Package: coMMpass 0.1.0

John Gavin

coMMpass: MMRF CoMMpass Data Analysis Pipeline

A reproducible data acquisition and analysis pipeline for the MMRF CoMMpass study using Targets and Nix.

Authors:John Gavin [aut, cre]

coMMpass_0.1.0.tar.gz
coMMpass_0.1.0.zip(r-4.7)coMMpass_0.1.0.zip(r-4.6)coMMpass_0.1.0.zip(r-4.5)
coMMpass_0.1.0.tgz(r-4.6-any)coMMpass_0.1.0.tgz(r-4.5-any)
coMMpass_0.1.0.tar.gz(r-4.7-any)coMMpass_0.1.0.tar.gz(r-4.6-any)
coMMpass_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
coMMpass/json (API)

# Install 'coMMpass' in R:
install.packages('coMMpass', repos = c('https://johngavin.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/johngavin/commpass-analysis/issues

Pkgdown/docs site:https://johngavin.github.io

On CRAN:

Conda:

softwarequarto

4.99 score 72 exports 108 dependencies

Last updated from:c6cb45c511. Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR312
source / vignettesOK453
linux-release-x86_64ERROR336
macos-release-arm64ERROR226
macos-oldrel-arm64ERROR282
windows-develERROR260
windows-releaseERROR275
windows-oldrelERROR272
wasm-releaseOK254

Exports:acquire_commpass_dataannotate_de_resultsannotate_genesapi_get_clinicalapi_get_de_resultsapi_get_pathwaysapi_get_survivalapi_list_datasetsapi_servecalculate_cooccurrencecalculate_qc_metricscheck_adjustmentclean_clinical_dataclean_expression_dataclean_treatment_datacommpass_dagcompute_pcacompute_risscorrelate_genescorrelate_genes_batchcreate_summary_tabledownload_clinical_datadownload_gdc_rnaseqdownload_s3_subsetexample_dataexport_h5adextract_cytogenetic_dataextract_risk_tableformat_file_sizeformat_with_commasgene_reportgenerate_api_endpointgenerate_api_indexget_adjustment_setsget_commpass_clinicalget_commpass_data_dictionaryget_commpass_tblget_counts_assayget_variable_docsintegrate_clinical_expressionlist_s3_commpassplot_cooccurrence_heatmapplot_cytogenetic_oncoprintplot_dagplot_enrichment_barplotplot_enrichment_dotplotplot_expression_by_subtypeplot_forestplot_gene_correlationplot_gsea_running_scoreplot_heatmap_deplot_kmplot_maplot_pcaplot_volcanoprepare_survival_dataquery_commpass_parquetquery_commpass_rnaresolve_gene_idrun_cox_regressionrun_deseq2run_gsearun_kaplan_meierrun_km_by_expressionrun_km_by_markersrun_orarun_pathway_analysisrun_vststrip_plotlysummarize_cytogeneticssummarize_de_methodssummarize_treatment

Dependencies:abindAnnotationDbiarrowaskpassassertthataws.s3aws.signaturebase64encBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicliprcpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdownloaderdplyrduckdbedgeRevaluatefarverfastmapfilelockgenericsGenomicRangesggplot2gluegtablehighrhmshttrhttr2IRangesisobandjsonliteKEGGRESTknitrlabelinglatticelifecyclelimmalocfitloggermagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplyrpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreadrrlangRSQLitervestS4ArraysS4VectorsS7scalesselectrSeqinfoSparseArraystatmodstringistringrSummarizedExperimentsysTCGAbiolinksTCGAbiolinksGUI.datatibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrxfunXMLxml2XVectoryaml

Pipeline DAG
Pipeline Overview | DAG Validation | Target Network | Pipeline by Layer | Recent Changes | Reproducibility
Rendered frompipeline-dag.qmdusingquarto::html

Last update: 2026-03-21
Started: 2026-02-25

Data Acquisition & Status
Overview | Data Flow | Pipeline Configuration | RNA-seq Data | Clinical Data | Data Completeness | Quality Control | Data Sources | Recent Changes | Reproducibility
Rendered fromdata-acquisition.qmdusingquarto::html

