seRNA-ESC

The raw data is stored using git-lfs

git pull https://github.com/haochunchang/seRNA-ESC.git

A starting docker image

Installed most of the packages needed.

docker run -it -v /path/to/seRNA-ESC:/seRNA-ESC/ \
           -p 8888:8888 \ # for displaying jupyter notebooks
           --name container_name \
           jr55662003/serna-esc:v1 bash

In this docker, use python3.5 to call scripts instead of python3.
Since some computation takes time, this image did not test all of the scripts.
Tested:
- Preprocessing
- NMF
- Co-expression analysis

Requirements

The following are the packages we used for developing the scripts: Please make sure you have those packages before running

apt-get install bedtools

Python 3.5

numpy 1.12.1
pandas 0.19.2
scikit-learn 0.18.1
networkx 1.11 (For stitching enhancers and BiCoxNet)
fastcluster 1.1.20 (For NMF & WGCNA)
matplotlib
seaborn

For checking python packages and install them, simply go into main directory and run:

pip3 install -r requirements.txt

R 3.3.2

WGCNA
limma
impute
MASS, class, cluster, data.table can all be installed from CRAN
doParallel (Enable WGCNA uses all CPUs in your machine)

For checking R packages and install them, you can run the R script in main directory:

Rscript check_requirement.R