sitongc / code-for-sc

The code for R & Linux & Python

Srcipts for Sitong Chen

This repository contains a comprehensive set of scripts and tools for analyzing RNA-seq, single-cell RNA-seq (SC-RNAseq), whole genome sequencing (WGS) data, machine learning, and various other tasks.

Project introduce

RNA-seq Analysis: Tools and scripts for processing and analyzing bulk RNA sequencing data.

SC-RNAseq Analysis: Methods for analyzing single-cell RNA sequencing data, including clustering and differential expression analysis.

Whole Genome Sequencing (WGS) Analysis: Pipelines for variant calling, genome assembly, and other WGS tasks.

Machine Learning: Machine learning models for classification, regression, and clustering of omics data.

Miscellaneous Tasks: Scripts for various random tasks related to omics data analysis.

All of the scripts are available in the Scripts/ folder.

Requirements

Basic Requirements: Python, R, Bash, reference genome.

RNA-seq Analysis: STAR, Salmon, DESeq2, DARTS, Leafcutter, rMATS, Snakemake.

SC-RNAseq Analysis: Seurat.

Whole Genome Sequencing (WGS) Analysis: BWA, GATK, bcftools.

Machine Learning: tensorflow, Enformer.

RNA-seq pipeline

Besides the softwares were mentions in the pipeline, this part also include 2 other splicing variant softwares, rMATS and Leafcutter.

It also provided the Snakemake version.

Contributors

Author: Sitong Chen

Email: [email protected]