Load Seurat RDS or qs/qs2 objects into the immunopipe pipeline.
npx skills add https://github.com/pwwang/immunopipe --skill loadingrnafromseurat
Please help me install this Agent Skill. Skill: loadingrnafromseurat Source: https://github.com/pwwang/immunopipe/tree/main/skills/loadingrnafromseurat Command: npx skills add https://github.com/pwwang/immunopipe --skill loadingrnafromseurat
Load pre-existing Seurat objects into the immunopipe pipeline instead of starting from raw count matrices via SampleInfo. This enables analysis on already processed single-cell RNA-seq data stored in Seurat objects.
Specify the Seurat object file in infile and run the pipeline, optionally skipping preprocessing if the object is already prepared.
High-intent search queries and answers about installing and using this skill.
Load a processed Seurat object into immunopipe by specifying the RDS or qs/qs2 file path in the infile parameter, bypassing the need for raw count matrices and SampleInfo.
Analyze multiple Seurat objects simultaneously by providing a list of RDS or qs/qs2 files to the infile parameter for batch single-cell RNA-seq downstream processing.
Immunopipe supports loading Seurat objects with TCR or BCR data by providing VDJ paths via SampleInfo alongside the processed single-cell RNA-seq data.
Skip preprocessing by setting the prepared environment flag, and use the clustered flag to indicate existing clusters when importing a Seurat object into immunopipe.
Loading Seurat RDS files directly serves as an alternative entry point when SampleInfo is not needed, allowing analysis of already processed single-cell RNA-seq data without starting from raw counts.
Use the optional sample environment flag to control sample labeling automatically when providing multiple Seurat files for immunopipe single-cell analysis.
ya-wayConvert single-cell data objects between Seurat and Scanpy formats.
pwwangLoad, preprocess, and integrate multi-sample scRNA-seq data into a Seurat object.
danilomongeRuns nf-core/airrflow immune-repertoire analysis from raw reads or assembled data.
zongtingweiPreprocess single-cell RNA-seq data into analysis-ready AnnData objects.
