Lab Algorithms for Download

GITHUB

For data analysis pipelines and scripts, please visit our GitHub:

https://github.com/KhavariLab

PROXIMITY ANALYSIS

A network generation tool using topological constraints. README for network generation and analysis scripts enclosed in package.

ProximityAnalysisPackage.zip

FOCIS

FOCIS (Feature Overlapper for Chromosomal Interval Subsets) performs an interval-based screen of a database of genomic features – ChIP-seq peaks, motif matches, and others – for overlap enrichment at a specific subset of genomic regions relative to a dataset-matched background.  Follow the link below for more details:

http://sourceforge.net/projects/focis/files/

RINS

A RINS package can be downloaded by clicking below. Included are all scripts, README, and virus reference file.  This is a package recommended for advanced users only. To install, type tar -xzvf which will create a folder with the contents entitled rins_core. Once installation is complete, please verify that all paths in the configuration file match your computer environment, else execution of RINS will be unsuccessful.

rins_core.tar.gz

A package including the above as well as the associated Bowtie and BLAST libraries/databases for running RINS on human sample data can be downloaded by visiting:

https://s3.amazonaws.com/changseq/kqu/rins/rins.tar.gz

This link will take you download a very large file, which can be installed in the same way and will open a folder called rins on your computer. If you would like to use these libraries/databases without downloaded such a large package, they are freely accessible from the sources described in the README.

If you encounter problems, please contact Ying Shen (yshen3@stanford.edu)