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TianGzlab 的 Skills 91
demo-skill
A fixture skill for the skill environment tests. Use it for nothing else.
fake-domains
Test fixture for the golden deployment in tests/entry. Load never; it has no script.
replace-me-skill
Load when copying this directory to bootstrap a new OmicsClaw skill. Skip when an existing skill already covers the request.
spatial-velocity
Load when estimating RNA velocity on a spatial AnnData with `layers["spliced"]` + `layers["unspliced"]` via scVelo (stochastic / deterministic / dynamical) or veloVI (deep generative). Skip when input lacks the spliced/unspliced layers (must be quantified upstream by velocyto / kb-python / STARsolo); non-spatial scRNA velocity (use sc-velocity).
spatial-trajectory
Load when inferring pseudotime / lineage trajectories on a preprocessed spatial AnnData via DPT (default — diffusion pseudotime), CellRank (terminal-state + fate-probability), or Palantir (waypoint branch probabilities). Skip when the data has spliced/unspliced layers and you want velocity-driven dynamics (use spatial-velocity); non-spatial scRNA pseudotime (use sc-pseudotime).
spatial-statistics
Load when running spatial autocorrelation / hotspot / co-occurrence / neighbourhood-enrichment / Ripley K stats on a clustered spatial AnnData via squidpy. Skip when ranking spatially variable genes (use spatial-genes); tissue domain detection (use spatial-domains).
spatial-register
Load when aligning multiple spatial slices into a common coordinate frame with PASTE or STalign. Skip single-slice data; for expression-space batch correction use spatial-integrate.
spatial-raw-processing
Load when converting spatial transcriptomics raw FASTQ pairs through ST-Pipeline into a `raw_counts.h5ad` ready for spatial-preprocess. Skip when input is already a count-matrix AnnData (use spatial-preprocess); non-spatial bulk / scRNA FASTQ (use bulkrna-read-qc).
spatial-preprocess
Load when running the foundational spatial transcriptomics QC + filtering + normalisation + HVG + PCA + neighbour-graph + Leiden pipeline on a Visium / Xenium / generic spatial AnnData. Skip when raw FASTQs need converting first (use spatial-raw-processing); tissue-domain detection on already-preprocessed data (use spatial-domains).
spatial-microenvironment-subset
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 neighbours. Skip when running global tissue-domain detection (use spatial-domains); cross-condition comparison (use spatial-condition).
spatial-integrate
Load when removing batch effects from multi-batch spatial AnnData with PCA using Harmony, BBKNN, or Scanorama. Skip physical coordinate alignment (use spatial-register) and single-batch data (use spatial-domains).
spatial-genes
Load when ranking spatially variable genes with Moran's I, SpatialDE, SPARK-X, or FlashS. Skip when detecting tissue domains (use spatial-domains) or differential expression between groups (use spatial-de).
spatial-enrichment
Load when running pathway or gene-set enrichment per cluster on spatial AnnData with over-representation, preranked GSEA, or ssGSEA group-mean scores. Skip when ranking spatially variable genes (use spatial-genes) or comparing conditions (use spatial-condition).
spatial-domains
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). Skip when ranking spatially variable genes (use spatial-genes); spot-level cell-type annotation (use spatial-annotate).
spatial-deconv
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). Skip when each spot is a single cell already (Xenium / MERFISH) (use spatial-annotate); tissue-domain detection (use spatial-domains).
spatial-de
Load when ranking spatial cluster markers or comparing two spatial groups. Skip when the data is single-cell (use sc-de), bulk (use bulkrna-de), or for spatially variable expression (use spatial-genes).
spatial-condition
Load when comparing conditions on spatial AnnData using biological-sample pseudobulk PyDESeq2 or Wilcoxon, with sample, condition and cluster labels. Skip one-condition per-cluster DE (use spatial-de) and experiments without independent replicates.
spatial-communication
Load when computing ligand-receptor communication on labelled spatial AnnData with LIANA, CellPhoneDB, FastCCC or CellChat. Skip unlabelled data (use spatial-annotate) and non-spatial scRNA analysis (use sc-cell-communication).