Provides eight functions to search ENCODE metadata, list and select files, plan and verify downloads, read local files, and create manifests.
Reads genomic intervals as GRanges objects and aligned expression matrices as SummarizedExperiment objects. Feature, file, query, request, and selection metadata are retained.
Applies per-file and total-size limits before downloading. Transfers use temporary files and are checked against reported sizes and MD5 values.
Includes an evaluated ENCODE microRNA-seq vignette covering search, file selection, download, count-matrix construction, and manifest creation.
Includes fixture-based unit tests, a separate live-service test, R CMD check workflows, and a coverage workflow.
Records successful requests used to construct file-search results, including parent-metadata requests.
Requires one featureCounts sample column for automatic simplification. Multi-sample tables can be retained with simplify_quant = FALSE.
Uses NA when an attribution retrieval date is unknown.