Stars
A small R package to make sequencing read coverage plots in R.
Identify which human reference genome was used to align a BAM/SAM/CRAM file
a set of SKILLS.md for doing bioinformatics with agents like claude code
A set of ready to use Agent Skills for research, science, engineering, analysis, finance and writing.
Examples of my Claude Code infrastructure with skill auto-activation, hooks, and agents
Scientific Inkscape: Inkscape extensions for figure resizing and editing
longcallR is a tool for SNP calling, haplotype phasing, and allele-specific analysis with long-read RNA-seq data.
An efficient CLI to extract sequences from the SRA
A lightweight version of R Markdown (without using Pandoc or knitr)
R/Bioconductor interface to Sanity single-cell normalization method
Visualising data frames as funky heatmaps 📊
Arc Virtual Cell Atlas
💌 Create simple, beautiful personal websites and landing pages using only R Markdown.
Integrative Composable Visualization Framework for ggplot2
📦 Repomix is a powerful tool that packs your entire repository into a single, AI-friendly file. Perfect for when you need to feed your codebase to Large Language Models (LLMs) or other AI tools lik…
A CLI tool to convert your codebase into a single LLM prompt with source tree, prompt templating, and token counting.
Specify a github or local repo, github pull request, arXiv or Sci-Hub paper, Youtube transcript or documentation URL on the web and scrape into a text file and clipboard for easier LLM ingestion
Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs
Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.
AI model evaluation with a focus on healthcare
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
tools in python and R for analyzing biological count data, especially from single cell RNAseq
A thorough tutorial on HLA imputation and association, accompanying our manuscript "Tutorial: A statistical genetics guide to identifying HLA alleles driving complex disease"
Visual exploratory analysis of gene expression data