Subversion Logs

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

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Revision: 120537
Author: h.bengtsson
Date: 2016-08-27T16:12:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/illuminaio/DESCRIPTION
Modified  /trunk/madman/Rpacks/illuminaio/NEWS
Added  /trunk/madman/Rpacks/illuminaio/R/zzz.R
Modified  /trunk/madman/Rpacks/illuminaio/README.md
Modified  /trunk/madman/Rpacks/illuminaio/vignettes/EncryptedFormat.Rnw
git-bioc: Copied updates from Git master branch to Bioconductor SVN

From: hb <hb@aroma-project.org>
Revision: 120536
Author: m.love
Date: 2016-08-27T12:49:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
Modified  /trunk/madman/Rpacks/DESeq2/R/AllClasses.R
fix nrow != ncol error msg
Revision: 120533
Author: a.mayakonda
Date: 2016-08-27T00:39:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/maftools/R/oncoplot.R
bug fix
Revision: 120531
Author: jspidlen
Date: 2016-08-26T21:35:43+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/man/calc_mean_sd_capture.Rd
Modified  /trunk/madman/Rpacks/flowQB/man/fit_led.Rd
Modified  /trunk/madman/Rpacks/flowQB/man/peak_gate-methods.Rd
Modified  /trunk/madman/Rpacks/flowQB/man/pick_parameters-methods.Rd
Modified  /trunk/madman/Rpacks/flowQB/man/qb_from_fits.Rd
Modified  /trunk/madman/Rpacks/flowQB/man/split_in_two-methods.Rd
Modified  /trunk/madman/Rpacks/flowQB/vignettes/flowQBVignettes.Rnw
This should now be complete with all documentation and all tests and checks passing without any warnings or considerations.
Revision: 120529
Author: c.warden
Date: 2016-08-26T21:02:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/COHCAP/CHANGES
Modified  /trunk/madman/Rpacks/COHCAP/DESCRIPTION
Modified  /trunk/madman/Rpacks/COHCAP/R/COHCAP.avg.by.island.R
Modified  /trunk/madman/Rpacks/COHCAP/R/COHCAP.site.R
Modified  /trunk/madman/Rpacks/COHCAP/inst/Perl/integrate_site.pl
output and delta-beta modifications
Revision: 120528
Author: mtmorgan
Date: 2016-08-26T20:37:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/DEGraph/DESCRIPTION
Modified  /trunk/madman/Rpacks/DEGraph/inst/CITATION
Modified  /trunk/madman/Rpacks/ENCODExplorer/DESCRIPTION
Modified  /trunk/madman/Rpacks/NOISeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/NOISeq/inst/CITATION
Modified  /trunk/madman/Rpacks/clippda/DESCRIPTION
Modified  /trunk/madman/Rpacks/switchBox/DESCRIPTION
Modified  /trunk/madman/Rpacks/switchBox/inst/CITATION
update DESCRIPTION / CITATION files

- malformed fields prevented citation() or readCitationFile() from
  forming correct citation without warnings / errors
Revision: 120527
Author: mtmorgan
Date: 2016-08-26T20:32:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/biocViews/DESCRIPTION
Modified  /trunk/madman/Rpacks/biocViews/R/repository.R
more robusts extractCitations()

