README.md

In mojaveazure/seurat-disk: Interfaces for HDF5-Based Single Cell File Formats

SeuratDisk v0.0.0.9015

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.

Installation

SeuratDisk is not currently available on CRAN. You can install it from GitHub with:

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
remotes::install_github("mojaveazure/seurat-disk")

Dependencies

SeuratDisk depends on the following non-standard packages:

| Package | CRAN Webpage | Source | Website | | :-------------------------: | :-----------------------------------------------------: | :----------------------------------------------------: | :--------------------------------------------------------------------------: | | cli | CRAN | GitHub | – | | crayon | CRAN | GitHub | – | | hdf5r | CRAN | GitHub | Website | | Matrix | CRAN | – | Website | | R6 | CRAN | GitHub | Website | | rlang | CRAN | GitHub | Website | | Seurat | CRAN | GitHub | Website | | SeuratObject | CRAN | GitHub | Website | | stringi | CRAN | – | [Website](https://stringi.gagolewski.com/ http://site.icu-project.org/ | | https://www.unicode.org/) | | | | | withr | CRAN | GitHub | Website |

mojaveazure/seurat-disk documentation built on Nov. 5, 2023, 9:40 a.m.