AI Agent Skills

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCoun…

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

Cell type annotation for single-cell RNA-seq using multi-LLM consensus

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

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

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, sin…

Unified biological database evidence owner. Use for gene annotation, variant clinical significance, cancer mutation evidence, GWAS trait associations, pathway mapping, t…

Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the ce…

rapids-singlecell: GPU-accelerated framework for scRNA analysis

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 Omic…

omics-plotting: publication-style figure authoring for omics / bioinformatics results with matplotlib / seaborn. Read this before writing any plotting or figure code in…

Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.

Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data

Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation.…

Predict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-function model outputting RNA-seq, CAGE, ATAC, and ChIP covera…