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Run Markdown Specifications

Process Details

  • Name: Run Markdown
  • Process UUID: ThzsIbXmzrRUEpHa6SbE3Azw6yg5fM
  • Process Group: Misc.

Overview

This process launches a Markdown script for analyzing read counts, groups, and comparison information in differential expression studies. It provides a flexible framework for custom analysis by executing user-provided R Markdown documents with access to count data, sample grouping information, and comparison specifications.

This process is implemented in Bash, which invokes R scripts through the rmarkdown package for dynamic report generation and analysis.

Key Functionality

  • R Markdown Execution: Renders user-provided R Markdown documents into HTML reports with embedded analysis results
  • Data Integration: Automatically organizes count files, group files, and comparison files into a structured input directory for analysis
  • Metadata Processing: Copies group information to create debrowser-compatible metadata files for downstream compatibility
  • Dynamic Analysis: Enables custom statistical analysis and visualization through user-defined R Markdown scripts

Input/Output Specification

Inputs

Required Inputs

  • Count File

    • Description: Gene or feature count matrix containing quantified expression data
    • Format: TSV

  • Group File

    • Description: Sample metadata file defining experimental groups and conditions
    • Format: TSV

  • Compare File

    • Description: Comparison specification file defining which groups to compare in differential expression analysis
    • Format: TSV

  • R Markdown Script

    • Description: User-provided R Markdown document containing custom analysis code and report structure
    • Format: RMD

Outputs

  • R Markdown Report
    • Description: Rendered HTML report containing analysis results, visualizations, and interpretations generated from the input R Markdown script
    • Format: RMD

References & Resources

  • Tool Documentation: Contact the team for details on R Markdown rendering and analysis framework
  • Related Papers: Xie, Y., Allaire, J.J., and Grolemund, G. (2018). R Markdown: The Definitive Guide. Chapman and Hall/CRC. ISBN 9781138359338.