# wjbsb/bulk_rnaseq_mna2_production architecture

> Architecture diagram of the GitHub repository wjbsb/bulk_rnaseq_mna2_production, generated by GitDiagram from its file tree, README and a sample of source files (last updated 2026-09-29). It is an AI-made overview: check details against the source.

- Interactive diagram: https://gitdiagram.com/wjbsb/bulk_rnaseq_mna2_production
- Repository: https://github.com/wjbsb/bulk_rnaseq_mna2_production

## Overview

This repository provides a downstream bulk RNA-seq analysis pipeline for consortium projects. The apparent user workflow is to run the downstream pipeline, which is organized around parameter building, quality control, clustering, and several downstream analyses. The README names DEG, FGSEA, CAMERA, similarity, and WGCNA capabilities; the tree also identifies their corresponding analysis scripts. Source excerpts were unavailable, so links between the runner, target definitions, and analysis stages are not asserted.

Main entry points: [`r_scripts/downstream/run_downstream_pipeline.R`](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/run_downstream_pipeline.R) (Pipeline runner)

## Diagram (Mermaid)

```mermaid
flowchart TD

subgraph group_orchestration["Pipeline orchestration"]
  node_runner["Pipeline runner"]
  node_targets["Target definitions<br/>[_targets.R]"]
end

subgraph group_analysis["Analysis stages"]
  node_parameters["Parameter building"]
  node_qc["Quality control<br/>[2_QC.R]"]
  node_clustering["Unsupervised clustering"]
  node_deg["Differential expression<br/>[4_DEG.R]"]
  node_gsea["GSEA<br/>[5_GSEA.R]"]
  node_camera["CAMERA<br/>[6_CAMERA.R]"]
  node_similarity["Similarity analysis<br/>[7_SIMILARITY.R]"]
  node_wgcna["WGCNA<br/>[8_WGCNA.R]"]
end

subgraph group_internal["Analysis support"]
  node_functions1["Analysis functions<br/>[functions_1.R]"]
  node_functions2["Analysis functions<br/>[functions_2.R]"]
  node_functions3["Analysis functions<br/>[functions_3.R]"]
  node_functions4["Analysis functions<br/>[functions_4.R]"]
  node_functions5["Analysis functions<br/>[functions_5.R]"]
  node_functions7["Analysis functions<br/>[functions_7.R]"]
  node_globalfunctions["Shared functions<br/>[global_functions.R]"]
end

node_user(("Project analyst"))

node_user -->|"runs"| node_runner

click node_runner "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/run_downstream_pipeline.R"
click node_targets "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/_targets.R"
click node_parameters "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/1_parameters_building.R"
click node_qc "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/2_QC.R"
click node_clustering "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/3_unsupervised_clustering.R"
click node_deg "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/4_DEG.R"
click node_gsea "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/5_GSEA.R"
click node_camera "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/6_CAMERA.R"
click node_similarity "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/7_SIMILARITY.R"
click node_wgcna "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/8_WGCNA.R"
click node_functions1 "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/utils/functions_1.R"
click node_functions2 "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/utils/functions_2.R"
click node_functions3 "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/utils/functions_3.R"
click node_functions4 "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/utils/functions_4.R"
click node_functions5 "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/utils/functions_5.R"
click node_functions7 "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/utils/functions_7.R"
click node_globalfunctions "https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/utils/global_functions.R"

classDef toneNeutral fill:#f8fafc,stroke:#334155,stroke-width:1.5px,color:#0f172a
classDef toneBlue fill:#dbeafe,stroke:#2563eb,stroke-width:1.5px,color:#172554
classDef toneAmber fill:#fef3c7,stroke:#d97706,stroke-width:1.5px,color:#78350f
classDef toneMint fill:#dcfce7,stroke:#16a34a,stroke-width:1.5px,color:#14532d
classDef toneRose fill:#ffe4e6,stroke:#e11d48,stroke-width:1.5px,color:#881337
classDef toneIndigo fill:#e0e7ff,stroke:#4f46e5,stroke-width:1.5px,color:#312e81
classDef toneTeal fill:#ccfbf1,stroke:#0f766e,stroke-width:1.5px,color:#134e4a
class node_runner,node_targets toneBlue
class node_parameters,node_qc,node_clustering,node_deg,node_gsea,node_camera,node_similarity,node_wgcna toneAmber
class node_functions1,node_functions2,node_functions3,node_functions4,node_functions5,node_functions7,node_globalfunctions toneMint
class node_user toneIndigo
```

## Components

### Pipeline orchestration

- [Pipeline runner](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/run_downstream_pipeline.R): `r_scripts/downstream/run_downstream_pipeline.R`
- [Target definitions](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/_targets.R): `r_scripts/downstream/_targets.R`

### Analysis stages

- [Parameter building](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/1_parameters_building.R): `r_scripts/downstream/1_parameters_building.R`
- [Quality control](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/2_QC.R): `r_scripts/downstream/2_QC.R`
- [Unsupervised clustering](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/3_unsupervised_clustering.R): `r_scripts/downstream/3_unsupervised_clustering.R`
- [Differential expression](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/4_DEG.R): `r_scripts/downstream/4_DEG.R`
- [GSEA](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/5_GSEA.R): `r_scripts/downstream/5_GSEA.R`
- [CAMERA](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/6_CAMERA.R): `r_scripts/downstream/6_CAMERA.R`
- [Similarity analysis](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/7_SIMILARITY.R): `r_scripts/downstream/7_SIMILARITY.R`
- [WGCNA](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/8_WGCNA.R): `r_scripts/downstream/8_WGCNA.R`

### Analysis support

- [Analysis functions](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/utils/functions_1.R): `r_scripts/downstream/utils/functions_1.R`
- [Analysis functions](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/utils/functions_2.R): `r_scripts/downstream/utils/functions_2.R`
- [Analysis functions](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/utils/functions_3.R): `r_scripts/downstream/utils/functions_3.R`
- [Analysis functions](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/utils/functions_4.R): `r_scripts/downstream/utils/functions_4.R`
- [Analysis functions](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/utils/functions_5.R): `r_scripts/downstream/utils/functions_5.R`
- [Analysis functions](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/utils/functions_7.R): `r_scripts/downstream/utils/functions_7.R`
- [Shared functions](https://github.com/wjbsb/bulk_rnaseq_mna2_production/blob/main/r_scripts/downstream/utils/global_functions.R): `r_scripts/downstream/utils/global_functions.R`

### Other components

- **Project analyst**

## Connections

- Project analyst → Pipeline runner: runs