Pinned Repositories
abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
cobra_analysis
cvn001.github.io
Hexo Blog
PAML_branch_sites_pipeline
PAML pipeline
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."
RecentHGT
A novel bioinformatics pipeline for recent horizontal gene transfer detecting.
secreted_protein_prediction
seq2Fun
seq2Fun provides function to annotate protein or coding sequences with KEGG pathways
srst2
Short Read Sequence Typing for Bacterial Pathogens
transflow
A snakemake workflow for WGS-based tuberculosis transmission analysis
cvn001's Repositories
cvn001/transflow
A snakemake workflow for WGS-based tuberculosis transmission analysis
cvn001/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."
cvn001/secreted_protein_prediction
cvn001/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。
cvn001/chewBBACA
BSR-Based Allele Calling Algorithm
cvn001/chicken-pangenome-paper
Scripts used to perform analyses in Rice et al. (2023)
cvn001/EnterobaseGenomeAssemblyDownload
Python script for downloading assemblies from enterobase
cvn001/GO_KEGG_annotation
GO KEGG annotation
cvn001/HIV-DRIVES
cvn001/HIV-DRM-machine-learning
This repo contains the data and software used to run the analyses in the "Using machine learning and Big data to explore the drug resistance landscape in HIV"
cvn001/HIVepisimAnalysis
cvn001/Lumix-V-log-LUTs
Free LUTs for Panasonic Lumix Vlog color grading
cvn001/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
cvn001/monkeypox
Monkeypox public repository
cvn001/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".
cvn001/panstripe
post processing of bacterial pangenome gene presence/absence matrices
cvn001/pathongs
Pathogen NGS Documentary
cvn001/plasmid-network-analysis
cvn001/plasnet
Clustering, visualising and exploring plasmid networks
cvn001/PopPIPE
Population analysis PIPEline 🛠🧬
cvn001/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
cvn001/QuasiFlow
A Nextflow Pipeline for Analysis of NGS-based HIV Drug Resistance Data
cvn001/ReporTree
A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
cvn001/riboviz
Analysis and Visualization of Ribosome Profiling Data
cvn001/snakepipes
Customizable workflows based on snakemake and python for the analysis of NGS data
cvn001/SNPanalysis
cvn001/sprog
Species Probes Generator
cvn001/superpangenome_construction
cvn001/TBSignatureProfiler
Profile RNA-seq data using published TB gene signatures
cvn001/Unicycler
hybrid assembly pipeline for bacterial genomes