Annotate scRNA-seq clustering results with cell type labels using multiple tools.
npx skills add https://github.com/pwwang/immunopipe --skill celltypeannotation
Please help me install this Agent Skill. Skill: celltypeannotation Source: https://github.com/pwwang/immunopipe/tree/main/skills/celltypeannotation Command: npx skills add https://github.com/pwwang/immunopipe --skill celltypeannotation
Annotates clustering results with biological cell type labels to give meaningful identities to clusters, enabling downstream interpretation and comparison across samples.
Supply your Seurat clustering results and run this workflow to obtain labeled cell types for each cluster.
High-intent search queries and answers about installing and using this skill.
Cell-type annotation for scRNA-seq data is performed by applying automated tools like ScType, scCATCH, hitype, or CellTypist to assign biological labels to clusters for downstream interpretation.
Yes, you can use CellTypist and scCATCH for immune cell datasets. The workflow seamlessly integrates with Seurat objects to deliver labeled cell types for each cluster.
Yes, the workflow supports h5ad inputs and applies to post-clustering analyses across multi-sample datasets, enabling configurable input formats and output columns for reproducible annotation.
You can compare direct assignment against automated tools like ScType, scCATCH, hitype, or CellTypist by configuring tool choices and tissue specifications within the same reproducible annotation workflow.
You can configure tissue specifications, database paths, tool choices, and output columns within the workflow to ensure annotation tools correctly match your specific scRNA-seq dataset context.
CHENyiru3Convert Python h5ad single-cell data into Seurat or SingleCellExperiment objects.
tony-zhelonkinModel sample identity as biological variation in multi-donor scRNA-seq data with MRVI.
robinbarvaagAnalyze single-cell RNA-seq data with preprocessing, clustering, and visualization.
awslabsAssign cell type labels to single-cell RNA-seq clusters using automated classifiers.
