UCSC GenomeBrowser Hub

This repository hosts the UCSC Genome Browser hub files for the Townsend Lab TCGA cancer effect size tracks.

It also includes a minimal reproducible BRCA workflow in scripts/ for:

1. installing dependencies,
2. recreating the BRCA CESAnalysis object,
3. exporting the mapped BED track, and
4. converting the BED file to bigBed.

Files added for BRCA reproducibility

Path	Purpose
scripts/01_install_dependencies.R	Installs the R package dependencies
scripts/02_run_brca_ces_analysis.R	Recreates the BRCA cesa object
scripts/03_build_bed_tracks.R	Builds the BRCA BED outputs from recurrent CES results
scripts/04_bed_to_bigbed.sh	Converts BED to bigBed with UCSC bedToBigBed

Required local inputs

Place these local files under data/raw/ before running the full workflow:

• hg38.chrom.sizes
• optionally TCGA-BRCA.maf.gz

If TCGA-BRCA.maf.gz is absent, the workflow downloads it automatically.

Run order

Rscript scripts/01_install_dependencies.R
Rscript scripts/02_run_brca_ces_analysis.R
Rscript scripts/03_build_bed_tracks.R
bash scripts/04_bed_to_bigbed.sh \
  outputs/tracks/BRCA_CES_All_mapped_ucsc.bed \
  data/raw/hg38.chrom.sizes \
  hg38/Breast_cancer_stage(0-IV)_TCGA_CES.bb

BRCA workflow notes

1. The analysis uses cancereffectsizeR with ces.refset.hg38.
2. The hub contains only recurrent-variant cancer effect size results from ces_variant; it does not include epistasis analyses.
3. Coordinate-style recurrent variants are parsed directly from variant_name.
4. Gene-level variants are mapped to the first matching gene interval in ces.refset.hg38$gr_genes.
5. The UCSC score is computed as round(10 * log10(selection_intensity) - 10) and clipped to the supported BED score range.