Added  /trunk/madman/Rpacks/Scale4C/man/addPointsOfInterest.Rd
Added  /trunk/madman/Rpacks/Scale4C/man/calculateFingerprintMap.Rd
Added  /trunk/madman/Rpacks/Scale4C/man/calculateScaleSpace.Rd
Added  /trunk/madman/Rpacks/Scale4C/man/findSingularities.Rd
Added  /trunk/madman/Rpacks/Scale4C/man/importBasic4CseqData.Rd
Added  /trunk/madman/Rpacks/Scale4C/man/liverData.Rd
Added  /trunk/madman/Rpacks/Scale4C/man/liverDataVP.Rd
Added  /trunk/madman/Rpacks/Scale4C/man/outputScaleSpaceTree.Rd
Added  /trunk/madman/Rpacks/Scale4C/man/plotInflectionPoints.Rd
Added  /trunk/madman/Rpacks/Scale4C/man/plotTesselation.Rd
Added  /trunk/madman/Rpacks/Scale4C/man/plotTraceback.Rd
Added  /trunk/madman/Rpacks/Scale4C/vignettes
Added  /trunk/madman/Rpacks/Scale4C/vignettes/images
Added  /trunk/madman/Rpacks/Scale4C/vignettes/images/Stadhouders_FL_Prom_traceback_1000_liverData.pdf
Added  /trunk/madman/Rpacks/Scale4C/vignettes/images/Stadhouders_FL_Prom_traceback_2000_liverData.pdf
Added  /trunk/madman/Rpacks/Scale4C/vignettes/images/Stadhouders_FL_Prom_traceback_2000_liverDataVP.pdf
Added  /trunk/madman/Rpacks/Scale4C/vignettes/images/Stadhouders_FL_Prom_traceback_2500_liverData.pdf
Added  /trunk/madman/Rpacks/Scale4C/vignettes/images/Stadhouders_FL_Prom_traceback_2500_liverDataVP.pdf
Added  /trunk/madman/Rpacks/Scale4C/vignettes/images/Stadhouders_FL_Prom_traceback_500_liverData.pdf
Added  /trunk/madman/Rpacks/Scale4C/vignettes/vignette.Rnw
Modified  /trunk/madman/Rpacks/bioc_3.6.manifest
Added  /trunk/madman/Rpacks/coexnet
Added  /trunk/madman/Rpacks/coexnet/.Rbuildignore
Added  /trunk/madman/Rpacks/coexnet/.gitignore
Added  /trunk/madman/Rpacks/coexnet/DESCRIPTION
Added  /trunk/madman/Rpacks/coexnet/NAMESPACE
Added  /trunk/madman/Rpacks/coexnet/R
Added  /trunk/madman/Rpacks/coexnet/R/CCP.R
Added  /trunk/madman/Rpacks/coexnet/R/cofVar.R
Added  /trunk/madman/Rpacks/coexnet/R/createNet.R
Added  /trunk/madman/Rpacks/coexnet/R/data.R
Added  /trunk/madman/Rpacks/coexnet/R/difExprs.R
Added  /trunk/madman/Rpacks/coexnet/R/exprMat.R
Added  /trunk/madman/Rpacks/coexnet/R/findThreshold.R
Added  /trunk/madman/Rpacks/coexnet/R/geneSymbol.R
Added  /trunk/madman/Rpacks/coexnet/R/getAffy.R
Added  /trunk/madman/Rpacks/coexnet/R/getInfo.R
Added  /trunk/madman/Rpacks/coexnet/R/internalfunctions.R
Added  /trunk/madman/Rpacks/coexnet/R/ppiNet.R
Added  /trunk/madman/Rpacks/coexnet/R/sharedComponents.R
Added  /trunk/madman/Rpacks/coexnet/README.md
Added  /trunk/madman/Rpacks/coexnet/coexnet.Rproj
Added  /trunk/madman/Rpacks/coexnet/data
Added  /trunk/madman/Rpacks/coexnet/data/info.rda
Added  /trunk/madman/Rpacks/coexnet/data/net1.rda
Added  /trunk/madman/Rpacks/coexnet/data/net2.rda
Added  /trunk/madman/Rpacks/coexnet/inst
Added  /trunk/madman/Rpacks/coexnet/inst/NEWS
Added  /trunk/madman/Rpacks/coexnet/inst/extdata
Added  /trunk/madman/Rpacks/coexnet/inst/extdata/GPL2025.soft
Added  /trunk/madman/Rpacks/coexnet/inst/extdata/GSE1234
Added  /trunk/madman/Rpacks/coexnet/inst/extdata/GSE1234/GSM1070311_1181.CEL.gz
Added  /trunk/madman/Rpacks/coexnet/inst/extdata/GSE1234/filelist.txt
Added  /trunk/madman/Rpacks/coexnet/inst/extdata/expression_example.txt
Added  /trunk/madman/Rpacks/coexnet/inst/extdata/ppi.txt
Added  /trunk/madman/Rpacks/coexnet/inst/unitTests
Added  /trunk/madman/Rpacks/coexnet/inst/unitTests/test_coexnet.R
Added  /trunk/madman/Rpacks/coexnet/man
Added  /trunk/madman/Rpacks/coexnet/man/CCP.Rd
Added  /trunk/madman/Rpacks/coexnet/man/affy.Rd
Added  /trunk/madman/Rpacks/coexnet/man/cofVar.Rd
Added  /trunk/madman/Rpacks/coexnet/man/createNet.Rd
Added  /trunk/madman/Rpacks/coexnet/man/difExprs.Rd
Added  /trunk/madman/Rpacks/coexnet/man/exprMat.Rd
Added  /trunk/madman/Rpacks/coexnet/man/findThreshold.Rd
Added  /trunk/madman/Rpacks/coexnet/man/geneSymbol.Rd
Added  /trunk/madman/Rpacks/coexnet/man/getAffy.Rd
Added  /trunk/madman/Rpacks/coexnet/man/getInfo.Rd
Added  /trunk/madman/Rpacks/coexnet/man/info.Rd
Added  /trunk/madman/Rpacks/coexnet/man/net1.Rd
