ggr-project

GGR Analysis

Python requirements

• Anaconda - v5+
• GPy - 1.8.4 (for DP_GP) (pip install)

Bioinformatics requirements

• bedtools/2.25.0+
• homer
• DP_GP (Englehardt) - commit: eec12e74219f916aa86e253783905f7b5e30f6f4
• deeptools

R requirements - v3.4

• seqLogo # check if this is used
• deseq2
• rGREAT
• RDAVIDWebService
• biomaRt
• qvalue
• gplots
• ggplot2
• reshape
• RColorBrewer
• fastcluster
• dendextend # check if this is used
• gridGraphics

NOTE: packages as of 2017-11-08

Other notes

pip install weblogo #3.6.0
pip install deeptools

Install homer according to homer instructions on UCSD website

Note that conda curl has issues for deeptools - do conda remove curl to use normal curl, also remove curl-config