Files in bic-mskcc/bicrnaseq
MSKCC Bioinformatics Core RNASeq
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/bic_analyze_counts.R
R/bic_plots.R
R/bic_util.R
README.md
bicrnaseq.Rproj
inst/extdata/c1.all.v4.0.symbols.gmt
inst/extdata/c2.all.v4.0.symbols.gmt
inst/extdata/c3.all.v4.0.symbols.gmt
inst/extdata/c3.mir.v4.0.symbols.gmt
inst/extdata/c3.tft.v4.0.symbols.gmt
inst/extdata/c5-1.all.v4.0.symbols.gmt
inst/extdata/c6-1.all.v4.0.symbols.gmt
inst/extdata/c7.all.v4.0.symbols.gmt
inst/extdata/canonical_pathways_in_genesymbols_fromGSEA.gmt
inst/extdata/curated_gene_sets_cgp.gmt
inst/extdata/go_biological_processes.gmt
inst/extdata/go_cellular_components.gmt
inst/extdata/go_molecular_functions.gmt
inst/extdata/mouse_c1.gmt
inst/extdata/mouse_c2.gmt
inst/extdata/mouse_c3.gmt
inst/extdata/mouse_c4.gmt
inst/extdata/mouse_c5.gmt
inst/extdata/test/test_alignment_summary_metrics.txt
inst/extdata/test/test_collect_rnaseq_metrics.txt
inst/extdata/test/test_htseq_counts.txt
inst/extdata/test/test_sample_comparisons.txt
inst/extdata/test/test_sample_key.txt
inst/extdata/test_alignment_summary_metrics.txt
inst/extdata/test_collect_rnaseq_summary_metrics.txt
man/bic.add.rownames2dat.Rd
man/bic.average.by.name.Rd
man/bic.check.line.chart.data.Rd
man/bic.check.picard.data.Rd
man/bic.check.read.distribution.data.Rd
man/bic.deseq.heatmap.Rd
man/bic.deseq.normalize.htseq.counts.Rd
man/bic.deseq.plot.pca.Rd
man/bic.file2matrix.Rd
man/bic.format.htseq.counts.Rd
man/bic.get.deseq.cds.Rd
man/bic.get.gene.sets.Rd
man/bic.get.package.info.Rd
man/bic.grid.arrange.shared.legend.Rd
man/bic.hclust.samples.Rd
man/bic.join.strings.Rd
man/bic.make.colnames.Rd
man/bic.make.rownames.Rd
man/bic.matrix2numeric.Rd
man/bic.mds.clust.samples.Rd
man/bic.non.empty.file.found.Rd
man/bic.pdf.hclust.Rd
man/bic.plot.5prime3prime.bias.Rd
man/bic.plot.alignment.distribution.Rd
man/bic.plot.alignment.summary.Rd
man/bic.plot.coverage.Rd
man/bic.plot.dispersion.estimates.Rd
man/bic.plot.ma.Rd
man/bic.plot.read.distribution.Rd
man/bic.plot.rseqc.line.chart.Rd
man/bic.process.gsa.res.Rd
man/bic.pval.histogram.Rd
man/bic.quantile.normalize.htseq.counts.Rd
man/bic.remove.sub.Rd
man/bic.run.deseq.comparison.Rd
man/bic.run.gsa.Rd
man/bic.sample.to.sample.distances.Rd
man/bic.scale.factor.quantile.Rd
man/bic.standard.heatmap.Rd
man/bic.write.dat.Rd
man/bic.write.deseq.results.Rd
man/bic.write.normalized.counts.file.Rd
tests/testthat.R
tests/testthat/test_plot_data.R
