Workflows: panoply_immune_analysis_workflow

panoply_immune_analysis_workflow

Description

This workflow performs immune analysis on transcriptomics data, assigning immune scores for understanding the tumor microenvironment; it also generates an interactive report. It executes the following modules:

module	description
panoply_immune_analysis	performs immune analysis
panoply_immune_analysis_report	creates an interactive R Markdown report of the immune analysis results

Input

Required inputs:

• inputData: (File) tarball output (.tar) for one of the other modules, or RNAseq data in gct format (when standalone is TRUE)
• type: (String) proteome data type
• standalone: (String) set to TRUE to run as a self-contained module; if TRUE the analysisDir input is required
• yaml: (.yaml file) parameters in yaml format
• label: (String) directory name within the tar file

Optional inputs:

• analysisDir: (String) name of analysis directory
• groupsFile: (.csv file) subset of sample annotations, providing classes for enrichment analysis
• fdr: (Float, default = 0.05) FDR cutoff value for significance in enrichment analysis
• heatmapWidth: (Int, default = 10) width of heatmap generated
• heatmapHeight: (Int, default = 15) height of heatmap generated

Output

panoply_immune_analysis_workflow produces the follow outputs:

• outputs: (.tar) An output tar file that contains the immune analysis results
• report: (.html file) Interactive R Markown report.