Man pages for bic-mskcc/bicrnaseq
MSKCC Bioinformatics Core RNASeq
| bic.add.rownames2dat | Add a column to matrix containing its row names |
| bic.average.by.name | Average all values in a matrix that have the same 'name' |
| bic.check.line.chart.data | Check formatting of input to bic.plot.rseqc.line.chart() |
| bic.check.picard.data | Validate data from PICARD CollectRnaSeqMetrics or... |
| bic.check.read.distribution.data | Check formatting of input to bic.plot.read.distribution() |
| bic.deseq.heatmap | Draw a heatmap of counts table |
| bic.deseq.normalize.htseq.counts | Use DESeq to normalize raw HTSeq counts |
| bic.deseq.plot.pca | Plot PCA |
| bic.file2matrix | Read data file and return as a matrix |
| bic.format.htseq.counts | Read in raw HTSeq count file and format for analysis |
| bic.get.deseq.cds | Normalize raw count matrix using DESeq scaling method |
| bic.get.gene.sets | Get the gene sets that meet criteria set by cut offs |
| bic.get.package.info | Get info for one or multiple packages installed in current R... |
| bic.grid.arrange.shared.legend | Arrange multiple plots on one page with one shared legend |
| bic.hclust.samples | Plot heirachical clustering of all samples |
| bic.join.strings | Convert a character vector to a delimited string |
| bic.make.colnames | Remove a row from matrix to use the values as column names |
| bic.make.rownames | Remove a column from a matrix and use its values as the... |
| bic.matrix2numeric | Convert all values in matrix to numeric |
| bic.mds.clust.samples | Plot MDS clustering of all samples |
| bic.non.empty.file.found | Search for a non-empty file by pattern |
| bic.pdf.hclust | Write PDF file containing heierarchical clustering tree |
| bic.plot.5prime3prime.bias | Plot coverage uniformity (5' and 3' bias) |
| bic.plot.alignment.distribution | Plot distibution of alignment across different genomic... |
| bic.plot.alignment.summary | Plot numbers of mapped and unmapped reads for each sample |
| bic.plot.coverage | Plot normalized coverage |
| bic.plot.dispersion.estimates | Plot dispersion estimates |
| bic.plot.ma | Plot MA |
| bic.plot.read.distribution | Plot RSeQC read distribution stats |
| bic.plot.rseqc.line.chart | Plot RSeQC sequential metrics in a line graph |
| bic.process.gsa.res | Format and filter results from piano::runGSA() |
| bic.pval.histogram | Histogram of p-values |
| bic.quantile.normalize.htseq.counts | Use quantile normalization to normalize raw HTSeq counts |
| bic.remove.sub | Remove a substring from a string |
| bic.run.deseq.comparison | Run a differential expression comparison between two... |
| bic.run.gsa | Run gene set analysis using the package 'piano' |
| bic.sample.to.sample.distances | Draw a heatmap showing sample-to-sample distances using... |
| bic.scale.factor.quantile | Non-deseq way to normalize counts(?) |
| bic.standard.heatmap | Create PDF of generic red/green/black heatmap showing... |
| bic.write.dat | Write file containing tab delimited data |
| bic.write.deseq.results | Write results for ALL genes and for DE genes |
| bic.write.normalized.counts.file | Write normalized counts matrix to file |
