Pipelines: panoply_main

panoply_main

Description

Performs proteogenomic analysis for a given ome (proteome, phosphoproteome, ubiquitylome, or acetylome). Use panoply_unified_workflow to run this pipeline on multiple ome types in parallel.

This pipeline executes the following modules:

• panoply_normalize_ms_data
• panoply_normalize_ms_data_report
• panoply_rna_protein_correlation
• panoply_rna_protein_correlation_report
• panoply_harmonize
• panoply_sampleqc
• panoply_sampleqc_report
• panoply_cna_setup
• panoply_cna_correlation
• panoply_cna_correlation_report
• panoply_association_workflow
• panoply_accumulate
• panoply_nmf
• panoply_ssgsea
• panoply_cmap_analysis (optional, proteome data only)
• panoply_download

Input

Required inputs:

• job_identifier: (String) An identifier name given to the job
• ome_type: (String) Type of omics data being run (ex: "proteome", "phosphoproteome" etc.)
• input_pome: (.gct file) Input ome data matrix
• input_rna: (.gct file, default = this.rna_ss) Input rna data matrix (optional)
• input_cna: (.gct file, default = this.cna_ss) Input cna data matrix (optional)
• sample_annotation: (File, default = this.annotation_ss) The annotation file for the given ome data
• groups_file: (File, default = this.groups_ss) The annotation file for the given ome data, subsetted to annotations of interest and used for analyses. Can be manually overriden for relevant modules (below).
• yaml: (.yaml file) parameters in yaml format

Optional inputs:

• run_ptmsea: (String, default = false) true if phosphoproteome data is being run and ptmsea analysis is desired or "false" to skip (this module takes additional time and higher cost to run)

• run_cmap: (String, default = false) true if proteome data is being run and cmap analysis is desired or false to skip (this module takes additional time and higher cost to run)

• cna_groups: please see groupsFile input parameter in panoply_cna_setup

• groups_file_association: please see groupsFile input parameter in panoply_association. Overrides default groups_file.

• groups_file_nmf: please see groupsFile input parameter in panoply_nmf. Overrides default groups_file.

• normalizeProteomics: please see normalizeProteomics input parameter in panoply_normalize_ms_data

• cmap_n_permutations: please see n_permutations input parameter in panoply_cmap_analysis

• groups_file_cmap_enrichment: please see cmap_enrichment_groups input parameter in panoply_cmap_analysis. Overrides default groups_file.

• subset_list_file: please see subset_list_file input parameter in panoply_cmap_analysis

• cmap_level5_data: please see cmap_level5_data input parameter in panoply_cmap_analysis

• annotation_pathway_db: please see annotation_pathway_db input parameter in panoply_cmap_analysis

• subset_bucket: please see subset_bucket input parameter in panoply_cmap_analysis

• ndigits: please see ndigits input parameter in panoply_normalize_ms_data

• na_max: please see naMax input parameter in panoply_normalize_ms_data

• sample_na_max: please see sample_na_max input parameter in panoply_association

• min_numratio_fraction: please see minNumratioFraction input parameter in panoply_normalize_ms_data

• nmiss_factor: please see nmiss_factor input parameter in panoply_association

• sd_filter_threshold: please see sdFilterThreshold input parameter in panoply_normalize_ms_data

• duplicate_gene_policy: please see duplicate_gene_policy input parameter in panoply_harmonize

• gene_id_col: please see gene_id_col input parameter in panoply_harmonize

• organism:

• standalone: (String, default = false) set to true to run as a self-contained module; when running panoply_main pipeline use false

• geneset_db: (String, default = this.gseaDB) please see gene_set_database input parameter in panoply_ssgsea

• ptm_db: (String, default = this.ptmseaDB) this is the gene_set_database for running ptmsea

Output

panoply_main produces the follow outputs:

• panoply_full.tar: When opened, contains the following folders:
  • association: all results from panoply_association_workflow
  • so_nmf: all results from panoply_nmf
  • cna: all results from panoply_cna_setup and panoply_cna_correlation
  • data: folder containing data needed to run panoply_main analysis
  • harmonized-data: all results from panoply_harmonize
  • normalized-data: all results from panoply_normalize_ms_data
  • rna: all results from panoply_rna_protein_correlation
  • sample-qc: all results from panoply_sampleqc
  • ssgsea_assoc: all results from running panoply_ssgsea after panoply_association. Please see panoply_ssgsea for more information
  • ssgsea_ome: all results from running panoply_ssgsea on the omics input data. Please see panoply_ssgsea for more information
  • ssgsea_rna: all results from running panoply_ssgsea on the rna input data. Please see panoply_ssgsea for more information
• summary_and_ssgsea.tar: contains a smaller version of panoply_full.tar with large data files removed for easier download and viewing. The directory structure and folders are the same as listed above but contain fewer data files and/or contain only pdf/png results from the given analysis.
• cmap_output.tar(if panoply_cmap_analysis is run): contains results for the cmap analysis in the cmap folder of the opened .tar file. Please see panoply_cmap_analysis for more information on these results.
• cmap_ssgsea_output.tar(if panoply_cmap_analysis is run): contains results for the cmap annotate ssgsea. Please see panoply_ssgsea for more information on these results.
• norm_report.html: report produced by panoply_normalize_ms_data_report
• rna_corr_report.html: report produced by panoply_rna_protein_correlation_report
• cna_corr_report.html: report produced by panoply_cna_correlation_report
• sample_qc_report.html: report produced by panoply_sampleqc_report
• association_report.html: report produced by panoply_association_report
• so_nmf_report.html: report produced by panoply_nmf_report
• so_nmf_ssgsea_report.html: report produced by panoply_ssgsea_report for NMF clustering results
• normalized_data_table.gct: normalized data matrix produced by panoply_normalize_ms_data