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1. bionmf bionmf Public

   NMF solver designed for identifying metagene programs in bioinformatics, adopted from Brunet et al. (available on PyPi)

   Python

2. peak-quant peak-quant Public

   Quantify peaks in BED format to a sparse count matrix for downstream analysis, such as DEseq2.

   Python

3. var-sim var-sim Public

   Simulation of probability distribution of minor allele frequencies of single-nucleotide polymorphisms.

   Python

4. ecotyper-py ecotyper-py Public

   Unofficial Python implementation of EcoTyper (R) for tumour-microenvironment classification in single-cell and bulk RNA-seq, incorporation with AnnData.

   Python