PECA2 gene regulatory network construction for single-cell data
Project description
scPECA
Introduction
This is a python version of PECA2 gene regulatory network construction software designed for single-cell data. It has a faster running speed and a lower memory footprint.
Installation
pip install scPECA
Or install via Github
git clone https://github.com/zhangjiahao1234/scPECA.git
cd scPECA
python setup.py install
Run scPECA
Input
scPECA requires to input the paired (sc)RNA-seq and (sc)ATAC-seq data, and it provides data pre-processing in some formats. (Pre-processing can also be done manually by the user)
Format 1
Paired bulk RNA-seq and ATAC-seq count data
sample_name_RNA.txt
gene1 | 10 |
gene2 | 3 |
sample_name_ATAC.txt
chr1_10000_10100 | 1 |
chr1_20000_20100 | 0 |
Format 2
scRNA-seq count data and scATAC-seq count data within the same cluster without meta information
sample_name_scRNA.csv
barcode1 | barcode2 | |
---|---|---|
gene1 | 1 | 19 |
gene2 | 3 | 6 |
sample_name_scATAC.csv
barcode1 | barcode2 | |
---|---|---|
chr1_10000_10100 | 1 | 0 |
chr1_20000_20100 | 0 | 1 |
Format 3
scRNA-seq count data and scATAC-seq count data with meta information
sample_name_scRNA.csv
barcode1 | barcode2 | |
---|---|---|
gene1 | 1 | 19 |
gene2 | 3 | 6 |
sample_name_scRNA_meta.csv
barcode1 | celltype1 |
barcode2 | celltype2 |
sample_name_scATAC.csv
barcode1 | barcode2 | |
---|---|---|
chr1_10000_10100 | 1 | 0 |
chr1_20000_20100 | 0 | 1 |
sample_name_scATAC_meta.csv
barcode1 | celltype1 |
barcode2 | celltype2 |
Run example
import scPECA
import os
data_path = os.path.join(os.path.dirname(scPECA.__file__), 'Cones') # demo data path
demo = scPECA.scPECA(data_path, 'Cones', 'hg38') # Create a scPECA class
demo.RNA_process(2) # Format 2 RNA data processing
demo.ATAC_process(2) # Format 2 ATAC data processing
demo.network('Cones', 20, 0) # PECA2 GRN construction
The details of each function can be viewed in python.
Output
sample_name_network.txt
System & Software Requirements
System: linux
Linux software: Homer
Python package: pybedtools, ismember, scipy, numpy_groupies,
Considerations
- RNA data preprocessing currently supports only hg38 and mm10 genomes.
- pybedtools may not support the latest version of python and will require the creation of a new environment.
Project details
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