AI Agent Skills

Single-cell analysis in Python. Scales to >100M cells.

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…

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill…

Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene…

Primary retained Python toolkit for molecular biology sequence work. Preferred for sequence manipulation, FASTA/FASTQ/GenBank parsing, Bio.Entrez, BLAST workflows, align…

Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use w…

Query the CZ CELLxGENE Census (61M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnDa…