Agent Skills by vvvv
Showing 27 vetted skills indexed across 1 GitHub repositories.
chenyhvvvvtrajectory-pseudotime
Infer cell developmental trajectories and pseudotime ordering from gene expression data.
chenyhvvvvspatial-domain-detection
Detect spatial domains in spot-level transcriptomics data using SpaGCN.
chenyhvvvvdeconvolution-flashdeconv
Estimate cell type proportions in spatial transcriptomics spots using an scRNA-seq reference.
chenyhvvvvintegration-scanorama
Correct batch effects across spatial slices using Scanorama integration.
chenyhvvvvregistration-paste
Align multiple spatial transcriptomics slices using PASTE optimal transport.
chenyhvvvvcell-communication-cellphonedb
Identify significant ligand-receptor interactions in human single-cell datasets using CellPhoneDB.
chenyhvvvvdifferential-expression
Identify differentially expressed genes across defined groups in AnnData objects.
chenyhvvvvenrichment-ora
Identify enriched pathways in gene lists using Fisher's exact test across KEGG, Reactome, MSigDB Hallmark, WikiPathways, and GO gene sets.
chenyhvvvvspatial-domain-stagate
Identify spatial domains in single-slice spatial transcriptomics data using STAGATE's graph-attention auto-encoder.
chenyhvvvvdeconvolution-cell2location
Estimate per-spot cell-type proportions with uncertainty using Bayesian deconvolution from scRNA-seq references.
chenyhvvvvcelltype-deconvolution
Automates RCTD cell-type deconvolution on spatial transcriptomics data, producing per-spot proportions and dominant celltype labels.
chenyhvvvvspatial-domain-graphst
Detect spatial domains in spot-level transcriptomics data using GraphST clustering.
chenyhvvvvspatial-statistics
Compute Moran's I, Ripley's K/L, co-occurrence, and centrality for spatial transcriptomics data.
chenyhvvvvcelltype-annotation-fast
Annotate cell types in spatial transcriptomics data using clustering, marker analysis, and LLM labeling.
chenyhvvvvniche-detection
Identify spatial cellular niches in single-slice spatial transcriptomics data using Harmonics hierarchical modeling.
chenyhvvvvpathway-go-enrichment
Perform GO enrichment analysis on gene lists using gseapy with FDR correction.
chenyhvvvvintegration-bbknn
Modifies neighbor graph with BBKNN to batch-correct across multiple slices and outputs joint UMAP embedding and Leiden clusters.
chenyhvvvvsvg-spatialde
Identify spatially variable genes in spatial transcriptomics data with SpatialDE.
chenyhvvvvspatial-stats-neighborhood-enrichment
Compute neighborhood enrichment z-scores from spatial neighbor graphs.
chenyhvvvvpathway-ssgsea
Compute per-cell pathway activity scores for spatial transcriptomics data using ssGSEA.
chenyhvvvvintegration-harmony
Align PCA embeddings across spatial transcriptomics slices with Harmony batch correction.
chenyhvvvvcnv-inference
Infer CNV scores and clone labels from spatial transcriptomics AnnData objects.
chenyhvvvvpathway-enrichment-compare
Compare enrichment between two gene lists and draw a mirrored bar plot.
chenyhvvvvalignment-stalign
Align cell-level spatial transcriptomics slices with STalign using landmark pairs and LDDMM.