Data ingestion for OmicsPlayground, split out of
playbase: delimited table readers
(read.as_matrix, read_counts, read_samples, read_contrasts,
read_annot, fread.csv), platform readers (Olink NPX, Spectronaut,
10X Cell Ranger, h5/h5ad), read.gmt, and the upload checks
(pgx.checkINPUT, pgx.crosscheckINPUT, validate_*, PGX_CHECKS).
A leaf package: it depends on nothing from playbase. Heavy readers (OlinkAnalyze, rhdf5, Seurat) are Suggests and checked at call time.
remotes::install_github("bigomics/playbase.ingest")
counts <- playbase.ingest::read_counts(playbase.ingest::example_file("counts.csv"))