Home Languages Developers Organizations Search You No Language Curated list of AI and deep learning tools for phage functional annotation and structural biology. A comprehensive course teaching R and the tidyverse for biology graduate students. Hands-on RMarkdown lessons from basics to RNA-seq, microbiome, and metagenomics analysis. Analysis of the oral bacterial microbiome by 16S amplicon analysis in HIV infected men R code associated with neurodegeneration study Code used to generate the results of the rotabiome study HTML Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since. A stenographic grammar for efficient human-AI coding collaboration. Terse commands, workflow tracking, and seamless Claude Code integration. AI-powered quick reference for R functions that provides concise, practical help using LLMs (Claude/OpenAI). Get example-focused documentation with customizable character voices, smart caching, and offline support. tldrAI makes R function documentation more accessible, efficient, and even entertaining. Analysis of 16S rRNA (dada2 amplicon sequence variants) from human volunteers given various vaccines following two different antibiotics treatments compared to no antibiotics. West Nile Virus Infection in mice treated with vehicle or various antibiotics: https://www.ncbi.nlm.nih.gov/pubmed/29590614 JavaScript Project dashboard for the National Institutes of Health Human Virome Program Jupyter Notebook Context and recommendations for using Claude code for bioinformatics Python A listing of software, tools and databases useful for virome analysis hecatomb is a virome analysis pipeline for analysis of Illumina sequence data Git-based viral taxonomy management system - track changes, migrate datasets, and cite specific versions. Website: https://shandley.github.io/ICTV-git/ Pipeline to analyze Claude Opus 4.5 writing patterns and generate a styleguide for avoiding LLM-isms Viral contig analysis (hecatomb-lite) Comprehensive QC pipeline for VLP-enriched virome sequencing (NovaSeq + RdAB) Hallmark gene panel for phage ecology fingerprinting Design viral hybrid capture probe panels, from taxonomy selection through synthesis-ready output. Pairs with virotaxa. Viral protein annotation using structural homology ViroForge: Synthetic virome data generator for benchmarking and validation Reproducible viral taxa selection from Virus-Host Database Detect chromosome-level scaffolds in genome assemblies with inconsistent naming conventions Claude Code skill that searches the last 30 days of scientific literature across OpenAlex, Semantic Scholar, PubMed, arXiv, and HuggingFace Hub Snakemake RNA-seq pipeline: snake venom gland vs other tissues (StringTie2 + Salmon + DESeq2) R Package to assist in integrative analysis of Female Genital Tract Microbiome Data Generalized dada2 workflow. Refer to the wiki for help and troubleshooting. R package that relates different microbiome diversity metrics to each other through information theory, so results can be compared across studies. R package for plotting biological culture plates and microplates, supporting several well naming schemes and both continuous and discrete values. A package for virome study power analysis Rust Composable primitives for differential abundance analysis of microbiome data High-performance virome-specific QC platform for the Human Virome Program Shell Miscellaneous scripts for handling Illumina sequencing of virus isolates. TypeScript Grammar of Graphics primitive catalog: 65 geoms, 73 scales, terminal and Vega-Lite backends, Claude Code AI integration A modern, web-based Hi-C contact map viewer and genome assembly curation tool
