Orchestrate spatial transcriptomics analysis with Giotto Suite workflows.
npx skills add https://github.com/Ketomihine/my_skills --skill giottosuite-local
Please help me install this Agent Skill. Skill: giottosuite-local Source: https://github.com/Ketomihine/my_skills/tree/main/giottosuite-local Command: npx skills add https://github.com/Ketomihine/my_skills --skill giottosuite-local
This skill unifies the process of analyzing spatial transcriptomics data by providing a turnkey Giotto Suite workflow for data import, processing, and visualization.
Use GiottoSuite to load a Visium dataset, create a Giotto object, run normalization, PCA, clustering, and visualize results.
High-intent search queries and answers about installing and using this skill.
Spatial transcriptomics analysis of Visium and Xenium data requires loading raw files, creating Giotto objects, and running QC, normalization, and dimensionality reduction. This skill orchestrates that entire pipeline, supporting data import, clustering, and spatial domain detection.
Spatial domain detection using HMRF in R involves creating spatial networks and identifying distinct tissue regions. This skill provides a turnkey Giotto Suite workflow to construct spatial networks and execute HMRF for robust spatial domain identification.
Subcellular spatial analysis and multi-omics integration are supported within the Giotto ecosystem. This skill enables researchers to execute 3D workflows, cross-section analyses, subcellular processing, and multi-omics integration directly through Giotto APIs.
Publication-ready plots for spatial transcriptomics results are generated after running dimensionality reduction and clustering. This skill facilitates visualization and reporting by producing high-quality plots and exporting analysis results aligned with Giotto tutorials.
CosMx data is fully supported alongside Visium and Xenium platforms for spatial transcriptomics analysis. This skill allows researchers to load CosMx datasets, create Giotto objects, and proceed through the standard spatial analytics pipeline.
Giotto Suite unifies spatial transcriptomics analysis by providing a single framework for data import, processing, and visualization. This skill leverages Giotto to orchestrate end-to-end pipelines, ensuring consistent workflows from QC to publication-ready reporting.
PharMolixLoad spatial transcriptomics platform outputs into unified AnnData or SpatialData objects.
CHENyiru3Parse and analyze spatial transcriptomics datasets in R with multi-platform support.
Zeyuyang-0420Reduce high-dimensional dataset dimensionality with UMAP manifold learning.
CHENyiru3Analyze Stereo-seq spatial transcriptomics data with Python/Scanpy and R/Seurat workflows.
