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00. Project Overview

Source: vignettes/project-overview.qmd

This vignette provides a visual overview of the coMMpass-analysis pipeline: its data flow, layer architecture, and a reading guide for navigating the vignettes. All diagrams use clickable nodes linking to the relevant vignette or external resource.

Data Flow Pipeline

Figure 1: Data flow pipeline for coMMpass-analysis. Data flows left-to-right from the GDC Portal through acquisition, cleaning, and QC stages into five parallel analysis tracks (DE, survival, pathway, EDA, cytogenetics), converging on gene reports, API endpoints, and the pkgdown website. The pipeline comprises 12 layers and ~183 targets. Colour key: blue = acquisition, yellow = cleaning/QC, red = analysis, green = outputs. Source: layer definitions in R/tar_plans/plan_dag_validation.R.

Layer Dependency Graph

Figure 2: Layer dependency graph showing the 12 pipeline layers. Each node represents a pipeline layer from plan_dag_validation.R. Solid arrows indicate allowed dependencies: data flows top-down from acquisition through cleaning/QC into parallel analysis tracks, then into storage and documentation. The dashed arrow from infrastructure to data-acquisition reflects the Nix/config bootstrap. Terminal layers: documentation (aggregates all outputs) and infrastructure (standalone). Colour key: blue = acquisition, yellow = cleaning/QC, red = analysis, green = storage/API, purple = documentation, grey = infrastructure. Source: R/tar_plans/plan_dag_validation.R, lines 13-48.

Vignette Reading Guide

Figure 3: Recommended reading paths through the 11 vignettes. Three paths serve different audiences: Clinical (blue) covers patient-level exploratory analysis and survival modelling; Genomics (red) covers RNA-seq acquisition, differential expression, and gene-level reporting; Developer/Pipeline (green) covers the targets DAG, pipeline telemetry, and API endpoints. All paths begin at Data Sources. Cross-cutting references: glossary (65 terms), data dictionary.

Session Information

Show code 
R version 4.5.3 (2026-03-11)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

time zone: UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
 [1] compiler_4.5.3  fastmap_1.2.0   cli_3.6.5       tools_4.5.3
 [5] htmltools_0.5.9 otel_0.2.0      yaml_2.3.12     rmarkdown_2.30
 [9] knitr_1.51      jsonlite_2.0.0  xfun_0.57       digest_0.6.39
[13] rlang_1.1.7     evaluate_1.0.5