sjcab_peak2anno_db

Gene-backed peak-to-annotation BED resources for SJ/CAB workflows. The package provides bundled annotations and downloads or generates resources from GENCODE, UCSC, Ensembl, Roadmap ChromHMM, Segway, blacklist, and CpG-island sources.

Use the navigation to find installation, configuration, resource-generation, and transcript-selection guides.

The install/download convention

install-* commands put resources under the configured database directory. download-* commands write to a staging directory, which defaults to the current working directory. Commands ending in -feature generate both gene GeneBED and derived FeatureBED resources.

Quick start

pip install sjcab_peak2anno_db
conda install stjudecab::sjcab_peak2anno_db
sjcab-peak2anno-db install
sjcab-peak2anno-db install def
sjcab-peak2anno-db install default
sjcab-peak2anno-db list def
sjcab-peak2anno-db list genebed
sjcab-peak2anno-db list feature

The default database directory is ~/.sjcab_peak2anno_db. Use --db-path or SJCAB_PEAK2ANNO_DB_PATH to select another location.

The original long-form references remain available in the repository: README.md and README.DEDUP.md.