louisfaure / deseq2py

python wrapper for DESeq2, compatible with scanpy

DESeq2py

Python wrapper of DESeq2 R package, combined with anndata object for easy access and plotting of the data.

Installation

The best way to get everything running smoothly is to use conda:

conda create -n deseq2py -c conda-forge -c bioconda python=3.8 bioconductor-deseq2 bioconductor-apeglm rpy2 -y
conda activate deseq2py
pip install git+https://github.com/LouisFaure/deseq2py.git

Usage

import scanpy as sc
import deseq2py as deseq
adata_bulk = sc.read("adata_bulk.h5ad")

deseq2.tl.run(adata_bulk,formula="~ condition")
deseq2.tl.vst(adata_bulk)
deseq2.tl.pca(adata_bulk)

deseq2.pl.pca(adata_bulk,color="condition",
              show_ellipses=True)

deseq2.tl.result(adata_bulk,lfc_shrink=True,name="condition_A_vs_B")

deseq2py's Issues

bechmark

Hi,
very useful work!
Why do you develop this tool and do you compare it with DEseq2 on some datasets ?

Count matrix to anndata

Hi,

Is it possible to convert a count matrix into an anndata to use deseq2py later? Do I have to run before bulk tools-py?

Thanks!

Victor