loadingrnafromseurat

Load Seurat RDS or qs/qs2 objects into the immunopipe pipeline.

22|4|Updated May 18, 2021

Search Tags:#single-cell #rds #loading #seurat #vdj #immunopipe

Ready to run

npx skills add https://github.com/pwwang/immunopipe --skill loadingrnafromseurat

💬 Prompt for ChatGPT / Claude Chat▼

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

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

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.

Core Features & Use Cases

Supports input as Seurat RDS or qs/qs2 objects.
Allows downstream analysis with immunopipe without SampleInfo.
Works with multiple samples by providing a list of files.

Quick Start

Specify the Seurat object file in infile and run the pipeline, optionally skipping preprocessing if the object is already prepared.

Frequently Asked Questions about loadingrnafromseurat

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I load a processed Seurat object into immunopipe without raw counts?▼

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.

Can I analyze multiple Seurat objects in a single immunopipe run?▼

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.

Does immunopipe support loading Seurat objects with existing TCR or BCR VDJ data?▼

Immunopipe supports loading Seurat objects with TCR or BCR data by providing VDJ paths via SampleInfo alongside the processed single-cell RNA-seq data.

How do I skip preprocessing when importing a clustered Seurat object?▼

Skip preprocessing by setting the prepared environment flag, and use the clustered flag to indicate existing clusters when importing a Seurat object into immunopipe.

What is the difference between using SampleInfo and loading Seurat RDS files in 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.

Do I need to label samples manually when loading multiple Seurat files?▼

Use the optional sample environment flag to control sample labeling automatically when providing multiple Seurat files for immunopipe single-cell analysis.