bubhub/de_toolkit repository overview

⁠Introduction

This is a collection of utilities to perform various operations on genomic count datasets involving determining differential expression.

⁠Documentation

There is work-in-progress documentation at (readthedocs.org):

• de_toolkit⁠

⁠Installing

⁠From pypi

pip install de_toolkit

⁠Installing R and packages

Certain functions in detk, particularly the de module, interface with R and bioconductor packages. You must have a version of R installed and the following packages to use the corresponding submodule functions:

• DESeq2⁠
• logistf⁠

⁠Development

First clone or fork and clone this repo:

git clone https://bitbucket.org/bubioinformaticshub/de_toolkit.git

We suggest using anaconda⁠ to create an environment that contains the software necessary, e.g.:

cd de_toolkit
conda create -n de_toolkit python=3.5
source activate de_toolkit
./install_conda_packages.sh
Rscript install_r_packages.R

In development, when you want to run the toolkit, use the setup.py script:

python setup.py install

This should make the detk and its subtools available on the command line. Whenever you make changes to the code you will need to run this command again.