AnnData agent skills, page 2

Load when scoring drug sensitivity per cluster on an annotated scRNA AnnData via simple-correlation against drug-target signatures or via CaDRReS-Sc pretrained models (GDSC / PRISM).

TianGzlab/OmicsClaw

Load when running bulk-style pathway enrichment (ORA / GSEA / GSEA-R / GSVA-R) on a per-group ranked DE / marker list against a gene-set library.

TianGzlab/OmicsClaw

Load when removing low-quality cells and lowly-detected genes from a single-cell AnnData using QC-derived thresholds or tissue presets.

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 inferring TF → target gene regulatory networks on a normalised scRNA AnnData via pySCENIC (GRNBoost2 + cisTarget + AUCell) or correlation-based GRN fallback (when arboreto is unavailable…

TianGzlab/OmicsClaw

Load when predicting in-silico gene knockout effects on a normalised scRNA AnnData via GRN-based propagation (Python) or scTenifoldKnk (R).

TianGzlab/OmicsClaw

Load when running a single batch-correction representation (none/Harmony/Scanorama/scVI) + clustering of single-cell data as one self-contained unit — normally fanned out as a member of…

TianGzlab/OmicsClaw

Load when ranking cluster-level marker genes from a clustered single-cell AnnData via Scanpy Wilcoxon / t-test / logreg or COSG specificity.

TianGzlab/OmicsClaw

Load when aggregating single cells into metacells (sample-aware coarse-grained pseudo-cells) on a normalised scRNA AnnData via SEACells or KMeans on a low-D embedding.

TianGzlab/OmicsClaw

Load when merging multiple single-sample scRNA-seq count matrices (one per sample-from-sc-count) into a single downstream-ready AnnData with sample labels.

TianGzlab/OmicsClaw

Load when computing per-cell pathway / gene-set scores on a normalised scRNA AnnData via AUCell (R or Python) or Scanpy scoregenes.

TianGzlab/OmicsClaw

Load when classifying perturbed vs non-perturbed cells in a Perturb-seq / CRISPR-screen scRNA AnnData via the pertpy Mixscape workflow.

TianGzlab/OmicsClaw

Load when attaching cell-barcode → sgRNA assignments from a mapping TSV/CSV onto a Perturb-seq expression AnnData, producing standardised perturbation / sgRNA / target-gene obs columns.

TianGzlab/OmicsClaw

Load when normalising QC'd scRNA into a PCA-ready AnnData via scanpy / Seurat / SCTransform / Pearson residuals.

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 per-cell QC metrics (ngenes, total counts, mt%, ribo%) on a single-cell AnnData before filtering.

TianGzlab/OmicsClaw

Load when an external single-cell h5ad/h5/loom/mtx needs to be canonicalised onto the OmicsClaw AnnData contract before downstream scRNA skills run.

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 generating spliced / unspliced layers from Cell Ranger BAM, FASTQ, STARsolo output, or velocyto loom — the prerequisite for sc-velocity.

TianGzlab/OmicsClaw

Load when preprocessing a single-cell ATAC peak × cell AnnData via Signac-style TF-IDF + LSI + Leiden, producing a clustered UMAP-ready object.

TianGzlab/OmicsClaw

Load when assigning per-spot cell-type labels on a spatial AnnData via marker-gene scoring or scRNA-reference mapping (Tangram / scANVI / CellAssign).

TianGzlab/OmicsClaw

Load when inferring copy-number variation per spot on a preprocessed spatial AnnData with chromosome-annotated genes via infercnvpy (default — log-ratio sliding-window) or Numbat (R, allele-aware…

TianGzlab/OmicsClaw

Load when computing ligand-receptor cell-cell communication on a preprocessed spatial AnnData with obs[celltypekey] (default leiden) via LIANA (default), CellPhoneDB, FastCCC, or CellChat (R).

TianGzlab/OmicsClaw

Load when comparing two or more experimental conditions (treatment vs control) on a multi-sample preprocessed spatial AnnData via PyDESeq2 pseudobulk or Wilcoxon DE — needs obs[conditionkey]…

TianGzlab/OmicsClaw

Load when ranking spatial cluster markers or comparing two spatial groups in spatial transcriptomics.

TianGzlab/OmicsClaw

Load when deconvolving spot-level cell-type proportions on a Visium-style spatial AnnData using a labelled scRNA reference (FlashDeconv / Cell2location / RCTD / DestVI / Tangram / others).

TianGzlab/OmicsClaw

Load when detecting tissue domains / niches on a preprocessed spatial AnnData via Leiden / Louvain (spatial-weighted) or graph-neural backends (SpaGCN / STAGATE / GraphST / BANKSY / CellCharter).

TianGzlab/OmicsClaw

Load when running pathway / gene-set enrichment per cluster on a preprocessed spatial AnnData via Enrichr (over-representation), GSEA (preranked), or ssGSEA (per-cell scores).

TianGzlab/OmicsClaw

Load when ranking spatially variable genes (SVGs) on a preprocessed spatial AnnData via Moran's I, SpatialDE, SPARK-X, or FlashS.

TianGzlab/OmicsClaw

Load when removing batch effects across multiple spatial samples on a multi-batch spatial AnnData via Harmony, BBKNN, or Scanorama before downstream analysis.

TianGzlab/OmicsClaw

Load when extracting a niche / microenvironment subset around a center cell-type by spatial radius from a labelled spatial AnnData, producing a smaller AnnData of centers + their within-radius…

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 converting spatial transcriptomics raw FASTQ pairs through ST-Pipeline into a rawcounts.h5ad ready for spatial-preprocess.

TianGzlab/OmicsClaw

Load when aligning multiple spatial slices into a common coordinate frame on a multi-slice spatial AnnData via PASTE optimal transport or STalign image-aware registration.

TianGzlab/OmicsClaw

Load when running spatial autocorrelation / hotspot / co-occurrence / neighbourhood-enrichment / Ripley K stats on a clustered spatial AnnData via squidpy.

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

Programmatically query the CZ CELLxGENE Census (61M+ cells) when you need cross-tissue, disease, or cell-type expression data for population-scale queries and reference atlas comparisons.

aipoch/medical-research-skills

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

VectorSpaceLab/AREX-Skill

Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.

majiayu000/claude-skill-registry