Welcome to Ma’ayanlab Bioinformatics’s documentation!¶

Indices and tables¶

Ma’ayanlab Bioinformatics¶

A collection of useful functions for bioinformatics data analysis.

This library contains many functions and methods I use again and again in different analyses including:

quantile normalization
other common normalizations
logcpm, zscore, filter variance
gmt parser
single-cell sparse matrix parsing
transcript to gene conversions
…
various dge including chdir, lima_voom, deseq2, etc..

Installation¶

# minimal
pip install "maayanlab-bioinformatics@git+https://github.com/Maayanlab/maayanlab-bioinformatics.git"

# complete
pip install "maayanlab-bioinformatics[all]@git+https://github.com/Maayanlab/maayanlab-bioinformatics.git"
# [OPTIONAL] for some R functionality like limma_voom & filter_by_expr
python -m maayanlab_bioinformatics.setup.R