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Arc Virtual Cell Atlas
💌 Create simple, beautiful personal websites and landing pages using only R Markdown.
Join subcellular Visium HD bins into cells
📦 Repomix (formerly Repopack) 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) o…
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
R implementation of the Reshef and Rumker CNA method (https://github.com/immunogenomics/cna)
A Python toolkit for subcellular analysis of spatial transcriptomics data
A comprehensive toolkit for mutational signature analysis
Visualizing Somatic Alterations of 10X Spatial Transcriptomics Data
A tool for detecting somatic variants in single cell data
A unified interface to spatial transcriptomics deconvolution tools
A performant scientific image visualization system.
Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq
Python and R SOMA APIs using TileDB’s cloud-native format. Ideal for single-cell data at any scale.