gnr

This file will become your README and also the index of your documentation.

Developer Guide

Setup

# create conda environment
$ mamba env create -f env.yml

# update conda environment
$ mamba env update -n gnr --file env.yml
# $ mamba env update -n gnr --file env.mac.yml

Install

pip install -e .

# install from pypi
pip install gnr

nbdev

# activate conda environment
$ conda activate gnr

# make sure the gnr package is installed in development mode
$ pip install -e .

# make changes under nbs/ directory
# ...

# compile to have changes apply to the gnr package
$ nbdev_prepare

Note: it might be useful to use the following snippet to enable hot reloading:

%load_ext autoreload
%autoreload 2

Publishing

# publish to pypi
$ nbdev_pypi

# publish to conda
$ nbdev_conda --build_args '-c conda-forge'

Usage

Installation

Install latest from the GitHub repository:

$ pip install git+https://github.com/dsm-72/gnr.git

or from conda

$ conda install -c dsm-72 gnr

or from pypi

$ pip install gnr

df_trj = make_mock_genes_x_tbins()
df_trj.head()

gc_op = GrangerCausality(n_jobs=2)

df_res = gc_op.fit_transform(df_trj, fit_params={'standard_scaler':True, 'signed_correlation': True})

df_res.head()

gc_op.plot_df_org(figsize=(4,4))

gc_op.plot_df_res(figsize=(4,4))

Documentation

Documentation can be found hosted on GitHub repository pages. Additionally you can find package manager specific guidelines on conda and pypi respectively.