Starred repositories
Local-first session search, analytics, insights, and token use statistics for coding agents, supporting Claude Code, Codex, and more than 20 other agents.
An open, curated collection of Agent Skills for scientific research — clone it, use it, extend it!
From agent user to agent builder: build a Claude Code-style coding agent from scratch in Python: 8 articles, 4 videos, one codebase
A linear decomposition model for testing microbiome association and mediation
Awesome lists of metagenome-assembled genome (MAG) datasets
🧬 The first region-scale, harmonized #metagenomic catalog for the Middle East & North Africa — 60,126 runs across 24 countries 🌍, featuring an interactive web platform 🖥️, ecological analytics 📊, a…
A structural variation pipeline for short-read sequencing
DPM: code and input files for the publication
Integrative pathway enrichment analysis of multivariate omics data
🧬 gget enables efficient querying of genomic reference databases
A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Code for doing minor analyses related to the IBDverse sc-eQTL propject
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
kapsakcj / amr
Forked from ncbi/amrAMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
A haplotype analysis toolkit for natural variation study.
This repository contains scripts used in the manuscript "Massive expansion of human gut bacteriophage diversity"
Genotype Imputation Pipeline for H3Africa