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bio-imaging-mass-cytometry-spatial-analysis

GPTomics/bioSkills

Analyze spatial cell-cell interactions, neighborhoods, and niches in IMC/MIBI data with squidpy and imcRtools, covering neighborhood-enrichment permutation nulls, the abundance-vs-density confound, inhomogeneous Ripley's K, cellular-neighborhood discovery, graph-construction (contact vs proximity), and edge effects. Use when testing whether cell types co-locate, choosing a spatial null, building a neighbor graph, discovering tissue niches, or deciding whether a spatial pattern is real or a density/segmentation artifact.

imaging-mass-cytometry-spatial-analysis

swaruplab/operon

Analyze spatial cell-cell interactions, neighborhoods, and niches in IMC/MIBI data with squidpy and imcRtools, covering neighborhood-enrichment permutation nulls, the abundance-vs-density confound, inhomogeneous Ripley's K, cellular-neighborhood discovery, graph-construction (contact vs proximity), and edge effects. Use when testing whether cell types co-locate, choosing a spatial null, building a neighbor graph, discovering tissue niches, or deciding whether a spatial pattern is real or a density/segmentation artifact.

alterlab-squidpy-spatial

AlterLab-IEU/AlterLab-Academic-Skills

Analyzes spatial transcriptomics with squidpy (1.8.x) on AnnData and SpatialData objects, routing platforms correctly: Visium spots use spatial_neighbors(coord_type='grid') and pair with deconvolution, while Xenium/MERFISH single-cell data use coord_type='generic'/Delaunay neighbors and spatialdata-io readers (xenium, visium_hd, merscope). Runs sq.gr.spatial_neighbors, nhood_enrichment, co_occurrence, spatial_autocorr (Moran's I for spatially variable genes), ripley, and ligrec. Use when the user wants spatial transcriptomics, squidpy, Visium/Xenium/MERFISH analysis, neighborhood enrichment, co-occurrence, or spatially variable genes; QC/clustering uses alterlab-scanpy and spot deconvolution (destVI/Tangram) uses alterlab-scvi-tools. Part of the AlterLab Academic Skills suite.

forge

Riley-Coyote/mnemos

Create new OpenClaw agents OR dispatch coding agents to visible terminal sessions. Use when: (1) user asks to create/spin up/forge a new agent, (2) user asks to build/dispatch/delegate a coding task to an agent, (3) user says 'have an agent work on this', (4) user wants parallel coding agents on separate tasks. Triggers: 'create agent', 'new agent', 'spin up agent', 'forge agent', 'build this', 'dispatch', 'send an agent', 'have an agent work on', 'use codex for this'.