/SLE

Primary LanguageJupyter Notebook

SLE

The Python Code for the analysis of bulk ATAC-seq and single cell RNA-seq data of SLE patients and healthy controls

1. Requirement

We analyzed the scRNA-seq data in a Linux system with Python (version 2.7),R (version 3.5) enviroment. The following software and packages are also required:

software version enviroment
ATAC-pipe - Linux
samtools 1.9 Linux
bedtools 2.26.0 Linux
bowtie2 2.3.0 Linux
macs2 2.1.1 Linux
picard 2.9.2 Linux
homer 4.9.0 Linux
numpy 1.11.0 python
pysam 0.11 python
matplotlib 2.0.2 python
pandas 0.20.3 python
seaborn 0.9.1 python
scipy 0.19.1 python
circlize - R

2. Installation

Users need to copy the scripts to the same path as the "SourceData" folder.

3. Analysis

Users can run these scripts in Jupyter notebook directly, and get the figures of our paper.