Last update: 2026-03-20
Started: 2026-02-25

Exploratory Data Analysis
Overview | Clinical Demographics | Age at Diagnosis | Gender Distribution | Race Distribution | Vital Status | ISS Staging | ISS Stage Distribution | Age by ISS Stage | Survival Endpoints | Biospecimen Overview | Sample Types | Samples per Patient | RNA-seq Quality | Library Size Distribution | Genes Detected per Sample | Sample Clustering (PCA) | Cytogenetic Landscape | Alteration Frequencies | Oncoprint | Co-occurrence Analysis | DuckDB Query Examples | Example: Simple Query | Example: Aggregation with DuckDB | Cross-dataset Integration | Clinical-Informed Normalisation | Reference Ranges | Clinical vs Z-Score Comparison | Missingness as Signal | Variable Missingness | Does Missingness Predict Survival? | Data Sources | Recent Changes | Reproducibility
Rendered fromexploratory-analysis.qmdusingquarto::html

Last update: 2026-03-20
Started: 2026-02-25

Differential Expression Analysis
Overview | Method Comparison | Principal Component Analysis | Volcano Plot | MA Plot | Heatmap of Top DE Genes | Consensus Genes | Paired Longitudinal DE | Annotated DE Results | Pathway Enrichment Visualizations | GSEA Enrichment Dot Plot | ORA Enrichment Bar Plot | Next Steps | Data Sources | Recent Changes | Reproducibility
Rendered fromdifferential-expression.qmdusingquarto::html

Last update: 2026-03-20
Started: 2026-02-25

Survival Analysis
Overview | Overall Survival | Survival by ISS Stage | Survival by Cytogenetic Risk Group | Survival by Individual Cytogenetic Markers | Cox Proportional Hazards | Basic Model: Age + Gender | Full Model: Age + Gender + ISS + Cytogenetic Risk | Forest Plot | Proportional Hazards Assumption | Model Comparison | Survival by Gene Expression | Expression by Cytogenetic Subtype | Next Steps | Data Sources | Recent Changes | Bayesian Survival Models | Frequentist vs Bayesian Comparison | Reproducibility
Rendered fromsurvival-analysis.qmdusingquarto::html

Last update: 2026-03-20
Started: 2026-02-25

Causal Analysis
Overview | Causal DAG | Key Causal Assumptions | Adjustment Sets | Model Adequacy Check | Interpretation | Implications for Analysis | References
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Last update: 2026-03-20
Started: 2026-03-15

Gene Report
r gene — Single Gene Characterization | Expression Distribution | Survival by Expression | Expression by Cytogenetic Subtype | Gene-Gene Correlations | Data Sources | Recent Changes | Reproducibility
Rendered fromgene-report.qmdusingquarto::html

Last update: 2026-03-20
Started: 2026-03-07

Pipeline Telemetry
Build Timing | Build Status Summary | Errors and Warnings | Outdated Targets | Size Distribution | Git Activity | Commit Velocity | Changes by Type | Changes by File Category | Recent Commits | GitHub Activity | Issues & Pull Requests | Codebase Metrics | Chunk-Target Audit | Reproducibility
Rendered fromtelemetry.qmdusingquarto::html

Last update: 2026-03-20
Started: 2026-03-04

Data Dictionary
Overview | Complete Data Dictionary | Clinical Data | Sample Rows | Biospecimen Data | RNA-seq Data | Treatment Data | Column Name Mappings | Units Reference | Data Sources & Links | R Code Examples | Loading Data | Exploring the Dictionary | Data Sources | Recent Changes | Reproducibility
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Last update: 2026-03-17
Started: 2026-02-25

Glossary
Definitions | Units Reference | Recent Changes | Reproducibility
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Last update: 2026-03-17
Started: 2026-02-25

API Usage
Overview | Available Endpoints | Example: curl | Example: R (jsonlite) | Example: Python (requests) | Raw Data Sources | Phase 2 Roadmap | Data Sources | Recent Changes | Reproducibility
Rendered fromapi-usage.qmdusingquarto::html

Last update: 2026-03-17
Started: 2026-02-25

Data Sources & Provenance
Overview | MMRF CoMMpass Study | Citation | Data at a Glance | Data Access Tiers | Pipeline Data Sources (Real) | GDC Documentation | Synthetic Test Data (example_data()) | MSigDB Gene Sets | Bundled Files | Recent Changes | Reproducibility
Rendered fromdata-sources.qmdusingquarto::html

Last update: 2026-03-17
Started: 2026-03-08

Project Overview
Data Flow Pipeline | Layer Dependency Graph | Vignette Reading Guide | Session Information
Rendered fromproject-overview.qmdusingquarto::html

