Scanpy Cat: Single-Cell RNA-seq Simple Analysis Pipeline

Installtation

before installtation,you must install *requirments" first(via pip install -r requirements.txt)

when use transform module(convert seurat inito anndata),you need to install packages : Seurat,SeuratDisk first,and also must have R env in this envrioment

git clone https://github.com/RyanYip-Kat/scpcat
cd scpcat 
python setup.py install

subcommand

there are several subcommand to reliaze functions,{create,reduction,findmarker,dotplot,embplot,heatmap,vlnplot,subset,enrich},and you can with --help to get usages eg.

scpCAT.py --help
scpCAT.py create --help

usages

create

scpCAT.py create -d /path/to/10X/outs/filtered_feature_bc_matrix -o output

reduction

scpCAT.py reduction -d /path/to/adata.h5ad --batch_correct --batch_key "sample" -o output

...

May be you will meet a bug when use

scpCAT.py transform -f pbmc_small.rds --name seurat -o test

A simple Bug(May be)

/path/lib/python3.8/site-packages/scpcat-1.0.0-py3.8.egg/scpcat/R/Seurat2Anndata.R': No such file or directory

you can fix it by ** cp -r scpcat/R /path/lib/python3.8/site-packages/scpcat-1.0.0-py3.8.egg/scpcat/