ShangBioLab

ShangBioLab/SpatialClaw

Instructions file CodexOpenCode

Instructions for ShangBioLab/SpatialClaw, covering agents.md — spatialclaw guide for ai coding agents, project overview, setup, commands and project structure.

ShangBioLab/SpatialClaw

Instructions file

Instructions for ShangBioLab/SpatialClaw, covering claude.md — spatialclaw agent instructions, spatial skill routing, cli reference, skill use rules and bot frontends.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Top-level spatial orchestration entry that delegates to the canonical spatial-orchestrator skill without restoring removed non-spatial skill trees.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Cell type annotation for spatial transcriptomics data using marker-based scoring, Tangram mapping, scANVI transfer, or CellAssign probabilistic models.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Cell-cell communication analysis via ligand-receptor scoring using built-in scoring, LIANA, CellPhoneDB, or FastCCC.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Copy number variation inference from spatial transcriptomics expression data using Python-native inferCNVpy.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Experimental condition comparison using pseudobulk differential expression with proper multi-sample statistics.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Differential expression analysis — find marker genes for clusters or compare two groups. Supports Wilcoxon rank-sum, t-test, and PyDESeq2 methods with publication-ready figures and CSV tables.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Cell-type deconvolution for spatial transcriptomics by mapping a single-cell RNA-seq reference onto spatial data.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Identify tissue regions and spatial niches from preprocessed spatial transcriptomics data using Leiden, Louvain, SpaGCN, STAGATE, GraphST, or BANKSY.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Pathway and gene set enrichment analysis for spatial transcriptomics data.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Python API skill for histology image analysis linked to spatial transcriptomics workflows, including tissue segmentation and nuclei/cell detection.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Multi-sample integration and batch correction for spatial transcriptomics data.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Identify spatial domains with DeepST or PearlST. This skill is directory-only: use --input /path/to/sample for single-sample runs; use --mode integration --input-list samples.txt only with DeepST.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Python API skill for morphology feature extraction and image-expression feature fusion in spatial analysis workflows.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Multi-sample spatial transcriptomics integration and batch correction with automatic method selection (STAligner, Harmony, BBKNN, Scanorama) and robust fallback.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Python API skill for spatial niche and tissue microenvironment discovery, characterization, and cross-condition comparison.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Integrate two aligned spatial omics modalities on the same cells using SpatialGlue or SpaDDM. Standard input contract: --input --omics2 . Supports demo mode and validated modality pairs such as RNA+Protein and RNA+ATAC.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Python API skill for oncology-focused spatial downstream analysis including tumor ecosystem mapping and exploratory response-associated pattern summaries.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Route natural language requests and file inputs to registered SpatialClaw skills, and run named spatial analysis pipelines.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Load spatial transcriptomics data (Visium, Xenium, MERFISH, Slide-seq, generic h5ad), perform QC filtering, normalization, HVG selection, PCA, UMAP, and Leiden clustering.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Spatial registration and multi-slice alignment for spatial transcriptomics data.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Python API skill for spatial transcription-factor activity and regulatory network inference.

ShangBioLab/SpatialClaw

Skill Claude CodeCodex

Python API skill for mapping reference single-cell annotations and expression programs onto spatial transcriptomics data.