Cancer Program Tool Resources
GenePattern is a powerful genomic analysis platform that provides access to more than 180 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.
GenomeSpace brings together diverse computational tools and enables scientists without programming skills to easily combine the capabilities of these tools. It offers a common space to create, manipulate, and share an ever-growing range of genomic analysis tools.
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 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 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.
|Molecular Signatures DB (MSigDB)||
The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software.
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 (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.