- tryCatch() each tarball
- check untar() results
- parse DESCRIPTION for enconding
- output only on error / warning
- structure output
Revision: 120526
Author: m.jiang
Date: 2016-08-26T20:31:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowWorkspace/tests/testthat/InternalTestSuite.R
bump
Revision: 120525
Author: m.jiang
Date: 2016-08-26T20:31:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/inst/cppTest/unitTest/gatingSet_test.cpp
Modified  /trunk/madman/Rpacks/flowWorkspace/src/R_GatingHierarchy.cpp
Modified  /trunk/madman/Rpacks/flowWorkspace/tests/testthat/InternalTestSuite.R
extend the gates after the transformation. #36
Revision: 120524
Author: l.zhu
Date: 2016-08-26T20:26:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/GUIDEseq/DESCRIPTION
added biocView CRISPR
Revision: 120523
Author: l.zhu
Date: 2016-08-26T20:25:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
added biocView CRISPR
Revision: 120522
Author: mtmorgan
Date: 2016-08-26T19:47:21+00:00
Paths:
Added  /trunk/madman/Rpacks/Anaquin
Added  /trunk/madman/Rpacks/Anaquin/DESCRIPTION
Added  /trunk/madman/Rpacks/Anaquin/NAMESPACE
Added  /trunk/madman/Rpacks/Anaquin/R
Added  /trunk/madman/Rpacks/Anaquin/R/LOQ.R
Added  /trunk/madman/Rpacks/Anaquin/R/anaquin.R
Added  /trunk/madman/Rpacks/Anaquin/R/graphics.R
Added  /trunk/madman/Rpacks/Anaquin/R/plotLODR.R
Added  /trunk/madman/Rpacks/Anaquin/R/plotLinear.R
Added  /trunk/madman/Rpacks/Anaquin/R/plotLogistic.R
Added  /trunk/madman/Rpacks/Anaquin/R/plotROC.R
Added  /trunk/madman/Rpacks/Anaquin/README.md
Added  /trunk/madman/Rpacks/Anaquin/data
Added  /trunk/madman/Rpacks/Anaquin/data/mixtureA.rda
Added  /trunk/madman/Rpacks/Anaquin/data/mixtureB.rda
Added  /trunk/madman/Rpacks/Anaquin/data/mixtureF.rda
Added  /trunk/madman/Rpacks/Anaquin/data/seqCuffcompare.rda
Added  /trunk/madman/Rpacks/Anaquin/data/seqCufflinks.rda
Added  /trunk/madman/Rpacks/Anaquin/data/seqDESeq2.rda
Added  /trunk/madman/Rpacks/Anaquin/inst
Added  /trunk/madman/Rpacks/Anaquin/inst/CITATION
Added  /trunk/madman/Rpacks/Anaquin/inst/NEWS
Added  /trunk/madman/Rpacks/Anaquin/man
Added  /trunk/madman/Rpacks/Anaquin/man/AnaquinData.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/analysis.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/input.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/isoformsToGenes.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/label.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/measured.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/mixtureA.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/mixtureB.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/mixtureF.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/plotLODR.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/plotLinear.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/plotLogistic.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/plotROC.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/pval.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/qval.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/ratio.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/score.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/seqCuffcompare.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/seqCufflinks.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/seqDESeq2.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/seqs.Rd
Added  /trunk/madman/Rpacks/Anaquin/man/std.Rd
Added  /trunk/madman/Rpacks/Anaquin/tests
Added  /trunk/madman/Rpacks/Anaquin/tests/tAnaquin.R
Added  /trunk/madman/Rpacks/Anaquin/tests/tPlotLODR.R
Added  /trunk/madman/Rpacks/Anaquin/tests/tPlotLinear.R
Added  /trunk/madman/Rpacks/Anaquin/tests/tPlotLogistic.R
Added  /trunk/madman/Rpacks/Anaquin/tests/tPlotROC.R
Added  /trunk/madman/Rpacks/Anaquin/vignettes
Added  /trunk/madman/Rpacks/Anaquin/vignettes/Anaquin.Rmd
Added  /trunk/madman/Rpacks/Anaquin/vignettes/AnaquinWorkflow.pdf
Added  /trunk/madman/Rpacks/YAPSA
Added  /trunk/madman/Rpacks/YAPSA/CONTRIBUTORS
Added  /trunk/madman/Rpacks/YAPSA/DESCRIPTION
Added  /trunk/madman/Rpacks/YAPSA/LICENSE.txt
Added  /trunk/madman/Rpacks/YAPSA/NAMESPACE
Added  /trunk/madman/Rpacks/YAPSA/NEWS
Added  /trunk/madman/Rpacks/YAPSA/R
Added  /trunk/madman/Rpacks/YAPSA/R/LCD.R
Added  /trunk/madman/Rpacks/YAPSA/R/SMC.R
Added  /trunk/madman/Rpacks/YAPSA/R/basic_functions.R
Added  /trunk/madman/Rpacks/YAPSA/R/compare_SMCs.R
Added  /trunk/madman/Rpacks/YAPSA/R/complex_functions.R
Added  /trunk/madman/Rpacks/YAPSA/R/data.R
Added  /trunk/madman/Rpacks/YAPSA/R/interact_foreign.R
Added  /trunk/madman/Rpacks/YAPSA/R/pkgname.R
Added  /trunk/madman/Rpacks/YAPSA/R/plot_functions.R
Added  /trunk/madman/Rpacks/YAPSA/README.md
Added  /trunk/madman/Rpacks/YAPSA/README_files
Added  /trunk/madman/Rpacks/YAPSA/README_files/figure-html
Added  /trunk/madman/Rpacks/YAPSA/README_files/figure-html/SMC_mut_density-1.png
Added  /trunk/madman/Rpacks/YAPSA/README_files/figure-html/apply_heatmap_exposures-1.png
Added  /trunk/madman/Rpacks/YAPSA/README_files/figure-html/cluster_PIDs_sig_info-1.png
Added  /trunk/madman/Rpacks/YAPSA/README_files/figure-html/exposures_barplot_LCD-1.png
Added  /trunk/madman/Rpacks/YAPSA/README_files/figure-html/exposures_barplot_LCD_sig_ind-1.png
Added  /trunk/madman/Rpacks/YAPSA/README_files/figure-html/exposures_barplot_abs_cutoffGen-1.png
Added  /trunk/madman/Rpacks/YAPSA/README_files/figure-html/exposures_barplot_abs_cutoffSpec-1.png
Added  /trunk/madman/Rpacks/YAPSA/README_files/figure-html/exposures_barplot_abs_cutoffZero-1.png
Added  /trunk/madman/Rpacks/YAPSA/README_files/figure-html/exposures_barplot_rel_cutoffGen-1.png
Added  /trunk/madman/Rpacks/YAPSA/README_files/figure-html/exposures_barplot_rel_cutoffSpec-1.png
Added  /trunk/madman/Rpacks/YAPSA/README_files/figure-html/exposures_barplot_rel_cutoffZero-1.png
Added  /trunk/madman/Rpacks/YAPSA/README_files/figure-html/make_rainfall_plot-1.png
Added  /trunk/madman/Rpacks/YAPSA/data
Added  /trunk/madman/Rpacks/YAPSA/data/cutoffs.rda
Added  /trunk/madman/Rpacks/YAPSA/data/exchange_colour_vector.rda
Added  /trunk/madman/Rpacks/YAPSA/data/lymphoma_Nature2013_raw.rda
Added  /trunk/madman/Rpacks/YAPSA/data/lymphoma_PID.rda
Added  /trunk/madman/Rpacks/YAPSA/data/lymphoma_cohort_LCD_results.rda
Added  /trunk/madman/Rpacks/YAPSA/data/lymphoma_test.rda
Added  /trunk/madman/Rpacks/YAPSA/data/sigs.rda
Added  /trunk/madman/Rpacks/YAPSA/data/targetCapture_cor_factors.rda
Added  /trunk/madman/Rpacks/YAPSA/inst
Added  /trunk/madman/Rpacks/YAPSA/inst/foreign
Added  /trunk/madman/Rpacks/YAPSA/inst/foreign/annotate_vcf.pl
Added  /trunk/madman/Rpacks/YAPSA/inst/foreign/kmer_frequencies.pl
Added  /trunk/madman/Rpacks/YAPSA/man
Added  /trunk/madman/Rpacks/YAPSA/man/LCD.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/LCD_complex_cutoff.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/YAPSA.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/add_annotation.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/add_as_fist_to_list.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/aggregate_exposures_by_category.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/annotate_intermut_dist_PID.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/annotate_intermut_dist_cohort.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/annotation_exposures_barplot.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/annotation_heatmap_exposures.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/attribute_nucleotide_exchanges.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/build_gene_list_for_pathway.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/compare_SMCs.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/compare_exposures.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/compare_sets.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/compare_to_catalogues.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/complex_heatmap_exposures.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/compute_comparison_stat_df.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/cosineDist.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/create_mutation_catalogue_from_VR.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/create_mutation_catalogue_from_df.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/cut_breaks_as_intervals.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/cutoffs.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/exampleYAPSA.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/exchange_colour_vector.