Package: cytome
Type: Package
Title: Native R Reader and Streaming Interface for the Cytome
        Single-Cell Store
Version: 0.1.3
Authors@R: c(
    person("Min", "Dai", role = c("aut", "cre"), email = "dai@broadinstitute.org"),
    person("PIASO Team", role = "cph"))
Description: Reads .cytome files - a SQLite-backed single-cell store -
        natively in R with zero Python dependency. A .cytome is a plain
        SQLite database, so the structural data (cells / genes / peaks,
        embeddings, graphs, fragments) is read with DBI; the chunked,
        compressed CSR count matrices are decoded via a small Rcpp
        layer (lz4-block / zstd / zlib). Constructs a
        SingleCellExperiment or a Seurat object, and provides
        cytome-native chunk streaming for out-of-core analysis without
        loading the full matrix. Part of the PIASO toolkit for
        single-cell omics (<https://piaso.org>).
License: MIT + file LICENSE
URL: https://github.com/genecell/cytome-r, https://piaso.org
BugReports: https://github.com/genecell/cytome-r/issues
Encoding: UTF-8
Depends: R (>= 4.1)
Imports: DBI, RSQLite, Matrix, Rcpp, methods
LinkingTo: Rcpp
Suggests: SingleCellExperiment, SummarizedExperiment, DelayedArray,
        S4Arrays, SparseArray, S4Vectors, SeuratObject, testthat (>=
        3.0.0)
SystemRequirements: liblz4, libzstd, zlib
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libzstd-dev zlib1g-dev
Repository: https://genecell.r-universe.dev
Date/Publication: 2026-09-29 01:48:15 UTC
RemoteUrl: https://github.com/genecell/cytome-r
RemoteRef: HEAD
RemoteSha: 04563025b39997e34c502aecc5ea0df3977ecbd2
NeedsCompilation: yes
Packaged: 2026-09-29 02:09:51 UTC; root
Author: Min Dai [aut, cre],
  PIASO Team [cph]
Maintainer: Min Dai <dai@broadinstitute.org>