srtdisk/DESCRIPTION at main · mianaz/srtdisk · GitHub

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Package: srtdisk
Type: Package
Title: Extended HDF5-Based Single Cell File Format Support
Version: 0.4.0
Date: 2026-09-16
Authors@R: c(
  person(given = 'Miana', family = 'Z', email = 'zzeng4@nd.edu', role = c('aut', 'cre')),
  person(given = 'Paul', family = 'Hoffman', email = 'phoffman@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0002-7693-8957')),
  person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-9448-8833'))
  )
Description: Extended implementation of SeuratDisk for Seurat v5 with enhanced
  support for HDF5-based single cell file formats. The h5Seurat file format is
  specifically designed for the storage and analysis of multi-modal single-cell
  and spatially-resolved expression experiments, for example, from CITE-seq or
  10X Visium technologies. It holds all molecular information and associated
  metadata, including (for example) nearest-neighbor graphs, dimensional
  reduction information, spatial coordinates and image data, and cluster labels.
  We also support rapid and on-disk conversion between h5Seurat and AnnData
  objects, with the goal of enhancing interoperability between Seurat and Scanpy.
  This version adds direct h5ad loading via LoadH5AD and includes Seurat v5
  Assay5 compatibility with improved spatial data handling.
URL: https://mianaz.github.io/srtdisk/, https://github.com/mianaz/srtdisk
BugReports: https://github.com/mianaz/srtdisk/issues
License: GPL-3 | file LICENSE
Encoding: UTF-8
Depends:
  R (>= 4.1.0)
Imports:
  cli (>= 2.0.1),
  crayon (>= 1.3.4),
  hdf5r (>= 1.3.0),
  Matrix (>= 1.2.18),
  methods (>= 3.6.0),
  R6 (>= 2.4.1),
  rlang (>= 0.4.4),
  Seurat (>= 3.2.0),
  SeuratObject (>= 4.0.0),
  stats,
  stringi (>= 1.4.6),
  tools,
  utils
Collate:
    'zzz.R'
    'AnnDataCompat.R'
    'GetObject.R'
    'UtilsH5Access.R'
    'AssembleObject.R'
    'AppendData.R'
    'TestObject.R'
    'TestH5.R'
    'h5info.R'
    'scdisk.R'
    'h5Seurat.R'
    'Connect.R'
    'PadMatrix.R'
    'sparse_matrix.R'
    'Transpose.R'
    'FormatRegistry.R'
    'Convert.R'
    'H5ADVersion.R'
    'H5ADVersionAPI.R'
    'H5DAccess.R'
    'LoadH5AD.R'
    'LoadH5Seurat.R'
    'loom.R'
    'loom_bindings.R'
    'LoadLoom.R'
    'LoadSpatialDemoData.R'
    'ReadH5.R'
    'UtilsAssayCompat.R'
    'WriteH5Group.R'
    'SaveH5Seurat.R'
    'SaveLoom.R'
    'SeuratVersion.R'
    'SeuratVersionAPI.R'
    'SpatialConversion.R'
    'SpatialFOV.R'
    'UtilsMatrix.R'
    'V5Compatibility.R'
    'V5LayerSupport.R'
    'h5Seurat_bindings.R'
Suggests:
    BiocGenerics,
    formatR,
    httr,
    knitr,
    reticulate,
    rmarkdown,
    SingleCellExperiment,
    SummarizedExperiment,
    testthat (>= 3.0.0),
    withr
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/roxygen2/version: 8.1.0