Stars
A thorough tutorial on HLA imputation and association, accompanying our manuscript "Tutorial: A statistical genetics guide to identifying HLA alleles driving complex disease"
An interactive explorer for single-cell transcriptomics data
Automatic DCR: a modified version of Decombinator for TCR annotation with automatic tag generation and allele-level output
Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info
Model Context Protocol Servers
A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/
add statistical significance annotations on seaborn plots. Further development of statannot, with bugfixes, new features, and a different API.
A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training.
Chai-1, SOTA model for biomolecular structure prediction
Anomaly detection related books, papers, videos, and toolboxes. Last update late 2025 for LLM and VLM works!
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
Pipeline for designing custom probes against human genes
Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also…
ReapTEC pipeline to simultaneously profile gene expression and enhancer activity in 5' scRNA-seq datasets
Interactive visualization of spatial omics data
Quantifying experimental perturbations at single cell resolution
Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also…
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
Python implementation of Milo for differential abundance testing on KNN graph
🦜🔗 The platform for reliable agents.