Cancer Program Tool Resources

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GISTIC

GISTIC is a tool to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, GISTIC estimates the background rates for each category as well as defines the boundaries of SCNA regions.

HAPSEG

HAPSEG is a tool to detect genomic segments of constant allele-specific copy-number based on SNP6.0 array data. 

ICBP Data & Analysis Portal

This portal provides access to information tools and data avilalle from all of the Centers for Cancer Systems Biology that are part of NCI's Integrative Cancer Biology Program including the Broad-Instiute/Dana Farber center.

Indelocator

Indelocator is a software tool for calling short indels in next generation sequencing data.

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.

JuncBASE

JuncBASE (Junction-Based Analysis of Splicing Events) is used to identify and classify alternative splicing events from RNA-Seq data. Alternative splicing events are identified from splice junction reads from RNA-Seq read alignments allowing for analysis of unannoated or aberrant alternative splicing. JuncBASE also uses read counts to quantify the relative expression of each isoform and identifies splice events that are significantly differentially expressed across two or more samples. 

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.

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.

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.

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