GISTIC2

This repository contains the Matlab source code for GISTIC (Genomic Identification of Significant Targets In Cancer), version 2.0.

Check out the <a href="https://broadinstitute.github.io/gistic2">GISTIC GitHub Page</a> for links to GISTIC downloads, user documentaion, and publications.

Cloning the gistic2 project

This repository contains a submodule of matlab functions for processing copy number data named 'snputil.' To ensure that the snputil subdirectory is populated with files, you should clone this repository using the --recursive option:

git clone --recursive  https://github.com/broadinstitute/gistic2.git

Repository directory structure

docs - HTML source for links and user documentation published in the GISTIC GitHub page.

refgenes - source code for creating reference genome input files (offered on an 'as is' basis).

Gencode.v22.170324 - download EMBL files and build a Gencode reference genome.

hg38.UCSC.add_mir.160920 - download UCSC files and build an hg38 reference genome.

snputil - git submodule of utility Matlab functions for analyzing copy number data.

@SegArray - defines the SegArray class, a data compression scheme for segmented copy number.

source - Matlab source code for GISTIC.

support - additional files needed to build a GISTIC tarball.

user_docs - HTML source for standalone documentation in the current GISTIC tarball (v2.0.23).