Computational method to calculate purity and ploidy of a given tumor sample. Determines the fraction of processed sample that actually contains tumor DNA from various data sources. Useful technique to distinguish between sub-clonal events and/or contamination.
The Integrative Genomics Viewer (IGV) is a stand alone piece of software developed at the Broad Institute to help visualize various types of genomic data including expression, sequence, copy number, etc. The full description and official software site is here.
The Genomic Identification of Significant Targets in Cancer (GISTIC) software package was developed at the Broad Institute to distinguish between actual molecular changes in copy number (amplifications and/or deletions) and noise from the array. The full description, publication, and software can be found on the site here.
This web portal is designed to facilitate the use and understanding of high resolution copy number data amassed from multiple cancer types specifically through the TCGA project. Pre-performed analyses include by gene and cancer type.
NCI Cancer Molecular Analysis (CMA) Portal
The NCI Cancer Molecular Analysis (CMA) Portal is an application created by caBIG that allows researchers to integrate, visualize, and explore clinical and genomic characterization data from translational research studies.
The Cancer Genome Workbench (CGWB) is an application developed by NCI that provides whole-genome and heatmap views of sample-level data.
cBio Cancer Genomics Portal
The cBio Cancer Genomics Portal provides visualization, analysis and download of large-scale cancer genomics data sets. The portal is developed and maintained by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center.
Lawrence Berkeley National Laboratory Biosig
Biosig allows the TCGA community to download computed histology-based information, and visualize images and overlaid computed information.
UCSC Cancer Genome Browser
The cancer specific version of the popular UCSC genome browser. Useful for integrating multiple data sets and information types including genomic and clinical data.