extract nucleotide counts for targeted variants from the BAM file.
Genotype known cancer hotspots from the tumor BAM file
Performs mutational enrichment analysis for a given clinical feature.
Draw two barplots side by side for cohort comparision.
Draw two oncoplots side by side for cohort comparision.
Compares identified denovo mutational signatures to known COSMIC signatures
Estimate number of signatures based on cophenetic correlation metric
Extract mutational signatures from trinucleotide context.
Draw forest plot for differences betweeen cohorts.
Extracts Tumor Sample Barcodes where the given genes are mutated.
Creates a Genotype Matrix for every variant
extract cytoband summary from GISTIC object
extract available fields from MAF object
extract gene summary from MAF or GISTIC object
extract sample summary from MAF or GISTIC object
Plot gistic results along linearized chromosome
Converts ICGC Simple Somatic Mutation format file to MAF
Clusters variants based on Variant Allele Frequencies (VAF).
Draws lollipop plot of amino acid changes on to Protein structure.
Convert MAF to MultiAssayExperiment object
Performs survival analysis for a geneset
calculates MATH (Mutant-Allele Tumor Heterogeneity) score.
Detect cancer driver genes based on positional clustering of variants.
draw an oncostrip similar to cBioportal oncoprinter output.
pfam domain annotation and summarization.
Plot differences between APOBEC enriched and non-APOBEC enriched samples.
Plot density plots from clutering results.
Draw an elbow plot of cophenetic correlation metric.
Plots results from clinicalEnrichment analysis
Plot Transition and Trasnversion ratios.
Rainfall plot to display hyper mutated genomic regions.
Performs sample stratification based on signature contribution and enrichment analysis.
Exact tests to detect mutually exclusive, co-occuring and altered genesets.
Predict genesets associated with survival
Compare mutation load against TCGA cohorts
Compare genes to known TCGA drivers and their biological pathways
Classifies SNPs into transitions and transversions
Extract single 5' and 3' bases flanking the mutated site for de-novo signature analysis. Also estimates APOBEC enrichment scores.
Writes GISTIC summaries to output tab-delimited text files.
Writes maf summaries to output tab-delimited text files.