Getting Started

Welcome Installing Bioconductor Command line tools (Docker) Getting the data

Quality Control

Overview Depth of Sequencing Coverage Cross Sample Contamination Tumor-in-normal Tumor Purity

Mutational Signatures

Overview SomaticSignatures (NMF) deconstructSigs (NNLS) SigMa (Likelihood) scarHRD (Homologous Recombination Deficiency) MSIsensor (Microsatellite Instability)

Mutational Significance Analysis

Overview MutSigCV OncodriveFML MutPanning Brown's Method (for combining p-values)

Tumor Phylogenetics

Overview Calculate Mutation Cancer Cell Fractions (CCFs) PhylogicNDT PyClone

Gene Set Analysis

Overview GSEA ssGSEA Pathway Overrepresentation

Differential Expression

Overview edgeR DESeq2 Independent Hypothesis Weighting (IHW)

Pathway Overrepresentation

My preferrential tool for performing pathway overrepresentation analysis is ConsensusPathDB hosted through the Max Planch Institute for Molecular Genetics. Like most overrepresentation analysis, the p-values are determined using a hypergeometric distribution

Coming soon

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