Cancer Program Tool Resources
|The Matrisome Project||
The Matrisome Project is a collaborative effort between scientists from the Hynes Lab at the Koch Institute for Integrative Cancer Research at MIT and the Broad Institute of MIT and Harvard, aimed at defining bioinformatically and experimentally the ensemble of genes encoding the "matrisome", i.e. the ensemble of extracellular matrix and ECM-associated proteins (Naba et al, 2011).
SegSeq is an algorithm to identify chromosomal breakpoints using massively parallel next generation sequence data.
RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data.
PathSeq is a computational tool for the identification and analysis of microbial sequences in high-throughput human sequencing data that is designed to work with large numbers of sequencing reads in a scalable manner.
Oncotator is a tool for annotating human genomic point mutations and indels with data relevant to cancer researchers. Annotations are aggregated from genomic annotations, protein annotations, and cancer annotations.
MutSig (for "Mutation Significance") is a package of tools for analyzing mutation data. It operates on a cohort of patients and identifies mutations, genes, and other genomic elements predicted to be driver candidates.
MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.
|Molecular Signatures DB (MSigDB)||
The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software.
|Integrative Genomics Viewer (IGV)||
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Indelocator is a software tool for calling short indels in next generation sequencing data.