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 (readthedocs.org):
pip install de_toolkit
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 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
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.