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/exposures_barplot.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/extract_names_from_gene_list.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/find_affected_PIDs.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/get_extreme_PIDs.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/hclust_exposures.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/makeVRangesFromDataFrame.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/make_catalogue_strata_df.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/make_comparison_matrix.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/make_strata_df.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/make_subgroups_df.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/melt_exposures.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/merge_exposures.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/normalizeMotifs_otherRownames.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/normalize_df_per_dim.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/plotExchangeSpectra.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/plot_SMC.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/plot_exposures.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/plot_strata.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/repeat_df.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/run_SMC.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/run_annotate_vcf_pl.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/run_comparison_catalogues.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/run_comparison_general.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/run_kmer_frequency_correction.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/run_kmer_frequency_normalization.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/run_plot_strata_general.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/shapiro_if_possible.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/sigs.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/split_exposures_by_subgroups.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/stat_plot_subgroups.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/stat_test_SMC.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/stat_test_subgroups.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/stderrmean.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/sum_over_list_of_df.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/targetCapture_cor_factors.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/test_exposureAffected.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/test_gene_list_in_exposures.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/transform_rownames_R_to_MATLAB.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/translate_to_hg19.Rd
Added  /trunk/madman/Rpacks/YAPSA/man/trellis_rainfall_plot.Rd
Added  /trunk/madman/Rpacks/YAPSA/tests
Added  /trunk/madman/Rpacks/YAPSA/tests/testthat
Added  /trunk/madman/Rpacks/YAPSA/tests/testthat/test_LCD.R
Added  /trunk/madman/Rpacks/YAPSA/tests/testthat/test_basic_functions.R
Added  /trunk/madman/Rpacks/YAPSA/tests/testthat/test_complex_functions.R
Added  /trunk/madman/Rpacks/YAPSA/tests/testthat.R
Added  /trunk/madman/Rpacks/YAPSA/vignettes
Added  /trunk/madman/Rpacks/YAPSA/vignettes/.directory
Added  /trunk/madman/Rpacks/YAPSA/vignettes/NMF.png
Added  /trunk/madman/Rpacks/YAPSA/vignettes/YAPSA.Rmd
Modified  /trunk/madman/Rpacks/bioc_3.4.manifest
Added  /trunk/madman/Rpacks/eegc
Added  /trunk/madman/Rpacks/eegc/DESCRIPTION
Added  /trunk/madman/Rpacks/eegc/NAMESPACE
Added  /trunk/madman/Rpacks/eegc/R
Added  /trunk/madman/Rpacks/eegc/R/barplotEnrich.R
Added  /trunk/madman/Rpacks/eegc/R/categorizeGene.R
Added  /trunk/madman/Rpacks/eegc/R/densityPlot.R
Added  /trunk/madman/Rpacks/eegc/R/diffGene.R
Added  /trunk/madman/Rpacks/eegc/R/dotPercentage.R
Added  /trunk/madman/Rpacks/eegc/R/eegc.R
Added  /trunk/madman/Rpacks/eegc/R/enrichment.R
Added  /trunk/madman/Rpacks/eegc/R/functionEnrich.R
Added  /trunk/madman/Rpacks/eegc/R/grnPlot.R
Added  /trunk/madman/Rpacks/eegc/R/heatmapPlot.R
Added  /trunk/madman/Rpacks/eegc/R/markerScatter.R
Added  /trunk/madman/Rpacks/eegc/R/networkAnalyze.R
Added  /trunk/madman/Rpacks/eegc/README.md
Added  /trunk/madman/Rpacks/eegc/data
Added  /trunk/madman/Rpacks/eegc/data/SandlerFPKM.rda
Added  /trunk/madman/Rpacks/eegc/data/cate.gene.rda
Added  /trunk/madman/Rpacks/eegc/data/cate.ratio.rda
Added  /trunk/madman/Rpacks/eegc/data/diffgene.genes.rda
Added  /trunk/madman/Rpacks/eegc/data/expr.filter.rda
Added  /trunk/madman/Rpacks/eegc/data/goenrich.rda
Added  /trunk/madman/Rpacks/eegc/data/human.gene.rda
Added  /trunk/madman/Rpacks/eegc/data/human.grn.rda
Added  /trunk/madman/Rpacks/eegc/data/human.tf.rda
Added  /trunk/madman/Rpacks/eegc/data/markers.rda
Added  /trunk/madman/Rpacks/eegc/data/mouse.gene.rda
Added  /trunk/madman/Rpacks/eegc/data/mouse.grn.rda
Added  /trunk/madman/Rpacks/eegc/data/mouse.tf.rda
Added  /trunk/madman/Rpacks/eegc/data/tissueGenes.rda
Added  /trunk/madman/Rpacks/eegc/data/tissueGroup.rda
Added  /trunk/madman/Rpacks/eegc/inst
Added  /trunk/madman/Rpacks/eegc/man
Added  /trunk/madman/Rpacks/eegc/man/SandlerFPKM.Rd
Added  /trunk/madman/Rpacks/eegc/man/barplotEnrich.Rd
Added  /trunk/madman/Rpacks/eegc/man/cate.gene.Rd
Added  /trunk/madman/Rpacks/eegc/man/cate.ratio.Rd
Added  /trunk/madman/Rpacks/eegc/man/categorizeGene.Rd
Added  /trunk/madman/Rpacks/eegc/man/densityPlot.Rd
Added  /trunk/madman/Rpacks/eegc/man/diffGene.Rd
Added  /trunk/madman/Rpacks/eegc/man/diffgene.genes.Rd
Added  /trunk/madman/Rpacks/eegc/man/dotPercentage.Rd
Added  /trunk/madman/Rpacks/eegc/man/eegc.Rd
Added  /trunk/madman/Rpacks/eegc/man/enrichment.Rd
Added  /trunk/madman/Rpacks/eegc/man/expr.filter.Rd
Added  /trunk/madman/Rpacks/eegc/man/functionEnrich.Rd
Added  /trunk/madman/Rpacks/eegc/man/goenrich.Rd
Added  /trunk/madman/Rpacks/eegc/man/grnPlot.Rd
Added  /trunk/madman/Rpacks/eegc/man/heatmapPlot.Rd
Added  /trunk/madman/Rpacks/eegc/man/human.gene.Rd
Added  /trunk/madman/Rpacks/eegc/man/human.grn.Rd
Added  /trunk/madman/Rpacks/eegc/man/human.tf.Rd
Added  /trunk/madman/Rpacks/eegc/man/markerScatter.Rd
Added  /trunk/madman/Rpacks/eegc/man/markers.Rd
Added  /trunk/madman/Rpacks/eegc/man/mouse.gene.Rd
Added  /trunk/madman/Rpacks/eegc/man/mouse.grn.Rd
Added  /trunk/madman/Rpacks/eegc/man/mouse.tf.Rd
Added  /trunk/madman/Rpacks/eegc/man/networkAnalyze.Rd
Added  /trunk/madman/Rpacks/eegc/man/tissueGenes.Rd
Added  /trunk/madman/Rpacks/eegc/man/tissueGroup.Rd
Added  /trunk/madman/Rpacks/eegc/vignettes
Added  /trunk/madman/Rpacks/eegc/vignettes/eegc.Rnw
Added  /trunk/madman/Rpacks/geneAttribution
Added  /trunk/madman/Rpacks/geneAttribution/DESCRIPTION
Added  /trunk/madman/Rpacks/geneAttribution/NAMESPACE
Added  /trunk/madman/Rpacks/geneAttribution/R
Added  /trunk/madman/Rpacks/geneAttribution/R/geneAttribution.R
Added  /trunk/madman/Rpacks/geneAttribution/README.md
Added  /trunk/madman/Rpacks/geneAttribution/inst
Added  /trunk/madman/Rpacks/geneAttribution/inst/NEWS
Added  /trunk/madman/Rpacks/geneAttribution/inst/extdata
Added  /trunk/madman/Rpacks/geneAttribution/inst/extdata/eqtlHaplotypeBlocks.b38.bed
Added  /trunk/madman/Rpacks/geneAttribution/inst/extdata/hiCRegions.b38.bed
Added  /trunk/madman/Rpacks/geneAttribution/man
Added  /trunk/madman/Rpacks/geneAttribution/man/geneAttribution.Rd
Added  /trunk/madman/Rpacks/geneAttribution/man/geneModels.Rd
Added  /trunk/madman/Rpacks/geneAttribution/man/loadBed.Rd
Added  /trunk/madman/Rpacks/geneAttribution/man/normP.Rd
Added  /trunk/madman/Rpacks/geneAttribution/tests
Added  /trunk/madman/Rpacks/geneAttribution/tests/testthat
Added  /trunk/madman/Rpacks/geneAttribution/tests/testthat/testGeneAttribution.R
Added  /trunk/madman/Rpacks/geneAttribution/tests/testthat.R
Added  /trunk/madman/Rpacks/geneAttribution/vignettes
Added  /trunk/madman/Rpacks/geneAttribution/vignettes/geneAttribution.Rmd
Adding Anaquin, eegc, YAPSA, geneAttribution
Revision: 120521
Author: m.riester
Date: 2016-08-26T19:47:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/R/PureCN-internal.R
Modified  /trunk/madman/Rpacks/PureCN/R/runAbsoluteCN.R
Modified  /trunk/madman/Rpacks/PureCN/man/runAbsoluteCN.Rd
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Added max.coverage.vcf argument.
Revision: 120520
Author: h.bengtsson
Date: 2016-08-26T19:09:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/illuminaio/NEWS
git-bioc: Copied updates from Git master branch to Bioconductor SVN

