How wjbsb/bulk_rnaseq_mna2_production works
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: run_downstream_pipeline.R Pipeline runner
Components 18
Pipeline orchestration
- Pipeline runner
r_scripts/downstream/run_downstream_pipeline.R - Target definitions
r_scripts/downstream/_targets.R
Analysis stages
- Parameter building
r_scripts/downstream/1_parameters_building.R - Quality control
r_scripts/downstream/2_QC.R - Unsupervised clustering
r_scripts/downstream/3_unsupervised_clustering.R - Differential expression
r_scripts/downstream/4_DEG.R - GSEA
r_scripts/downstream/5_GSEA.R - CAMERA
r_scripts/downstream/6_CAMERA.R - Similarity analysis
r_scripts/downstream/7_SIMILARITY.R - WGCNA
r_scripts/downstream/8_WGCNA.R
Analysis support
- Analysis functions
r_scripts/downstream/utils/functions_1.R - Analysis functions
r_scripts/downstream/utils/functions_2.R - Analysis functions
r_scripts/downstream/utils/functions_3.R - Analysis functions
r_scripts/downstream/utils/functions_4.R - Analysis functions
r_scripts/downstream/utils/functions_5.R - Analysis functions
r_scripts/downstream/utils/functions_7.R - Shared functions
r_scripts/downstream/utils/global_functions.R
Other components
- Project analyst
Connections 1
- Project analyst → Pipeline runner: runs