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)

Welcome

Welcome!

Prerequisites

The tutorials presented here assume that you have R and/or Python installed, and that you have a basic understanding of the programming syntax of each language (e.g. variables, functions, classes). For most of the bioinformatics and computational biology tutorials, the statistics and theory behind the methods are briefly disucessed in the Overview section. While it is not neccessary to learn or understand the statistics behind each method in order to run the tutorials, I highly recommend taking the time to do so.

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