Pipeline Overview
The CoMMpass analysis pipeline is organized into isolated layers. Each layer corresponds to a functional area of the analysis, with explicit allowed dependencies between layers.
| data-acquisition |
Download RNA-seq and clinical data from GDC |
| data-cleaning |
Standardize and integrate datasets |
| cytogenetics |
Extract FISH markers and classify risk |
| quality-control |
Sample QC, filtering, normalization |
| differential-expression |
DESeq2, edgeR, limma-voom analysis |
| survival |
Kaplan-Meier, Cox PH regression |
| pathway |
GSEA, ORA, gene annotation |
| eda |
Exploratory summaries |
| storage |
DuckDB/parquet querying |
| api |
Plumber API for programmatic access |
| documentation |
Vignette pre-computed outputs |
| infrastructure |
Nix sync, pkgctx, DAG validation |
DAG Validation
Validation checks on the targets pipeline DAG: no orphaned targets, no circular dependencies, and all vignette targets are reachable from raw data inputs. A passing validation confirms the pipeline is structurally sound.
Target Network
Interactive DAG showing the targets pipeline network with layer-based coloring. Nodes are colored by functional layer. Hover for target details, use the dropdown to search by name.
Interactive DAG available in local builds only.
Run targets::tar_visnetwork(targets_only = TRUE) locally.
Pipeline by Layer
To explore the full interactive DAG locally, run:
targets::tar_visnetwork(targets_only = TRUE, label = "time")
Recent Changes
Recent project commits with lines added, files changed, and change categories.
Reproducibility
Session Info (click to expand)
Show code
sessionInfo()
#> R version 4.6.1 (2026-06-24)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 26.04 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-r0.3.32.so; LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: Etc/UTC
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] targets_1.12.0
#>
#> loaded via a namespace (and not attached):
#> [1] vctrs_0.7.3 cli_3.6.6 knitr_1.51 rlang_1.3.0
#> [5] xfun_0.60 otel_0.2.0 processx_3.9.0 jsonlite_2.0.0
#> [9] data.table_1.18.4 glue_1.8.1 prettyunits_1.2.0 DT_0.34.0
#> [13] buildtools_1.0.0 backports_1.5.1 htmltools_0.5.9 maketools_1.3.2
#> [17] sys_3.4.3 ps_1.9.3 sass_0.4.10 rmarkdown_2.31
#> [21] jquerylib_0.1.4 crosstalk_1.2.2 tibble_3.3.1 evaluate_1.0.5
#> [25] base64url_1.4 fastmap_1.2.0 yaml_2.3.12 lifecycle_1.0.5
#> [29] compiler_4.6.1 codetools_0.2-20 igraph_2.3.3 htmlwidgets_1.6.4
#> [33] pkgconfig_2.0.3 digest_0.6.39 R6_2.6.1 tidyselect_1.2.1
#> [37] pillar_1.11.1 callr_3.8.0 magrittr_2.0.5 bslib_0.11.0
#> [41] withr_3.0.3 tools_4.6.1 secretbase_1.3.0 cachem_1.1.0