Scott Handley http://evomics.org handley.scott@gmail.comProfessor @ Washington University in St. Louis. Founder and occasional director of some bioinformatics Workshops. 68 2 84 204 69 No Language awesome-phage-structure 2 0 HIV-Oral 1 1 Analysis of the oral bacterial microbiome by 16S amplicon analysis in HIV infected men neurodegeneration_16S 1 0 R code associated with neurodegeneration study rotabiome 1 0 Code used to generate the results of the rotabiome study r-tidyverse-for-biologists 1 0 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.HTML awesome-virome 75 13 A listing of software, tools and databases useful for virome analysis Microbiome-Analysis-Using-R 28 21 Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since. stenograph 1 0 A stenographic grammar for efficient human-AI coding collaboration. Terse commands, workflow tracking, and seamless Claude Code integration. tldrAI 1 1 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. human_volunteer_rotabiome 0 5 Analysis of 16S rRNA (dada2 amplicon sequence variants) from human volunteers given various vaccines following two different antibiotics treatments compared to no antibiotics. WNV-antibiotics 0 2 West Nile Virus Infection in mice treated with vehicle or various antibiotics: https://www.ncbi.nlm.nih.gov/pubmed/29590614Jupyter Notebook claude-for-bioinformatics 11 0 Context and recommendations for using Claude code for bioinformaticsPython hecatomb 60 13 hecatomb is a virome analysis pipeline for analysis of Illumina sequence data ICTV-git 2 0 Git-based viral taxonomy management system - track changes, migrate datasets, and cite specific versions. Website: https://shandley.github.io/ICTV-git/ claude-style-guide 1 0 Pipeline to analyze Claude Opus 4.5 writing patterns and generate a styleguide for avoiding LLM-isms decatomb 1 0 Viral contig analysis (hecatomb-lite) lab-virome-QC 1 2 Comprehensive QC pipeline for VLP-enriched virome sequencing (NovaSeq + RdAB) phageprint 1 0 Hallmark gene panel for phage ecology fingerprinting probesmith 1 0 vhold 1 0 Viral protein annotation using structural homology viroforge 1 1 ViroForge: Synthetic virome data generator for benchmarking and validation virotaxa 1 0 Reproducible viral taxa selection from Virus-Host Database chromdetect 0 1 Detect chromosome-level scaffolds in genome assemblies with inconsistent naming conventions research30 0 1 Claude Code skill that searches the last 30 days of scientific literature across OpenAlex, Semantic Scholar, PubMed, arXiv, and HuggingFace HubR microFGT 2 1 Package to assist in integrative analysis of Female Genital Tract Microbiome Data dada2-workflow 1 1 Generalized dada2 workflow. Refer to the wiki for help and troubleshooting. diversityGPT 1 0 ggplateplus 1 0 viromePower 1 0 A package for virome study power analysisRust composable-daa 1 1 Composable primitives for differential abundance analysis of microbiome data virome-qc 0 1 High-performance virome-specific QC platform for the Human Virome ProgramShell virus_isolate_sequencing 2 1 Miscellaneous scripts for handling Illumina sequencing of virus isolates. dotfiles 1 0 macOS dotfiles for bioinformatics on Apple Silicon — zsh, Homebrew, Claude Code, modern CLI tools viral_genome_sop 0 1 TypeScript ggterm 2 2 Grammar of Graphics primitive catalog: 65 geoms, 73 scales, terminal and Vega-Lite backends, Claude Code AI integration
