Xiangchen Li's repositories
abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
cvn001.github.io
Hexo Blog
Pangenome-Graphs-in-Infectious-Disease
This repository contains simulated datasets and scripts used for the research paper titled "Pangenome Graphs in Infectious Disease: A Promising and Practical Implementation for Comprehensive Genetic Variation Analysis."
awesome-chatgpt-prompts-zh
ChatGPT 中文调教指南。各种场景使用指南。学习怎么让它听你的话。
chewBBACA
BSR-Based Allele Calling Algorithm
EasyMicrobiome
Scripts and databases for amplicon and metagenome
EnterobaseGenomeAssemblyDownload
Python script for downloading assemblies from enterobase
GO_KEGG_annotation
GO KEGG annotation
Lumix-V-log-LUTs
Free LUTs for Panasonic Lumix Vlog color grading
metaGEM
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
MethylSnake
A Snakemake pipeline for RRBS data analysis
MR_HEM
The code used to conduct the analysis for the study "Li et al., Drug targets for haemorrhoidal disease: proteome-wide Mendelian randomisation and colocalization analyses. Gut 2024".
panstripe
post processing of bacterial pangenome gene presence/absence matrices
pathongs
Pathogen NGS Documentary
PopPIPE
Population analysis PIPEline 🛠🧬
ProteoDisco
Generates protein variant sequences based on imported mutations from VCF, MAF and additional files to generate a protein-variant database for use in proteogenomics studies
quanttb
QuantTB is a SNP based method to identify and quantify individual strains present in tuberculosis whole genome sequencing datasets.
QuasiFlow
A Nextflow Pipeline for Analysis of NGS-based HIV Drug Resistance Data
riboviz
Analysis and Visualization of Ribosome Profiling Data
snakepipes
Customizable workflows based on snakemake and python for the analysis of NGS data
sprog
Species Probes Generator
TBProfiler
Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
TBSignatureProfiler
Profile RNA-seq data using published TB gene signatures
Unicycler
hybrid assembly pipeline for bacterial genomes
VGEA
VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.