How sajjadeslamkhah/drg-pancancer works
DRG-PanCancer is a reproducible TCGA pan-cancer analysis, not a general-purpose software service. Its main workflow downloads public cohort data, prepares tumour samples and DRG scores, runs biological and prognostic analyses, and produces manuscript results. A separate revision program adds robustness and adjustment analyses; figure and table scripts consume pipeline outputs. The README documents these capabilities, but the excerpts do not expose most internal call paths, so the graph keeps those links at the documented pipeline level.
Main entry points: drg_pancancer_pipeline.py Pan-cancer pipeline · drg_v3_revision.py Revision analyses · make_main_figures.py Figure assembly · make_tables.py Table assembly
Components 21
Main analysis
- Pan-cancer pipeline
src/drg_pancancer_pipeline.py - Data acquisition
src/drg_pancancer_pipeline.py - Cohort and scores
src/drg_pancancer_pipeline.py - Tumour-normal tests
src/drg_pancancer_pipeline.py - Survival analyses
src/drg_pancancer_pipeline.py - Metabolic programmes
src/drg_pancancer_pipeline.py - Clinical and genomic
src/drg_pancancer_pipeline.py - LASSO-Cox validation
src/drg_pancancer_pipeline.py - Main result tables
src/drg_pancancer_pipeline.py
Revision analyses
- Revision analyses
src/drg_v3_revision.py - Matched-set nulls
src/drg_v3_revision.py - Clinical adjustments
src/drg_v3_revision.py - Proportional-hazards checks
src/drg_v3_revision.py - LASSO benchmarks
src/drg_v3_revision.py - Revision result files
src/drg_v3_revision.py
Manuscript outputs
- Figure assembly
src/make_main_figures.py - Manuscript figures
src/make_main_figures.py - Table assembly
src/make_tables.py - Manuscript tables
src/make_tables.py
Other components
- Researcher
- Public TCGA data
Connections 23
- Researcher → Pan-cancer pipeline: runs
README.md - Public TCGA data → Data acquisition: provides data
README.md - Pan-cancer pipeline → Data acquisition: downloads
README.md - Pan-cancer pipeline → Cohort and scores: prepares samples
README.md - Pan-cancer pipeline → Tumour-normal tests: compares
README.md - Pan-cancer pipeline → Survival analyses: analyses survival
README.md - Pan-cancer pipeline → Metabolic programmes: analyses programmes
README.md - Pan-cancer pipeline → Clinical and genomic: tests subgroups
README.md - Pan-cancer pipeline → LASSO-Cox validation: validates models
README.md - Pan-cancer pipeline → Main result tables: writes results
README.md - Researcher → Revision analyses: runs
README.md - Revision analyses → Main result tables: reads outputs
src/drg_v3_revision.py - Revision analyses → Matched-set nulls: tests nulls
README.md - Revision analyses → Clinical adjustments: adjusts models
README.md - Revision analyses → Proportional-hazards checks: checks hazards
README.md - Revision analyses → LASSO benchmarks: benchmarks models
README.md - Revision analyses → Revision result files: writes results
README.md - Researcher → Figure assembly: runs
README.md - Main result tables → Figure assembly: reads tables
src/make_main_figures.py - Figure assembly → Manuscript figures: assembles
README.md - Researcher → Table assembly: runs
README.md - Main result tables → Table assembly: reads tables
src/make_tables.py - Table assembly → Manuscript tables: builds
README.md