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scViewer Stork Pipeline Specification

Pipeline Details

  • Name: scViewer Stork
  • Pipeline UUID: 9f4ir0r5y0llapfsyizl07ncd1uxgf
  • Version: 1.0.0
  • View Pipeline:

Overview

scViewer Stork pipeline is designed for seamless integration of existing Seurat analysis results with Viafoundry's powerful scViewer Shiny application. This "Stork" pipeline serves as a bridge for researchers who have completed their single-cell RNA sequencing analysis using Seurat and want to visualize their results using the interactive scViewer platform.

Key Use cases:

  • Seurat Object Visualization: Import and visualize pre-analyzed Seurat objects in the interactive scViewer application.
  • Cross-Platform Data Integration: Convert existing R-based Seurat analyses for web-based visualization and sharing.
  • Interactive Data Exploration: Enable collaborative analysis and presentation of single-cell data through web-based visualization tools.

Features

  • Seurat Object Compatibility: Directly accepts Seurat objects in .rds format from existing analyses.
  • Dual Format Support: Generates both Seurat-compatible (.rds) and Python-compatible (.h5ad) output formats.
  • Metadata Preservation: Maintains all metadata and factor variables from the original Seurat object.
  • scViewer Integration: Optimized output formatting for seamless integration with Viafoundry's scViewer application.
  • Cross-Language Compatibility: Converts R Seurat objects to h5ad format for Python-based downstream analysis.

Input/Output Specification

Inputs

Required

Seurat Object File

  • Description: A Seurat object file containing pre-analyzed single-cell RNA sequencing data with embedded metadata, dimensionality reductions, and clustering results.
  • Format: .rds
  • Example File Path: /path/to/input/seurat_analysis.rds

Outputs

Reported Outputs

  • scViewer-Ready Seurat Object:
  • Description: Processed Seurat object formatted for scViewer visualization
  • Format: .rds
  • Example File Path: /output/directory/sample_scViewer.rds
  • Visualization App: scViewer

  • Location: Output Folder

  • H5AD File:

  • Description: AnnData-formatted file compatible with Python-based single-cell analysis tools
  • Format: .h5ad
  • Example File Path: /output/directory/sample.h5ad
  • Visualization App: Python scanpy, cellxgene
  • Location: Output Folder

Supporting Outputs

  • Intermediate H5Seurat File:
  • Description: Intermediate Seurat object in HDF5 format used for conversion to h5ad
  • Format: .h5Seurat
  • Example File Path: /intermediate/directory/sample.h5Seurat

Associated Processes

References & Additional Documentation

  • Related Tools: Seurat R package, SeuratDisk, scViewer Shiny Application
  • Pipeline Repository: Viafoundry Pipeline Repository
  • Workflow Diagram: Available in pipeline description page