Added  /trunk/madman/Rpacks/coexnet/man/net2.Rd
Added  /trunk/madman/Rpacks/coexnet/man/ppiNet.Rd
Added  /trunk/madman/Rpacks/coexnet/man/sharedComponents.Rd
Added  /trunk/madman/Rpacks/coexnet/tests
Added  /trunk/madman/Rpacks/coexnet/tests/runTests.R
Added  /trunk/madman/Rpacks/coexnet/vignettes
Added  /trunk/madman/Rpacks/coexnet/vignettes/coexnet.Rmd
Added  /trunk/madman/Rpacks/coexnet/vignettes/coexnet.pdf
Added  /trunk/madman/Rpacks/zinbwave
Added  /trunk/madman/Rpacks/zinbwave/.Rbuildignore
Added  /trunk/madman/Rpacks/zinbwave/.gitignore
Added  /trunk/madman/Rpacks/zinbwave/.travis.yml
Added  /trunk/madman/Rpacks/zinbwave/DESCRIPTION
Added  /trunk/madman/Rpacks/zinbwave/NAMESPACE
Added  /trunk/madman/Rpacks/zinbwave/R
Added  /trunk/madman/Rpacks/zinbwave/R/AllClasses.R
Added  /trunk/madman/Rpacks/zinbwave/R/AllGenerics.R
Added  /trunk/madman/Rpacks/zinbwave/R/helper_methods.R
Added  /trunk/madman/Rpacks/zinbwave/R/orthogonalizeTraceNorm.R
Added  /trunk/madman/Rpacks/zinbwave/R/solveRidgeRegression.R
Added  /trunk/madman/Rpacks/zinbwave/R/zinb_fit.R
Added  /trunk/madman/Rpacks/zinbwave/README.md
Added  /trunk/madman/Rpacks/zinbwave/data
Added  /trunk/madman/Rpacks/zinbwave/data/toydata.rda
Added  /trunk/madman/Rpacks/zinbwave/inst
Added  /trunk/madman/Rpacks/zinbwave/inst/CITATION
Added  /trunk/madman/Rpacks/zinbwave/inst/NEWS
Added  /trunk/madman/Rpacks/zinbwave/man
Added  /trunk/madman/Rpacks/zinbwave/man/ZinbModel-class.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getAlpha_mu.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getAlpha_pi.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getBeta_mu.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getBeta_pi.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getEpsilon_W.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getEpsilon_alpha.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getEpsilon_beta_mu.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getEpsilon_beta_pi.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getEpsilon_gamma_mu.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getEpsilon_gamma_pi.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getEpsilon_zeta.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getGamma_mu.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getGamma_pi.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getLogMu.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getLogitPi.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getMu.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getPhi.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getPi.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getTheta.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getV_mu.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getV_pi.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getW.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getX_mu.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getX_pi.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/getZeta.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/loglik.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/nFactors.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/nFeatures.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/nSamples.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/orthogonalizeTraceNorm.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/penalty.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/solveRidgeRegression.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/toydata.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/zinb.loglik.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/zinb.loglik.dispersion.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/zinb.loglik.dispersion.gradient.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/zinb.loglik.regression.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/zinb.loglik.regression.gradient.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/zinb.regression.parseModel.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/zinbFit.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/zinbInitialize.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/zinbModel.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/zinbOptimize.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/zinbOptimizeDispersion.Rd
