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Initialisation of notebook (suitable for print)

%config InlineBackend.figure_format = 'retina'
%matplotlib inline
import os
import pandas as pd
import numpy as np
import seaborn as sns
from matplotlib import pyplot as plt

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from __future__ import print_function
import libsbml
import argparse

def _parser():

    parser = argparse.ArgumentParser(description="Parse stoichiometry matrix of SBML file")
    parser.add_argument('file', metavar="filename", type=argparse.FileType('r'),
                        help="Filename of SBML file to parse")

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Cavadas et al., Scientific Reports, 2016 Supplements

This gist pre-processes supplementary data from Cavadas et al. paper in Scientific Reports, citation below:

Cavadas, M.A.S., Mesnieres, M., Crifo, B., Manresa, M.C., Selfridge, A.C., Keogh, C.E., Fabian, Z., Scholz, C.C., Nolan, K.A., Rocha, L.M.A., et al. (2016). REST is a hypoxia-responsive transcriptional repressor. Sci Rep-Uk 6, 31355

Each of the notebooks downloads the data directly from the journal, converts it into an easier-to-work tsv format, and augments it with uniprot, ensembl and entrez identifiers.

The notebooks make extensive use of MyGene.info which can be cited as:

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Converting deeptools matrix to pd.DataFrame

import matplotlib

# Deeptools will mess with matplotlib settings, fix that
_mpl_backend = matplotlib.rcParams['backend']
from deeptools.heatmapper import heatmapper as deeptools_heatmapper
matplotlib.use(_mpl_backend)
del _mpl_backend

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