Cancer Program Tool Resources

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TumorPortal

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

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. The main purpose of MSigDB is to provide gene sets for genomic analysis using GSEA software. The gene sets can also be downloaded for other purposes as well. In addition, the MSigDB web site hosts a number of online query and analysis tools.

Molecular Signatures DB (MSigDB)

The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets. The main purpose of MSigDB is to provide gene sets for genomic analysis using GSEA software. The gene sets can also be downloaded for other purposes as well. In addition, the MSigDB web site hosts a number of online query and analysis tools.

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