capseuratconverter

The capseuratconverter package provides functions to convert AnnData (.h5ad) files to Seurat v5 objects and saves them as RDS files. The package was created specically for the Cell Annotation Project (CAP), so please test it first to see it it meets your requirements. It is written in pure R, with no reticulate dependencies. The package currently supports AnnData (.h5ad) files created via AnnData v0.10+ and converts the following fields: X, obs, var, raw.X, raw.var, obsm, and uns.

Installation

The package isn't published on CRAN, so it can be installed using devtools:

install.packages('devtools')
devtools::install_github('cellannotation/capseuratconverter')

Alternatively, you can install it from GitHub releases (the fastest way):

destfile <- "capseuratconverter.tar.gz"
url <- "https://github.com/cellannotation/capseuratconverter/releases/download/v0.6/capseuratconverter_0.6.tar.gz"
download.files(url=url, destfile=destfile)
install.packages(destfile, repos = NULL, type='source')
file.remove(destfile)

Usage

There are two main functions in the package:

• h5ad_to_seurat(h5ad_path, ignore_bad_format) Takes the path to an .h5ad file and returns a Seurat v5 object.
• h5ad2rds(h5ad_path, ignore_bad_format) Takes the path to an .h5ad file, runs h5ad_to_seurat, and saves the object to the same path as the input but replaces the .h5ad extension with .rds. Returns the path to the RDS file.

If ignore_bad_format is set to TRUE, the function will ignore bad formats in obs/var/uns/obsm/varm fields and will continue convertion. If set to FALSE, the function will throw an error if any bad formats are detected.

Dependencies

• R version >= 4.0.0
• SeuratObject >= 5.0.0
• Matrix
• rhdf5
• log4r

Contribution

Fill free to contribute with new issues or PRs! The project is small so there are no special guidlines for that.