GISTIC2

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

Check out the GISTIC GitHub Page 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).