Load spatial transcriptomics data and perform quality control with scverse tools.
npx skills add https://github.com/Minions-Land/AutOmicScience --skill omics-spatial
Please help me install this Agent Skill. Skill: omics-spatial Source: https://github.com/Minions-Land/AutOmicScience/tree/main/skills/omics/spatial Command: npx skills add https://github.com/Minions-Land/AutOmicScience --skill omics-spatial
This Skill addresses the complexity of spatial transcriptomics by providing a standardized, reproducible framework for loading, quality-controlling, and analyzing spatial data across multiple platforms like Visium, Xenium, and MERFISH.
Use the omics-spatial skill to load your spatial data and perform initial quality control by running the omics_runtime read_spatial command followed by the spatial_qc method.
High-intent search queries and answers about installing and using this skill.
Spatial transcriptomics quality control across Visium and Xenium is performed by loading data into spatialdata containers and applying standardized spatial_qc methods. This ensures reproducible, evidence-backed biological insights across multi-modal platforms.
Identifying spatially contiguous tissue domains in a Visium slide requires running domain detection algorithms integrated with squidpy. This process maps cell-type composition to help understand the tumor microenvironment.
Yes, scRNA-seq references can be integrated for spot deconvolution and label transfer in spatial data using cell2location and Tangram. This integrates with scverse tools to map cell-type composition accurately.
Spatial transcriptomics analysis supports MERFISH, Stereo-seq, Visium, Xenium, and CosMx platforms through unified loading and validation. Multi-platform support ensures standardized data handling across diverse bioinformatics research.
Detecting spatially variable genes and performing neighborhood enrichment analysis utilizes advanced spatial statistics via squidpy. This includes co-occurrence analysis to provide evidence-backed biological insights within spatialdata containers.
KetomihineOrganize, query, and visualize spatial omics data with a unified Python framework.
omicverseAnnotate tumor single-cell AnnData objects with MetaTiME cell-state labels.
ya-wayCompute spatial statistics for spatial transcriptomics data with Squidpy and Scanpy.
ya-wayAutomate spatial transcriptomics analysis for Visium and Xenium data.