From: hb <hb@aroma-project.org>
Revision: 120517
Author: hpages
Date: 2016-08-26T17:55:04+00:00
Paths:
Added  /trunk/madman/Rpacks/CellMapper/.BBSoptions
Force installation of package on build system in order to break chicken-egg
situation with CellMapperData.
Revision: 120516
Author: l.zhu
Date: 2016-08-26T17:35:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/GUIDEseq/R/GUIDEseqAnalysis.R
Modified  /trunk/madman/Rpacks/GUIDEseq/man/GUIDEseqAnalysis.Rd
preset some of the parameters in GUIDEseqAnalysis as integer
Revision: 120515
Author: a.johnston
Date: 2016-08-26T17:02:49+00:00
Paths:
Modified  /trunk/madman/Rpacks/SMITE/DESCRIPTION
merge_conflicts

Merge branch 'master' into devel

* master:
  Version bump to trigger package rebuilding now that purl()'ing issue has been correctly identified. knitr does not create purl()'ed (Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which the build system was setting. Now it's not set, so these .R files are now created. See https://github.com/yihui/knitr/issues/1212 for more.
  Bump version of all packages that use knitr for vignettes. This is because of an issue (now fixed) in knitr which failed to create purl()'ed R files from vignette sources and include them in the package. This version bump will cause these packages to propagate with those R files included.
  bump version after creating 3.3 branch
  Bump versions prior to creation of 3.3 branch
  fixed dependency issue that prevented the vignette from loading
  Fixed vignette error in CMD check r
  remove duplicate info
  Added PI as Author
  Added PI as Author
  Added PI as Author
  Added PI as Author
  git_fix2
  git_fix2
  svn_git Fix

# Conflicts:
#	DESCRIPTION
#	R/SMITE.R

From: Andrew Johnston <Andrew.Johnston@med.einstein.yu.edu>
Revision: 120514
Author: l.zhu
Date: 2016-08-26T16:45:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/CRISPRseek/DESCRIPTION
Modified  /trunk/madman/Rpacks/CRISPRseek/R/compare2Sequences.R
Modified  /trunk/madman/Rpacks/CRISPRseek/R/writeHits.R
fixed a bug for 5prime PAM in compare2Sequences
Revision: 120513
Author: m.boenn
Date: 2016-08-26T16:01:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/geecc/DESCRIPTION
Modified  /trunk/madman/Rpacks/geecc/NAMESPACE
Modified  /trunk/madman/Rpacks/geecc/R/zzz.R
Modified  /trunk/madman/Rpacks/geecc/man/plotConCub.Rd
Modified  /trunk/madman/Rpacks/geecc/man/runConCub.Rd
should pass BUILD now, second try
Revision: 120512
Author: r.cavalcante
Date: 2016-08-26T15:37:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/README.md
Update README.md

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120511
Author: r.cavalcante
Date: 2016-08-26T15:20:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/NEWS
Update NEWS

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120510
Author: r.cavalcante
Date: 2016-08-26T15:20:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/README.md
Include coveralls badge in README

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120509
Author: r.cavalcante
Date: 2016-08-26T15:20:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_dist_to_tss.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_gene_coverage.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_spline_length.R
Update collate in DESCRIPTION

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120508
Author: r.cavalcante
Date: 2016-08-26T15:20:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/NAMESPACE
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich_package_doc.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_dist_to_tss.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_gene_coverage.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_spline_length.R
Modified  /trunk/madman/Rpacks/chipenrich/R/supported.R
Modified  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.html
Modified  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_peak_input.R
Fix supported_*() checks and more

* Forgot to change the checks in chipenrich.R, plot_dist_to_tss.R,
plot_gene_coverage.R, and plot_spline_length.R to match new data.frame
output.
* Now checks combinations of genome, organism, locusdef, genesets,
read_lengths.
* Need to remove 'mer' from read_lengths for checks
* Added stringr::str_sub() to clarify function sources.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120507
Author: r.cavalcante
Date: 2016-08-26T15:20:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_gene_coverage.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_spline_length.R
Modified  /trunk/madman/Rpacks/chipenrich/R/supported.R
Modified  /trunk/madman/Rpacks/chipenrich/man/supported_genesets.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/supported_locusdefs.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/supported_read_lengths.Rd
Update documentation and checks for supported_*()

* Now that a data.frame is returned, change the documentation
description and change all checks in corresponding functions relating
to these.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120506
Author: r.cavalcante
Date: 2016-08-26T15:20:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/NAMESPACE
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich_package_doc.R
Update NAMESPACE

* Import only required functions from stringr and plyr.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120505
Author: r.cavalcante
Date: 2016-08-26T15:20:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/supported.R
Improve supported_*() functions

* Locus definitions, genesets, and read lengths (for mappability) are
not the same for all organisms. Instead of giving a character vector
the generally available options, output data.frames that specify for
which genomes/organisms the items are available.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120504
Author: r.cavalcante
Date: 2016-08-26T15:20:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_dist_to_tss.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_gene_coverage.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_spline_length.R
Load data() into their own environment

* Trying to solve the NOTE and follow data() best practices

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120503
Author: r.cavalcante
Date: 2016-08-26T15:20:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Fix NOTES in chipenrich.R

* Add :: to calls
* Use df_name$column formulation in subset() rather than column.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120502
Author: r.cavalcante
Date: 2016-08-26T15:20:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/test_gam.R
Fix NOTES in test_gam.R

* Reformat code (tabs equiv. to 4 spaces)
* Add :: to calls
* Use df_name$column formulation in subset() rather than column.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120501
Author: r.cavalcante
Date: 2016-08-26T15:20:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/test_fisher.R
Fix NOTES for test_fisher.R

* Reformat code (tabs equiv. to 4 spaces)
* Add :: to calls
* Use df_name$column formulation in subset() rather than column.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120500
Author: r.cavalcante
Date: 2016-08-26T15:19:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/test_binomial.R
Fix NOTES from binomial.R

* Reformat code (tabs equiv. to 4 spaces)
* Add :: to calls
* Use df_name$column formulation in subset() rather than column.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120499
Author: r.cavalcante
Date: 2016-08-26T15:19:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/test_approx.R
Fix NOTES from test_approx.R

* Reformat code (tabs equiv. to 4 spaces)
* Add :: to calls
* Use df_name$column formulation in subset() rather than column.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120498
Author: r.cavalcante
Date: 2016-08-26T15:19:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/setup.R
Fix NOTES from setup.R

* Reformat code (tabs equiv. to 4 spaces)
* Add :: to calls
* Use df_name$column formulation in subset() rather than column.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120497
Author: r.cavalcante
Date: 2016-08-26T15:19:45+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/randomize.R
Fix NOTES from randomize.R

