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


There is work-in-progress documentation at (


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:


First clone or fork and clone this repo:

git clone

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
Rscript install_r_packages.R

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

python 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.