Cancer Program Tool Resources

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Gene Set Enrichment Analysis (GSEA)

GSEA is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).

GENE-E

GENE-E is a Java desktop application developed to allow the rapid visual exploration of data sets derived from RNAi and chemical screens.

GeneCruiser

GeneCruiser is a web service allowing users to annotate their genomic data by mapping microarray feature identifiers to gene identifiers.

GenePattern

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

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

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.

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.

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