* Add :: to calls
* Use df_name$column formulation in subset() rather than column.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120496
Author: r.cavalcante
Date: 2016-08-26T15:19:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Update collate in DESCRIPTION

* After removing two files related to previous commit

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120495
Author: r.cavalcante
Date: 2016-08-26T15:19:35+00:00
Paths:
Deleted  /trunk/madman/Rpacks/chipenrich/R/plot_expected_peaks.R
Deleted  /trunk/madman/Rpacks/chipenrich/R/plot_spline_mappa.R
Remove two unused plot_*() functions

* plot_expected_peaks() was not used
* plot_spline_mappa() was also not used
* Suspect both of these were functions used in development, but the
resulting plots did not make into QC.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120494
Author: r.cavalcante
Date: 2016-08-26T15:19:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.R
Modified  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.Rmd
Modified  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.html
Modified  /trunk/madman/Rpacks/chipenrich/vignettes/chipenrich-vignette.Rmd
Alter DESCRIPTION and vignette

* Remove duplicate Author block
* Remove Chee as maintainer
* Using load(chipenrich) instead of devtools::load_all() in vignette
seems to get rid of bizarre vignette warning about malformed line.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120493
Author: r.cavalcante
Date: 2016-08-26T15:19:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/man/chipenrich.Rd
Bugfix: Remove max_geneset_size from chipenrich() example

* Causes no genesets to be tested

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120492
Author: r.cavalcante
Date: 2016-08-26T15:19:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_dist_to_tss.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_gene_coverage.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_spline_length.R
Modified  /trunk/madman/Rpacks/chipenrich/man/plot_dist_to_tss.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/plot_gene_coverage.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/plot_spline_length.Rd
More peak subsetting for examples

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120491
Author: r.cavalcante
Date: 2016-08-26T15:19:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/read.R
Modified  /trunk/madman/Rpacks/chipenrich/man/chipenrich.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/load_peaks.Rd
Modified  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_assign_peaks.R
Modified  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_peaks_per_gene.R
Bugfixes

* Somehow annotatr function references were still in some tests.
* Subsetting of peaks in examples to improve runtime.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120490
Author: r.cavalcante
Date: 2016-08-26T15:19:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/read.R
Modified  /trunk/madman/Rpacks/chipenrich/R/setup.R
Modified  /trunk/madman/Rpacks/chipenrich/vignettes/chipenrich-vignette.Rmd
Subset peaks for use in vignette to reduce runtime

* Was taking > 10 min to build the package. Sad!

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120488
Author: r.cavalcante
Date: 2016-08-26T15:18:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Added  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.R
Added  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.Rmd
Added  /trunk/madman/Rpacks/chipenrich/inst/doc/chipenrich-vignette.html
Modified  /trunk/madman/Rpacks/chipenrich/man/chipenrich.Rd
Added  /trunk/madman/Rpacks/chipenrich/vignettes/chipenrich-vignette.Rmd
Deleted  /trunk/madman/Rpacks/chipenrich/vignettes/chipenrich.Rnw
Rewrite vignette in Rmarkdown and fixes

* Vignette is in Rmarkdown
* Reduced max_geneset_size in vignette and examples to speed up package
builds
* Moved FET and Binomial warning block in chipenrich.R.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120487
Author: r.cavalcante
Date: 2016-08-26T15:18:47+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/NAMESPACE
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich_package_doc.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_dist_to_tss.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_gene_coverage.R
Modified  /trunk/madman/Rpacks/chipenrich/R/plot_spline_length.R
Modified  /trunk/madman/Rpacks/chipenrich/R/read.R
Modified  /trunk/madman/Rpacks/chipenrich/R/supported.R
Modified  /trunk/madman/Rpacks/chipenrich/man/chipenrich.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/plot_dist_to_tss.Rd
Deleted  /trunk/madman/Rpacks/chipenrich/man/plot_expected_peaks.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/plot_gene_coverage.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/plot_spline_length.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/read_bedgff.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/supported_genesets.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/supported_genomes.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/supported_locusdefs.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/supported_methods.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/supported_read_lengths.Rd
roxygen2 documentation overhaul

* All exported functions are documented in roxygen2 blocks
* Fixed numerous errors in example code
* Replaced manually written .Rd manuals with roxygen2 auto-generated
versions
* Added some importFroms to the NAMESPACE
* Various code formatting changes (2 space indents to tabs (=4 spaces)
indents

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120486
Author: r.cavalcante
Date: 2016-08-26T15:18:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/assign_peaks.R
Modified  /trunk/madman/Rpacks/chipenrich/R/peaks_per_gene.R
Modified  /trunk/madman/Rpacks/chipenrich/R/read.R
Modified  /trunk/madman/Rpacks/chipenrich/man/assign_peak_segments.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/calc_peak_gene_overlap.Rd
Modified  /trunk/madman/Rpacks/chipenrich/man/num_peaks_per_gene.Rd
Fix read_bed() related items

* Add peak names since not using annotatr::read_regions() anymore.
* Fix examples to use read_bed().

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120485
Author: r.cavalcante
Date: 2016-08-26T15:18:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/NAMESPACE
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich_package_doc.R
Update NAMESPACE and DESCRIPTION

* Harmonize DESCRIPTION Imports with NAMESPACE
* Attempt to collate for chipenrich().

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120484
Author: r.cavalcante
Date: 2016-08-26T15:18:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/NAMESPACE
Modified  /trunk/madman/Rpacks/chipenrich/R/assign_peaks.R
Modified  /trunk/madman/Rpacks/chipenrich/R/read.R
Modified  /trunk/madman/Rpacks/chipenrich/man/assign_peaks.Rd
Added  /trunk/madman/Rpacks/chipenrich/man/load_peaks.Rd
Added  /trunk/madman/Rpacks/chipenrich/man/read_bed.Rd
Added  /trunk/madman/Rpacks/chipenrich/man/read_bedgff.Rd
More read_*() updates

* Fix example in assign_peaks.R to use read_bed() again.
* Make roxygen2 documentation blocks for the read_*() functions.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120483
Author: r.cavalcante
Date: 2016-08-26T15:18:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/.travis.yml
Modified  /trunk/madman/Rpacks/chipenrich/NAMESPACE
Modified  /trunk/madman/Rpacks/chipenrich/R/assign_peaks.R
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich_package_doc.R
Modified  /trunk/madman/Rpacks/chipenrich/R/read.R
Modified  /trunk/madman/Rpacks/chipenrich/R/utils.R
Modified  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_user_geneset.R
Remove annotatr import and change previous read_*() functions

* Rather than use annotatr's read_*() functions, change Ryan's original
built-in read_*() functions to output a GRanges object instead of a
list of IRanges.
* Comment out enrichment test in test_user_geneset.R because it takes
forever. Will add custom genesets with tiny test peak sets for faster
enrichment testing later.
* Alter .travis.yml to have coveralls output, and use package cache's
like annotatr.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120482
Author: r.cavalcante
Date: 2016-08-26T15:18:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/utils.R
Refactor chipenrich()

