Package: GenomicDataStream Type: Package Title: Read Genomic Data Files (VCF, BCF, BGEN, PGEN, BED, H5AD) into R/Rcpp in Chunks Version: 0.99.28 Date: 2026-09-29 Authors@R: c(person("Gabriel", "Hoffman", role=c("aut", "cre"), email="gabriel.hoffman@mssm.edu", comment=c(ORCID="0000-0002-0957-0224")), person("Zilong", "Li", , "zilong.dk@gmail.com", role = c("aut"), comment = c(ORCID = "0000-0001-5859-2078"))) Description: Read genomic data files (i.e. VCF, BCF, BGEN, PGEN, BED, H5AD, DelayedArray) into R/Rcpp in chunks for analysis with Armadillo / Eigen / Rcpp libraries. Modern datasets are often too big to fit into memory, and many analyses operate on a small chunk features at a time. GenomicDataStream provides interfaces at both the C++ and R levels for out-of-core analysis. URL: https://github.com/GabrielHoffman/GenomicDataStream BugReports: https://github.com/GabrielHoffman/GenomicDataStream/issues License: Artistic-2.0 Suggests: BiocStyle, RUnit, muscat, VariantAnnotation, knitr, rmarkdown Depends: R (>= 4.5.0), methods, stats, utils Imports: Rcpp, beachmat.hdf5, DelayedArray, RcppParallel, HDF5Array, rhdf5filters, SingleCellExperiment, anndataR, stringr, dplyr, h5mread, S4Vectors, withr, magrittr LinkingTo: Rcpp, RcppArmadillo, RcppEigen (>= 0.3.4.0.2), RcppParallel, beachmat (>= 2.21.9), assorthead, BH (>= 1.87.0), vcfppR (>= 0.8.1) biocViews: DataImport, Infrastructure Encoding: UTF-8 SystemRequirements: GNU make, Intel TBB, libcurl: libcurl-devel (rpm) or libcurl4-openssl-dev (deb) VignetteBuilder: knitr Config/roxygen2/version: 8.1.0 Config/pak/sysreqs: cmake make libicu-dev libpng-dev libssl-dev python3 zlib1g-dev Repository: https://biocstaging.r-universe.dev Date/Publication: 2026-09-29 20:25:28 UTC RemoteUrl: https://github.com/BiocStaging/GenomicDataStream RemoteRef: HEAD RemoteSha: 834e39c3206d892b1023a3cc2f3a514b25b8a18a NeedsCompilation: yes Packaged: 2026-09-30 00:45:53 UTC; root Author: Gabriel Hoffman [aut, cre] (ORCID: ), Zilong Li [aut] (ORCID: ) Maintainer: Gabriel Hoffman