Data & Analytics · AnnData · For researchers

Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.

davila7/claude-code-templates

Runs differential gene expression analysis on bulk RNA-seq counts with PyDESeq2: design formulas, Wald tests, FDR correction and volcano or MA plots.

davila7/claude-code-templates

Runs a seven-step quality-control and exploration pipeline on scRNA-seq, CyTOF or flow cytometry data and writes a plain-language report of what it found.

LigphiDonk/Oh-my--paper

Data structure for annotated matrices in single-cell analysis; use when reading/writing .h5ad (or zarr) and exchanging data with the scverse ecosystem.

aipoch/medical-research-skills

Load when removing ambient RNA contamination from droplet-based scRNA-seq using a simple subtraction path, CellBender, or SoupX.

TianGzlab/OmicsClaw

Load when computing cell-cell ligand-receptor communication on an annotated scRNA AnnData via builtin scorer, LIANA, CellPhoneDB, CellChat (R), or NicheNet (R).

TianGzlab/OmicsClaw

Load when testing whether cell-type / cluster proportions or neighbourhood densities differ between conditions in a multi-sample scRNA AnnData via Milo, scCODA, simple proportion screen, or R…

TianGzlab/OmicsClaw

Load when extracting gene programs (NMF / cNMF factorisation) and per-cell program usage scores from a non-negative scRNA AnnData.

TianGzlab/OmicsClaw

Load when ordering cells along a developmental trajectory in a normalised scRNA AnnData via DPT, Palantir, VIA, CellRank, Slingshot (R), or Monocle3 (R).

TianGzlab/OmicsClaw

Load when computing RNA velocity vectors on a scRNA AnnData with spliced / unspliced layers via scVelo (stochastic / dynamical / steady-state); dynamical mode additionally exports latent time.

TianGzlab/OmicsClaw

Load when running the foundational spatial transcriptomics QC + filtering + normalisation + HVG + PCA + neighbour-graph + Leiden pipeline on a Visium / Xenium / generic spatial AnnData.

TianGzlab/OmicsClaw

Load when inferring pseudotime / lineage trajectories on a preprocessed spatial AnnData via DPT (default — diffusion pseudotime), CellRank (terminal-state + fate-probability), or Palantir (waypoint…

TianGzlab/OmicsClaw

Load when estimating RNA velocity on a spatial AnnData with layers["spliced"] + layers["unspliced"] via scVelo (stochastic / deterministic / dynamical) or veloVI (deep generative).

TianGzlab/OmicsClaw

A skill your agent uses for OmicVerse bulk RNA-seq, enrichment/signature scoring, metabolomics, proteomics, microbiome, and statistical table workflows.

VectorSpaceLab/AREX-Skill