Cancer Program Tool Resources


D-ToxoG is a tool for removing the OxoG artifact from a set of SNV calls.


dRanger is a tool to identify somatic rearrangements as clusters of aberrant paired-end sequencing reads in a tumor sample where the the normal sample has read-pairs consistent with the reference. Candidate rearrangement breakpoints from dRanger are passed into Breakpointer, which applies a modified Smith-Waterman algorithm to all reads in the region to identify split-read support for  the rearrangement. 


FireBrowse is a simple and elegant way to explore cancer data, backed by a powerful computational infrastructure, application programming interface (API), graphical tools and online reports.  It sits above the TCGA GDAC Firehose, one of the deepest and most integratively characterized open cancer datasets in the world--with over 80K sample aliquots from 11,000+ cancer patients, spanning 38 unique disease cohorts.  FireBrowse makes it possible to find any of thousands of data archives generated by Firehose in just 2 clicks.  Likewise, two clicks are all that's needed to find any of the ~1500 analysis resports created by Firehose in each analysis run.  For programmers a powerful RESTful API is provided, with bindings to the UNIX command line, Python and R.  And for scientists we provide graphical tools like viewGene to explore expression levels, and iCoMut to explore the comprehensive analysis profile of each TCGA disease study within a single, interactive figure.


Firehose is an analysis infrastructure developed at The Broad Institute to coordinate the flow of terabyte-scale datasets through scores of quantitative algorithms.  Firehose is used to coordinate the various tools utilized by the Cancer Genome Analysis team to analyze cancer genome projects. 

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


GenePattern is an open source genomic analysis platform that provides access to hundreds of tools for the analysis and visualization of gene expression, sequence variation, proteomic, and other data types. 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.


GeNets is a biological pathway analysis and visualization platform that helps scientists
elucidate the biology driving the patterns found in high-throughput experimental data.


GenomeSpace is a cloud-based resource that supports “frictionless” interaction between bioinformatics tools and data resources. It allows researchers to address complex biomedical questions requiring the use of multiple software tools in concert. A key element of the GenomeSpace environment is a collection of “recipes,” guides for short workflows utilizing 2-3 tools that can serve as building blocks in larger integrative analyses.


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.