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A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Differential expression of RNA-seq data using the Negative Binomial

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

🛠️ Build tools for Web Components.

Combined RNA and ATAC Footprint Training of Gene Regulatory Network

197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Powers OmicsHorizon.