* Reorganized the blocks for clarity.
* Improved comments to distinguish what each block and component of
each block does.
* Reformatted code style to use tabs (equivalent to 4 spaces) instead
of two spaces for indenting.
* Reformatted code with more space around = and , to make more readable.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120481
Author: r.cavalcante
Date: 2016-08-26T15:18:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/NAMESPACE
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Modified  /trunk/madman/Rpacks/chipenrich/R/chipenrich_package_doc.R
Remove dplyr import

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120480
Author: r.cavalcante
Date: 2016-08-26T15:18:07+00:00
Paths:
Added  /trunk/madman/Rpacks/chipenrich/R/chipenrich.R
Deleted  /trunk/madman/Rpacks/chipenrich/R/main.R
Change main.R to chipenrich.R

* Files now contain the functions their names describe

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120479
Author: r.cavalcante
Date: 2016-08-26T15:18:01+00:00
Paths:
Added  /trunk/madman/Rpacks/chipenrich/R/constants.R
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Move constants

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120478
Author: r.cavalcante
Date: 2016-08-26T15:17:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Added  /trunk/madman/Rpacks/chipenrich/R/setup.R
Move functions to setup mappa, ldef, and genesets

* For user supplied versions

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120477
Author: r.cavalcante
Date: 2016-08-26T15:17:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Added  /trunk/madman/Rpacks/chipenrich/R/plot_expected_peaks.R
Move plot_expected_peaks() related functions

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120476
Author: r.cavalcante
Date: 2016-08-26T15:17:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Added  /trunk/madman/Rpacks/chipenrich/R/plot_spline_mappa.R
Move plot_spline_mappa() related functions

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120475
Author: r.cavalcante
Date: 2016-08-26T15:17:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Added  /trunk/madman/Rpacks/chipenrich/R/utils.R
Move utility functions

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120474
Author: r.cavalcante
Date: 2016-08-26T15:17:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Added  /trunk/madman/Rpacks/chipenrich/R/test_approx.R
Added  /trunk/madman/Rpacks/chipenrich/R/test_binomial.R
Added  /trunk/madman/Rpacks/chipenrich/R/test_fisher.R
Added  /trunk/madman/Rpacks/chipenrich/R/test_gam.R
Move test_*() functions

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120473
Author: r.cavalcante
Date: 2016-08-26T15:17:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Added  /trunk/madman/Rpacks/chipenrich/R/supported.R
Move supported_*() functions

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120472
Author: r.cavalcante
Date: 2016-08-26T15:17:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Added  /trunk/madman/Rpacks/chipenrich/R/plot_dist_to_tss.R
Move plot_dist_to_tss() related functions

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120471
Author: r.cavalcante
Date: 2016-08-26T15:17:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Added  /trunk/madman/Rpacks/chipenrich/R/plot_gene_coverage.R
Move plot_gene_coverage() related functions

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120470
Author: r.cavalcante
Date: 2016-08-26T15:17:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Added  /trunk/madman/Rpacks/chipenrich/R/randomize.R
Move randomize_*() functions

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120469
Author: r.cavalcante
Date: 2016-08-26T15:17:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Added  /trunk/madman/Rpacks/chipenrich/R/plot_spline_length.R
Move plot_spline_length() related functions

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120468
Author: r.cavalcante
Date: 2016-08-26T15:17:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Remove unused make_gpw()

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120467
Author: r.cavalcante
Date: 2016-08-26T15:16:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/NAMESPACE
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Modified  /trunk/madman/Rpacks/chipenrich/R/peaks_per_gene.R
Added  /trunk/madman/Rpacks/chipenrich/man/calc_peak_gene_overlap.Rd
Added  /trunk/madman/Rpacks/chipenrich/man/num_peaks_per_gene.Rd
Added  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_peaks_per_gene.R
Add documentation for peaks per gene functions

* Cleaned up code formatting.
* Added unit tests.
* Thinking about replacing base functions with dplyr, but not sure if
it's really worth the extra dependency.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120466
Author: r.cavalcante
Date: 2016-08-26T15:16:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Added  /trunk/madman/Rpacks/chipenrich/R/peaks_per_gene.R
Breakout peaks per gene related functions

* Refactoring in a later commit

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120465
Author: r.cavalcante
Date: 2016-08-26T15:16:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/chipenrich/DESCRIPTION
Modified  /trunk/madman/Rpacks/chipenrich/NAMESPACE
Added  /trunk/madman/Rpacks/chipenrich/R/assign_peaks.R
Added  /trunk/madman/Rpacks/chipenrich/R/chipenrich_package_doc.R
Modified  /trunk/madman/Rpacks/chipenrich/R/main.R
Added  /trunk/madman/Rpacks/chipenrich/R/read.R
Added  /trunk/madman/Rpacks/chipenrich/inst/extdata/test_assign.bed
Added  /trunk/madman/Rpacks/chipenrich/man/assign_peak_segments.Rd
Added  /trunk/madman/Rpacks/chipenrich/man/assign_peaks.Rd
Added  /trunk/madman/Rpacks/chipenrich/tests/testthat/test_assign_peaks.R
Breakout read functions and assign_*() functions

* Read functions are broken out into their own file for backwards
compatibility at the moment. Eventually, I think
annotatr::read_regions() will take their place for the flexibility.
* Using annotatr::read_regions() also gives a GRanges object with is
preferable to deal with over a data.frame or a list of IRanges per
chromosome.
* assign_peaks() and assign_peak_segments() have been refactored to use
GenomicRanges representation instead of a for loop of chromosomal
IRanges. Code is clearer.
* Documented assign_*() functions in a roxygen2 block.