Added  /trunk/madman/Rpacks/zinbwave/man/zinbSim.Rd
Added  /trunk/madman/Rpacks/zinbwave/tests
Added  /trunk/madman/Rpacks/zinbwave/tests/testthat
Added  /trunk/madman/Rpacks/zinbwave/tests/testthat/test_accessors.R
Added  /trunk/madman/Rpacks/zinbwave/tests/testthat/test_design.R
Added  /trunk/madman/Rpacks/zinbwave/tests/testthat/test_value.R
Added  /trunk/madman/Rpacks/zinbwave/tests/testthat.R
Added  /trunk/madman/Rpacks/zinbwave/vignettes
Added  /trunk/madman/Rpacks/zinbwave/vignettes/biblio.bib
Added  /trunk/madman/Rpacks/zinbwave/vignettes/intro.Rmd
Added  /trunk/madman/Rpacks/zinbwave/zinb.Rproj
Adding Scale4C, zinbwave, RTNsurvival, coexnet
Revision: 130618
Author: w.luo
Date: 2017-06-22T16:41:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/pathview/R/cpdname2kegg.R
new release version 1.17.1 with cpdname2kegg.R updated
Revision: 130615
Author: b.uyar
Date: 2017-06-22T15:32:05+00:00
Paths:
Added  /trunk/madman/Rpacks/RCAS/README.md
added README file

From: Bora Uyar <bora.uyar@embl.de>
Revision: 130612
Author: k.horan
Date: 2017-06-22T14:59:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/ChemmineR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChemmineR/NAMESPACE
Modified  /trunk/madman/Rpacks/ChemmineR/R/draw_sdf.R
Modified  /trunk/madman/Rpacks/ChemmineR/vignettes/ChemmineR.Rmd
Merge branch 'master' into devel

From: khoran <khoran@cs.ucr.edu>
Revision: 130611
Author: p.angerer
Date: 2017-06-22T13:50:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/destiny/DESCRIPTION
Modified  /trunk/madman/Rpacks/destiny/R/diffusionmap.r
Modified  /trunk/madman/Rpacks/destiny/R/eig_decomp.r
allow n_eigs=0 again
Revision: 130610
Author: p.angerer
Date: 2017-06-22T13:39:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/destiny/R/aaa.r
Modified  /trunk/madman/Rpacks/destiny/src/RcppExports.cpp
R 3.4
Revision: 130609
Author: r.castelo
Date: 2017-06-22T12:53:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/GSVA/DESCRIPTION
Modified  /trunk/madman/Rpacks/GSVA/NAMESPACE
Added  /trunk/madman/Rpacks/GSVA/R/methods-shinyapp.R
Added  /trunk/madman/Rpacks/GSVA/man/igsva.Rd
Added first version of a GSVA shiny app.
Revision: 130608
Author: v.kim
Date: 2017-06-22T11:26:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/lpsymphony/DESCRIPTION
Modified  /trunk/madman/Rpacks/lpsymphony/configure
With this configure script compile source using Clang/Clang++ on Mac OS X >= 10.11 (El Capitan and higher)
Revision: 130607
Author: a.lun
Date: 2017-06-22T10:48:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/csaw/DESCRIPTION
Modified  /trunk/madman/Rpacks/csaw/NAMESPACE
Deleted  /trunk/madman/Rpacks/csaw/R/paramList.R
Modified  /trunk/madman/Rpacks/csaw/R/windowCounts.R
Deleted  /trunk/madman/Rpacks/csaw/man/paramList.Rd
Cleaned up windowCounts, removed paramList.
Revision: 130605
Author: a.lun
Date: 2017-06-22T09:18:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/scran/tests/testthat/test-convert.R
Fixed check in convert tests.
Revision: 130604
Author: a.lun
Date: 2017-06-22T09:10:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/scran/DESCRIPTION
Modified  /trunk/madman/Rpacks/scran/R/findMarkers.R
Modified  /trunk/madman/Rpacks/scran/R/mnnCorrect.R
Modified  /trunk/madman/Rpacks/scran/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/scran/man/findMarkers.Rd
Modified  /trunk/madman/Rpacks/scran/man/mnnCorrect.Rd
Modified  /trunk/madman/Rpacks/scran/tests/testthat/test-markers.R
Added up/down option to findMarkers, bug fix to mnnCorrect.

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