Man pages for bic-mskcc/bicrnaseq
MSKCC Bioinformatics Core RNASeq

bic.add.rownames2datAdd a column to matrix containing its row names
bic.average.by.nameAverage all values in a matrix that have the same 'name'
bic.check.line.chart.dataCheck formatting of input to bic.plot.rseqc.line.chart()
bic.check.picard.dataValidate data from PICARD CollectRnaSeqMetrics or...
bic.check.read.distribution.dataCheck formatting of input to bic.plot.read.distribution()
bic.deseq.heatmapDraw a heatmap of counts table
bic.deseq.normalize.htseq.countsUse DESeq to normalize raw HTSeq counts
bic.deseq.plot.pcaPlot PCA
bic.file2matrixRead data file and return as a matrix
bic.format.htseq.countsRead in raw HTSeq count file and format for analysis
bic.get.deseq.cdsNormalize raw count matrix using DESeq scaling method
bic.get.gene.setsGet the gene sets that meet criteria set by cut offs
bic.get.package.infoGet info for one or multiple packages installed in current R...
bic.grid.arrange.shared.legendArrange multiple plots on one page with one shared legend
bic.hclust.samplesPlot heirachical clustering of all samples
bic.join.stringsConvert a character vector to a delimited string
bic.make.colnamesRemove a row from matrix to use the values as column names
bic.make.rownamesRemove a column from a matrix and use its values as the...
bic.matrix2numericConvert all values in matrix to numeric
bic.mds.clust.samplesPlot MDS clustering of all samples
bic.non.empty.file.foundSearch for a non-empty file by pattern
bic.pdf.hclustWrite PDF file containing heierarchical clustering tree
bic.plot.5prime3prime.biasPlot coverage uniformity (5' and 3' bias)
bic.plot.alignment.distributionPlot distibution of alignment across different genomic...
bic.plot.alignment.summaryPlot numbers of mapped and unmapped reads for each sample
bic.plot.coveragePlot normalized coverage
bic.plot.dispersion.estimatesPlot dispersion estimates
bic.plot.maPlot MA
bic.plot.read.distributionPlot RSeQC read distribution stats
bic.plot.rseqc.line.chartPlot RSeQC sequential metrics in a line graph
bic.process.gsa.resFormat and filter results from piano::runGSA()
bic.pval.histogramHistogram of p-values
bic.quantile.normalize.htseq.countsUse quantile normalization to normalize raw HTSeq counts
bic.remove.subRemove a substring from a string
bic.run.deseq.comparisonRun a differential expression comparison between two...
bic.run.gsaRun gene set analysis using the package 'piano'
bic.sample.to.sample.distancesDraw a heatmap showing sample-to-sample distances using...
bic.scale.factor.quantileNon-deseq way to normalize counts(?)
bic.standard.heatmapCreate PDF of generic red/green/black heatmap showing...
bic.write.datWrite file containing tab delimited data
bic.write.deseq.resultsWrite results for ALL genes and for DE genes
bic.write.normalized.counts.fileWrite normalized counts matrix to file
bic-mskcc/bicrnaseq documentation built on April 29, 2018, 5:37 a.m.