Exploratory Week 3 scripts¶
← Previous: Differential accessibility · Workflow contents
These scripts operate on nominal candidate sets after the primary analysis returned zero FDR-significant DARs.
07_annotate_nominal_candidates.Rannotates the strict 21-region nominal set with GENCODE Release 50 and nearest-transcript-TSS hypotheses.08_prepare_gprofiler_inputs.pyprepares direction-aware gene queries and a custom background for manual g:Profiler submission.09_run_homer_nominal_sensitivity.shrecords the one-worker HOMER sensitivity analysis using 1,562 nominal target regions, the 59,186-region primary background universe, and central 200-bp windows.
The annotation and g:Profiler preparation scripts require the full omitted
peak-level result tables plus verified GENCODE resources. The HOMER script
requires explicit PROJECT_ROOT, HOMER_ROOT, GENOME_FASTA, and
GENOME_FASTA_GZ environment variables. Its paths must use the syntax expected
by the shell in which HOMER is installed.
None of these analyses establishes a significant DAR, target gene, transcription-factor activity, or regulatory mechanism.