scutil 0.1.1

A Python package utils to support scanpy usage

Installation

pip install scutil

This is for scRNAseq data analysis where

usage

for qc and low dim visualization, starting from h5ad file,

as in the tests/

import scutil as su
import scanpy as sc
import json
su.check_workdir("../")
adata = sc.read_h5ad("tests/_data/test.h5ad")

with open('tests/config/params.json', 'r') as f:
    config = json.load(f)

name = config['project_name']
adata = sc.read_h5ad(f"tests/_data/{name}.h5ad")
su.filter_adata(adata, **config['filter_params'])
su.norm_hvg(adata, name, n_top_genes=1000)
su.pca(adata, name, 30, pearson=False)
su.tsne_and_umap(adata, name, n_comps=10, pearson=False, key='celltype')

su.write_adata(adata, f'tests/_data/{name}_qc_vis.h5ad')