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Most Viewed Resources


Tumorscape
Tumor microenvironment and Drug resistance
The Matrisome Project
TCGA Tumorscape
TCGA Data and Analyses (Broad GDAC)
SegSeq
RNA-SeQC
Prostate Cancer Genome Sequencing
PathSeq
Oncotator

Recently Updated


Tumorscape	06/11/12
Tumor microenvironment and Drug resistance	08/08/12
The Matrisome Project	01/14/13
TCGA Tumorscape	06/12/12
TCGA Data and Analyses (Broad GDAC)	06/08/12
SegSeq	06/08/12
RNA-SeQC	06/11/12
Prostate Cancer Genome Sequencing	06/08/12
PathSeq	06/08/12
Oncotator	06/08/12

Cancer Program Tool Resources


The Matrisome Project		The Matrisome Project is a collaborative effort between scientists from the Hynes Lab at the Koch Institute for I ntegrative Cancer Research at MIT and the Broad Institute of MIT and Harvard, aimed at defining bioinformatically and experimentally the ensemble of genes encoding the "matrisome", i.e. the ensemble of extracellular matrix and ECM-associated proteins (Naba et al, 2011). The purpose of the Matrisome Project web page is to provide information and resources relevant to research on ECM proteins and to be a platform for deploying data collections, methods, and protocols. Our aim is to facilitate the use of our protocols by other scientists and to allow their widespread use in future studies.
SegSeq		SegSeq is an algorithm to identify chromosomal breakpoints using massively parallel next generation sequence data.
RNA-SeQC		RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data.
PathSeq		PathSeq is a computational tool for the identification and analysis of microbial sequences in high-throughput human sequencing data that is designed to work with large numbers of sequencing reads in a scalable manner.
Oncotator		Oncotator is a tool for annotating human genomic point mutations and indels with data relevant to cancer researchers. Annotations are aggregated from genomic annotations, protein annotations, and cancer annotations.
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.
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.
Molecular Signatures DB (MSigDB)		The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software.
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.
Indelocator		Indelocator is a software tool for calling short indels in next generation sequencing data.

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