From: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Revision: 120464
Author: s.wieczorek
Date: 2016-08-26T13:52:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/Prostar/DESCRIPTION
Modified  /trunk/madman/Rpacks/Prostar/NEWS
Modified  /trunk/madman/Rpacks/Prostar/inst/ProstarApp/global.R
Modified  /trunk/madman/Rpacks/Prostar/inst/ProstarApp/server.R
Modified  /trunk/madman/Rpacks/Prostar/inst/ProstarApp/ui.R
Version 1.5.3 : manage xlsx files
Revision: 120463
Author: s.wieczorek
Date: 2016-08-26T13:49:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/DAPAR/DESCRIPTION
Modified  /trunk/madman/Rpacks/DAPAR/NAMESPACE
Modified  /trunk/madman/Rpacks/DAPAR/NEWS
Modified  /trunk/madman/Rpacks/DAPAR/R/inOutFiles.R
Modified  /trunk/madman/Rpacks/DAPAR/man/writeMSnsetToExcel.Rd
Version 1.5.5 : xlsx files
Revision: 120462
Author: p.angerer
Date: 2016-08-26T13:18:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/destiny/R/diffusionmap-plotting.r
Modified  /trunk/madman/Rpacks/destiny/R/dpt_plotting.r
Modified  /trunk/madman/Rpacks/destiny/man/plot.DiffusionMap.Rd
added NAs to plots
Revision: 120461
Author: p.angerer
Date: 2016-08-26T13:18:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/destiny/ROADMAP
updated roadmap
Revision: 120460
Author: a.mayakonda
Date: 2016-08-26T11:38:29+00:00
Paths:
Modified  /trunk/madman/Rpacks/maftools/DESCRIPTION
Modified  /trunk/madman/Rpacks/maftools/R/oncoplot.R
Modified  /trunk/madman/Rpacks/maftools/R/read_maf_dt.R
Modified  /trunk/madman/Rpacks/maftools/R/subsetMaf.R
Modified  /trunk/madman/Rpacks/maftools/inst/NEWS
bug fixes
Revision: 120458
Author: l.gatto
Date: 2016-08-26T07:40:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/mzR/DESCRIPTION
Modified  /trunk/madman/Rpacks/mzR/NEWS
Modified  /trunk/madman/Rpacks/mzR/R/methods-mzRpwiz.R
Modified  /trunk/madman/Rpacks/mzR/R/zzz.R
Modified  /trunk/madman/Rpacks/mzR/README.md
Modified  /trunk/madman/Rpacks/mzR/src/Makevars
Modified  /trunk/madman/Rpacks/mzR/src/Makevars.win
Modified  /trunk/madman/Rpacks/mzR/src/RcppExports.cpp
Modified  /trunk/madman/Rpacks/mzR/src/RcppPwiz.cpp
Modified  /trunk/madman/Rpacks/mzR/src/RcppPwiz.h
Modified  /trunk/madman/Rpacks/mzR/src/RcppPwizModule.cpp
Added  /trunk/madman/Rpacks/mzR/src/boost/chrono/src
Added  /trunk/madman/Rpacks/mzR/src/boost/chrono/src/chrono.cpp
Added  /trunk/madman/Rpacks/mzR/src/boost/chrono/src/process_cpu_clocks.cpp
Added  /trunk/madman/Rpacks/mzR/src/boost/chrono/src/thread_clock.cpp
Modified  /trunk/madman/Rpacks/mzR/src/boost/regex/src/regex_raw_buffer.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/Jamroot.jam
Added  /trunk/madman/Rpacks/mzR/src/pwiz/SVN_info.txt
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/clean.bat
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/BinaryIndexStream.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/CVTranslator.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/Jamfile.jam
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/MemoryIndex.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/ParamTypes.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/ParamTypes.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/Unimod.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/UnimodTest.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/cv.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/cv.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/cvgen.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/cvtest.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/diff_std.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/obo.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/psi-ms.obo
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/common/unimod.obo
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/DefaultReaderList.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/Diff.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/DiffTest.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/IO.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/IO.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/IdentData.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/IdentData.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/IdentDataFile.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/IdentDataTest.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/Jamfile.jam
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/KwCVMap.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/KwCVMap.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/KwCVMapTest.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/MascotReader.cpp
Added  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/MascotReader.hpp
Added  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/MascotReaderTest.cpp
Added  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/MascotReaderTest.data
Added  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/MascotReaderTest.data/F003081.dat
Added  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/MascotReaderTest.data/F02.mzid.gz
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/Pep2MzIdent.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/Reader.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/Reader.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/Serializer_Text.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/Serializer_pepXML.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/Serializer_pepXML_Test.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/Serializer_protXML.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/TextWriter.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/identdata/examples.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/BinaryDataEncoder.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/ChromatogramListBase.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/ChromatogramList_mz5.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/DefaultReaderList.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/Diff.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/IO.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/IOTest.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/Jamfile.jam
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/LegacyAdapter.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/MSData.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/MSData.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/MSDataFile.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/MSDataMerger.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/MSDataTest.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/MSNumpress.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/MSNumpress.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/RAMPAdapter.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/RAMPAdapter.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/Reader.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/Reader.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/Serializer_MGF.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/Serializer_MSn.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/Serializer_mzXML.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumListBase.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumListCache.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumListCache.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumListCacheTest.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumListWrapper.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumList_BTDX.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumList_MGF.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumList_MSn.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumList_MSn_Test.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumList_mz5.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumList_mz5_Test.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumList_mzML.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumList_mzML_Test.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumList_mzXML.cpp
Added  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp
Added  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/SpectrumWorkerThreads.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/Version.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/mz5/Connection_mz5.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/mz5/Connection_mz5.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/ramp/ramp.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/msdata/ramp/ramp.h
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/proteome/AminoAcid.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/proteome/Diff.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/proteome/Digestion.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/proteome/Digestion.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/proteome/DigestionTest.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/proteome/Jamfile.jam
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/proteome/Modification.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/proteome/Peptide.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/proteome/ProteinListCache.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/proteome/ProteomeData.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/proteome/ProteomeDataFile.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/proteome/Reader.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/proteome/Serializer_FASTA.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/data/proteome/examples.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/pwiz.sln
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/pwiz.vcxproj
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/pwiz.vcxproj.filters
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/quickbuild.bat
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/chemistry/Chemistry.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/chemistry/Chemistry.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/chemistry/ChemistryData.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/chemistry/ChemistryTest.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/chemistry/IsotopeCalculator.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/chemistry/IsotopeEnvelopeEstimator.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/chemistry/IsotopeTable.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/chemistry/MZTolerance.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/chemistry/iso.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/chemistry/parse_isotopes.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/math/Parabola.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/math/Stats.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/math/erf.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/minimxml/Jamfile.jam
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/minimxml/SAXParser.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/minimxml/XMLWriter.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/Base64.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/COMInitializer.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/ClickwrapPrompter.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/FailTest.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/Filesystem.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/Filesystem.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/FilesystemTest.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/Image.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/IntegerSet.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/MSIHandler.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/MSIHandler.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/SHA1.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/SHA1.h
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/TabReader.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/TabReader.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/TabReaderTest.cpp
Added  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/TabReaderTest.data/MSITest.tab
Added  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/TabReaderTest.data/TabTest.tab
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/VendorReaderTestHarness.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/VendorReaderTestHarness.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/automation_vector.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/automation_vector.h
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/automation_vector_test.cpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/cpp_cli_utilities.hpp
Modified  /trunk/madman/Rpacks/mzR/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp
Modified  /trunk/madman/Rpacks/mzR/src/win/i386/libpwiz.a
Modified  /trunk/madman/Rpacks/mzR/src/win/x64/libpwiz.a
upgrade pwiz and close connection for pwiz backend
Revision: 120457
Author: f.kramer
Date: 2016-08-26T07:39:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/rBiopaxParser/DESCRIPTION
Modified  /trunk/madman/Rpacks/rBiopaxParser/NEWS
Populated NEWS and fixed DESCRIPTION. Added code for pathway2Graph from Nirupama Benis nirupama.benis@wur.nl

From: Frank Kramer <dev@frankkramer.de>
Revision: 120456
Author: f.kramer
Date: 2016-08-26T07:32:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/rBiopaxParser/R/downloadBiopaxData.R
fixed Reactome download link

