Cancer Program Tool Resources

sort ascending
TumorPortal

Genes, Cancers, and DNA Mutations
http://TumorPortal.org

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).
The purpose of the Matrisome Project web page is to provide information and resources relevant to research on ECM proteins and to be a platform for deploying data collections, methods, and protocols. Our aim is to facilitate the use of our protocols by other scientists and to allow their widespread use in future studies.

SegSeq

SegSeq is an algorithm to identify chromosomal breakpoints using massively parallel next generation sequence data.

RNA-SeQC

RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data.

PathSeq

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

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.

Oncotator

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

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

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.

Pages