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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