PaCMAP: Large-scale Dimension Reduction Technique Preserving Both Global and Local Structure

CellWhisperer bridges the gap between transcriptomics data and natural language, enabling intuitive interaction with scRNA-seq datasets

igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

Scalable framework for integrating single-cell omics with genetic data using AnnData.

Seismic R package. Discover cell type-trait associations in minutes for GWAS and single-cell RNA-sequencing data

A 'ggplot2' extension that focusses on expanding the plotter's arsenal of guides, such as axes, legends and colour bars. It brings various improvements to existing guides by re-implementation, as w…

Single-cell eQTL GWAS colocalization tool

Python tool for converting files and office documents to Markdown.

The lean application framework for Python. Build sophisticated user interfaces with a simple Python API. Run your apps in the terminal and a web browser.

The AnnSQL package enables SQL based queries on AnnData objects.

Highlight points and lines in ggplot2

Universal multi-language runner and smart REPL written in Rust.

An extensible, state of the art columnar file format. Formerly at @spiraldb, now an Incubation Stage project at LFAI&Data, part of the Linux Foundation.

Easy genomic regions for short-read variant calling

GeneSetCluster 2.0: a comprehensive toolset for summarizing and integrating gene-sets analysis

Public repo for rbio, a biologically-informed reasoning model trained on virtual cell models as verifiers

Expose the contents of .docx files without leaving your terminal. Fast, safe, and smart — no Office required!

A Rust-Based suite of utilities for ultra-fast genomic feature extraction

Distance-based Phylogenetic Placer

Detection and quantify alternative polyA site

PerturbNet is a deep generative model that can predict the distribution of cell states induced by chemical or genetic perturbation

Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome

A geom for ggplot to create bump plots

Quantification of isoform usage and alternative polyadenylation (APA) from single-cell RNA-seq using a Nextflow-based pipeline.

This API provides programmatic access to the AlphaGenome model developed by Google DeepMind.