From: Frank Kramer <dev@frankkramer.de>
Revision: 120455
Author: f.kramer
Date: 2016-08-26T07:31:51+00:00
Paths:
Added  /trunk/madman/Rpacks/rBiopaxParser/.Rbuildignore
Added  /trunk/madman/Rpacks/rBiopaxParser/.gitignore
Modified  /trunk/madman/Rpacks/rBiopaxParser/DESCRIPTION
Modified  /trunk/madman/Rpacks/rBiopaxParser/NAMESPACE
Modified  /trunk/madman/Rpacks/rBiopaxParser/R/pathway2Graph.R
Modified  /trunk/madman/Rpacks/rBiopaxParser/R/rBiopaxParser-package.R
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/CLASS_INHERITANCE_BP2.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/CLASS_INHERITANCE_BP3.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/CLASS_PROPERTIES_BP2.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/CLASS_PROPERTIES_BP3.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/DATABASE_BIOPAX.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/addBiochemicalReaction.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/addBiopaxInstance.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/addBiopaxInstances.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/addControl.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/addPathway.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/addPathwayComponents.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/addPhysicalEntity.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/addPhysicalEntityParticipant.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/addPropertiesToBiopaxInstance.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/addhash.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/addns.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/biopax.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/calcGraphOverlap.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/checkValidity.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/colorGraphNodes.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/combineNodes.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/createBiopax.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/diffGraphs.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/downloadBiopaxData.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/generateNewUniqueID.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/getClassProperties.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/getInstanceClass.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/getInstanceProperty.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/getNeighborhood.Rd
Added  /trunk/madman/Rpacks/rBiopaxParser/man/getParticipants.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/getReferencedIDs.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/getReferencingIDs.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/getSubClasses.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/getSuperClasses.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/getXrefAnnotations.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/hasProperty.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/internal_NrOfXMLNodes.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/internal_XMLInstance2DF.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/internal_checkArguments.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/internal_generateXMLfromBiopax.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/internal_getBiopaxModelAsDataFrame.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/internal_propertyListToDF.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/internal_resolvePhysicalEntityParticipant.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/intersectGraphs.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/isOfClass.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/isOfNamespace.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/isURL.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/layoutRegulatoryGraph.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/listComplexComponents.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/listInstances.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/listInteractionComponents.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/listPathwayComponents.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/listPathways.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/mergePathways.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/pathway2AdjacancyMatrix.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/pathway2Geneset.Rd
Added  /trunk/madman/Rpacks/rBiopaxParser/man/pathway2Graph.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/pathway2RegulatoryGraph.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/plotRegulatoryGraph.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/print.biopax.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/rBiopaxParser-package.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/readBiopax.Rd
Added  /trunk/madman/Rpacks/rBiopaxParser/man/removeDisconnectedParts.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/removeInstance.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/removeNodes.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/removeProperties.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/selectInstances.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/splitComplex.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/striphash.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/stripns.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/transitiveClosure.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/transitiveReduction.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/unfactorize.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/uniteGraphs.Rd
Modified  /trunk/madman/Rpacks/rBiopaxParser/man/writeBiopax.Rd
Added  /trunk/madman/Rpacks/rBiopaxParser/rBiopaxParser.Rproj
Integrated changed from Nirupama Benis. Added function pathway2Graph

From: Frank Kramer <dev@frankkramer.de>
Revision: 120454
Author: f.kramer
Date: 2016-08-26T07:31:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/rBiopaxParser/R/pathway2Graph.R
pathway2graph, changed

From: Benis, Nirupama <nirupama.benis@wur.nl>
Revision: 120453
Author: f.kramer
Date: 2016-08-26T07:31:14+00:00
Paths:
Added  /trunk/madman/Rpacks/rBiopaxParser/R/pathway2Graph.R
Added  /trunk/madman/Rpacks/rBiopaxParser/data/biopaxLevel3Example.RData
pathway2graph, exampleData added

From: Benis, Nirupama <nirupama.benis@wur.nl>
Revision: 120452
Author: f.kramer
Date: 2016-08-26T07:23:35+00:00
Paths:
Deleted  /trunk/madman/Rpacks/rBiopaxParser/R/parseBiopax.R.orig
merge local, github, svn - 3

From: Frank Kramer <dev@frankkramer.de>
Revision: 120451
Author: f.kramer
Date: 2016-08-26T07:23:30+00:00
Paths:
Deleted  /trunk/madman/Rpacks/rBiopaxParser/DESCRIPTION.orig
Deleted  /trunk/madman/Rpacks/rBiopaxParser/NEWS.orig
Deleted  /trunk/madman/Rpacks/rBiopaxParser/R/selectBiopax.R.orig
Deleted  /trunk/madman/Rpacks/rBiopaxParser/README.md.orig
merge local, github, svn - 2

From: Frank Kramer <dev@frankkramer.de>
Revision: 120449
Author: l.chavez
Date: 2016-08-26T06:30:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/MEDIPS/DESCRIPTION
Modified  /trunk/madman/Rpacks/MEDIPS/R/MEDIPS.correlation.R
Correlation Analysis Update
Revision: 120448
Author: h.bengtsson
Date: 2016-08-26T01:37:26+00:00
Paths:
Modified  /trunk/madman/Rpacks/affxparser/NEWS
git-bioc: Copied updates from Git master branch to Bioconductor SVN

From: hb <hb@aroma-project.org>
Revision: 120447
Author: m.love
Date: 2016-08-26T00:26:42+00:00
Paths:
Modified  /trunk/madman/Rpacks/DESeq2/DESCRIPTION
old affiliations
Revision: 120446
Author: a.pickering
Date: 2016-08-25T23:32:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/crossmeta/DESCRIPTION
Modified  /trunk/madman/Rpacks/crossmeta/R/meta_utils.R
Merge branch 'master' into remotes/hedgehog
Revision: 120445
Author: a.pickering
Date: 2016-08-25T23:32:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/crossmeta/R/diff_utils.R
Modified  /trunk/madman/Rpacks/crossmeta/R/meta_utils.R
Modified  /trunk/madman/Rpacks/crossmeta/R/setup_prev.R
Modified  /trunk/madman/Rpacks/crossmeta/tests/testthat/test-all.R
Merge branch 'master' into remotes/hedgehog

Conflicts:
	R/meta_utils.R
Revision: 120444
Author: jspidlen
Date: 2016-08-25T23:25:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/man/peak_gate-methods.Rd
More documentation.
Revision: 120443
Author: jspidlen
Date: 2016-08-25T23:04:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/man/get_results_for_dyes.Rd
More documentation.
Revision: 120442
Author: m.jiang
Date: 2016-08-25T22:55:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
bump
Revision: 120441
Author: m.jiang
Date: 2016-08-25T22:55:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/R/GatingSetList_Methods.R
Modified  /trunk/madman/Rpacks/flowWorkspace/tests/testthat/GatingSetList-testSuite.R
add validity check in save_gslist to avoid the target folder being written by multiple gslists
Revision: 120440
Author: m.riester
Date: 2016-08-25T22:51:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Changed title.
Revision: 120439
Author: jspidlen
Date: 2016-08-25T22:45:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/man/calc_mean_sd_capture_all.Rd
More documentation.
Revision: 120437
Author: jspidlen
Date: 2016-08-25T22:23:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowQB/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowQB/man/calc_mean_sd_197.Rd
Modified  /trunk/madman/Rpacks/flowQB/man/calc_mean_sd_background.Rd
Modified  /trunk/madman/Rpacks/flowQB/man/calc_mean_sd_capture.Rd
More documentation.

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