Cancer Program Tool Resources
ABSOLUTE generates absolute copy number data from a mixed population of tumor and normal DNA. This process begins by generation of segmented copy number data, which is input to the ABSOLUTE algorithm together with pre-computed models of recurrent cancer karyotypes and, optionally, allelic fraction values for somatic point mutations. ABSOLUTE then provides information on the absolute cellular copy number of local DNA segments and, for point mutations, the number of mutated alleles.
The goal of the Achilles Project is to create a genome-wide catalog of tumor dependencies to identify vulnerabilities associated with genetic alterations.
BreakPointer is a tool to pinpoint rearrangement breakpoints using paired-end next generation sequencing reads.
|Connectivity Map (CMAP)||
The Connectivity Map is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms that together enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes.
ContEst is a tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data. Using a Bayesian framework, contamination levels are estimated from array based genotypes and sequencing reads.
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.
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.
GeneCruiser is a web service allowing users to annotate their genomic data by mapping microarray feature identifiers to gene identifiers.