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Pipelines
wcorinne edited this page Aug 29, 2025
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Pipelines link together multiple, disparate analyses, to ease analysis of a given dataset. The following links provide documentation on each PANOPLY pipeline:
- Home
- PANOPLY Tutorial
- Data Preparation Modules
-
Data Analysis Modules
- panoply_association
- panoply_blacksheep
- panoply_clumps_ptm_diffexp
- panoply_clumps_ptm
- panoply_clumps_ptm_postprocess
- panoply_cmap_analysis
- panoply_cna_correlation
- panoply_cons_clust
- panoply_immune_analysis
- panoply_metaboanalyst
- panoply_mimp
- panoply_nmf
- panoply_nmf_postprocess
- panoply_omicsev
- panoply_quilts
- panoply_rna_protein_correlation
- panoply_sankey
- panoply_ssgsea
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Report Modules
- panoply_association_report
- panoply_blacksheep_report
- panoply_clumps_ptm_report
- panoply_cna_correlation_report
- panoply_cons_clust_report
- panoply_immune_analysis_report
- panoply_metaboanalyst_report
- panoply_mimp_report
- panoply_nmf_report
- panoply_normalize_ms_data_report
- panoply_rna_protein_correlation_report
- panoply_sampleqc_report
- panoply_sankey_report
- panoply_ssgsea_report
- Support Modules
- Navigating Results
- PANOPLY without Terra
- Customizing PANOPLY
-
Workflows
- panoply_association_workflow
- panoply_blacksheep_workflow
- panoply_clumps_ptm_workflow
- panoply_immune_analysis_workflow
- panoply_metaboanalyst_workflow
- panoply_nmf_workflow
- panoply_nmf_internal_workflow
- panoply_normalize_filter_workflow
- panoply_process_SM_table
- panoply_sankey_workflow
- panoply_ssgsea_workflow
- Pipelines