encodeUtils queries the ENCODE Portal REST API and converts nested metadata into traceable experiment and file tables. It standardizes fields used in scripted analyses, including accessions, assays, biosamples, organisms, targets, assemblies, output types, file sizes, checksums, and download URLs.
Details
Use it to search RNA-seq, ChIP-seq, and ATAC-seq experiments, list files from ENCODE accessions, select common outputs, preview downloads before transfer, load supported local files into native R objects, and write reproducibility manifests for downstream R and Bioconductor workflows. The introductory vignette and help pages use deliberately small live requests; the separate live smoke test is opt-in.
This package is not affiliated with or endorsed by the ENCODE Project.
The package uses a conservative default request throttle below the ENCODE REST API limit for programmatic GET requests.
Development provenance
AI (Codex 5.6 Sol) was used to write code for the test suite. All other code was written primarily by a human. AI-generated code for the testing suite was manually reviewed, edited, and tested by the maintainer. The maintainer assumes responsibility for all package code and its ongoing maintenance.
Author
Maintainer: Zoheb Khan zohebkhan600@gmail.com (ORCID)
Authors:
Zoheb Khan zohebkhan600@gmail.com (ORCID)