TerenceDong's repositories
seqkit
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
CoverM
Read coverage calculator for metagenomics
sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
GutMircobiome_WomenHealth
Disentangling the age-dependent manner in the associations between gut microbiome and women’s health: a multi-cohort microbiome study
rush
A cross-platform command-line tool for executing jobs in parallel
args_oap
ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
xMarkerFinder
Microbial marker identification from cross-cohort datasets
EasyMetagenome
Easy Metagenome Pipeline
MolecularGraph
Notebook tutorials for MolecularGraph.jl
TrimGalore
A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
abricate_ARG
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
EasyMicrobiomeR
Using R language in microbiome analysis
chat-gpt-google-extension
A browser extension to display ChatGPT response alongside Google Search results
metaWRAP
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
COPD_multiomics
This repository contains computer codes for main analyses of the manuscript titled 'Multi-omic Landscape of Airway Microbe-Host Interaction in Chronic Obstructive Pulmonary Disease'.
fastspar
Rapid and scalable correlation estimation for compositional data
interpretable-ai-book
Code associated with my Interpretable AI Book (https://www.manning.com/books/interpretable-ai)
cmseq
Set of utilities on sequences and BAM files
MobileGeneticElementDatabase
Contains a fasta format database of a large variety of mobile genetic elements and an annotation file
microeco
An R package for data analysis in microbial community ecology
AGS-and-ACN-tools
Fast and accurate Average Genome Size and 16S rRNA gene Average Copy Number computation in metagenomic data
GMHI_2020
Scripts for reproducing results shown in Gupta VK et al. "A Predictive Index for Health Status using Species-level Gut Microbiome Profiling". Nature Communications, 2020. https://doi.org/10.1038/s41467-020-18476-8.
MetagenomeProcessing
A pipeline for assembly, annotation and taxonomic classification of metagenomes after sequencing