Last update: 2026-03-17
Started: 2026-03-11

Readme and manuals

Help Manual

Help pageTopics
Main data acquisition functionacquire_commpass_data
Add gene symbol column to DE results tableannotate_de_results
Annotate Ensembl gene IDs with symbols and descriptionsannotate_genes
Get clinical data for API responseapi_get_clinical
Get DE results for API responseapi_get_de_results
Get pathway analysis results for API responseapi_get_pathways
Get survival data for API responseapi_get_survival
List available API datasetsapi_list_datasets
Launch the plumber APIapi_serve
Calculate pairwise co-occurrence of cytogenetic alterationscalculate_cooccurrence
Calculate QC metrics for RNA-seq datacalculate_qc_metrics
Compare model covariates against DAG-implied adjustmentscheck_adjustment
Check package dependenciescheck_dependencies
Clean Clinical Dataclean_clinical_data
Clean Expression Dataclean_expression_data
Clean and standardize treatment dataclean_treatment_data
Define the CoMMpass causal DAGcommpass_dag
Compute PCA from transformed expression datacompute_pca
Compute Revised International Staging System (R-ISS)compute_riss
Correlate two genes across samplescorrelate_genes
Batch correlation: one gene vs manycorrelate_genes_batch
Create project directoriescreate_project_dirs
Create Summary Statistics Tablecreate_summary_table
Download data from AWS S3 open access bucketdownload_aws_data
Download clinical data from GDCdownload_clinical_data
Download RNA-seq data from GDCdownload_gdc_rnaseq
Download a Sample of RNA-seq Files from S3download_s3_subset
Load example coMMpass datasetsexample_data
Export SummarizedExperiment to H5AD (AnnData) formatexport_h5ad
Extract cytogenetic markers from clinical dataextract_cytogenetic_data
Extract risk table from Kaplan-Meier resultsextract_risk_table
Filter low-quality samples and genesfilter_low_quality
Find consensus DE genes across methodsfind_consensus_genes
Format File Size in Human-Readable Formatformat_file_size
Format Number with Thousands Separatorformat_with_commas
Render a single-gene characterization reportgene_report
Generate a single API endpoint JSON stringgenerate_api_endpoint
Generate API index metadatagenerate_api_index
Generate summary reportgenerate_summary_report
Get adjustment sets for a given analysisget_adjustment_sets
Query GDC for CoMMpass Clinical Dataget_commpass_clinical
Get CoMMpass Data Dictionaryget_commpass_data_dictionary
Get Lazy DuckDB Table for CoMMpass Dataget_commpass_tbl
Get counts assay from SummarizedExperimentget_counts_assay
Get Extended Documentation for a Variableget_variable_docs
Create Integrated Datasetintegrate_clinical_expression
List AWS S3 CoMMpass Bucket Contentslist_s3_commpass
Normalize RNA-seq datanormalize_rnaseq
Plot co-occurrence heatmap of cytogenetic alterationsplot_cooccurrence_heatmap
Plot cytogenetic oncoprintplot_cytogenetic_oncoprint
Plot the CoMMpass causal DAGplot_dag
Bar plot of enrichment resultsplot_enrichment_barplot
Dot plot of enrichment resultsplot_enrichment_dotplot
Plot gene expression by cytogenetic subtypeplot_expression_by_subtype
Plot forest plot of Cox hazard ratiosplot_forest
Scatter plot of gene-gene correlationplot_gene_correlation
GSEA running enrichment score plotplot_gsea_running_score
Heatmap of top DE genesplot_heatmap_de
Plot Kaplan-Meier curveplot_km
MA plot of DE resultsplot_ma
PCA plotplot_pca
Volcano plot of DE resultsplot_volcano
Prepare survival data from clinical and cytogenetic dataprepare_survival_data
Query CoMMpass Parquet Filesquery_commpass_parquet
Query GDC for CoMMpass RNA-seq Metadataquery_commpass_rna
Render DE analysis reportrender_de_report
Run Cox proportional hazards regressionrun_cox_regression
Run DESeq2 differential expression analysisrun_deseq2
Run edgeR differential expression analysisrun_edger
Run Gene Set Enrichment Analysis (GSEA)run_gsea
Run Kaplan-Meier analysisrun_kaplan_meier
Run KM analysis stratified by gene expression levelrun_km_by_expression
Run KM analysis for each individual cytogenetic markerrun_km_by_markers
Run limma differential expression analysisrun_limma
Run Over-Representation Analysis (ORA)run_ora
Run pathway enrichment analysisrun_pathway_analysis
Run variance stabilizing transformationrun_vst
Save results with timestampsave_timestamped
Setup loggingsetup_logging
Strip plotly closure bloat for compact serializationstrip_plotly
Summarize cytogenetic alteration frequenciessummarize_cytogenetics
Generate summary statisticssummarize_data
Summarize DE results across methodssummarize_de_methods
Summarize treatment lines per patientsummarize_treatment