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