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Copy file name to clipboardExpand all lines: vignettes/articles/software_design.Rmd
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# Introduction
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`r Biocpkg("anndataR")` is designed to be an R native implementation of the `AnnData` object, inspired by the of the following packages:
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`r Biocpkg("anndataR")` is designed to be an R native implementation of the `AnnData` object, inspired by the following packages:
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*[_anndata_](https://anndata.readthedocs.io/en/stable/) ([scverse/anndata](https://github.com/scverse/anndata)): The Python `anndata` package and on-disk specification
*`r Githubpkg("mtmorgan/h5ad")`: Read/write `*.h5ad` files natively using `r Biocpkg("rhdf5")`
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*`r CRANpkg("anndataR")` ([dynverse/anndata](https://github.com/dynverse/anndata)): An R implementation of the `AnnData` data structures, uses `r CRANpkg("reticulate")` to read/write `*.h5ad` files
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*`r CRANpkg("anndata")` ([dynverse/anndata](https://github.com/dynverse/anndata)): An R implementation of the `AnnData` data structures, uses `r CRANpkg("reticulate")` to read/write `*.h5ad` files
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Ideally, this package will be a complete replacement for all of these packages, and will be the go-to package for working with `AnnData` files in R.
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It is want you will want to use in most cases where you want to interact with an `AnnData` object.
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- The `HDF5AnnData` provides an interface to a H5AD file and minimal data is stored in memory until it is requested by the user.
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It is primarily designed as an intermediate object when reading/writing H5AD files but can be useful for accessing parts of large files.
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- The `ReticulateAnnData`access data stored in an `AnnData` object in a concurrent Python session.
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- The `ReticulateAnnData`accesses data stored in an `AnnData` object in a concurrent Python session.
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This comes with the overhead and complexity of using `r CRANpkg("reticulate")` but is sometimes useful to access functionality that has not yet been implemented in `r Biocpkg("anndataR")`.
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- The planned `ZarrAnnData` will provide an interface to an `AnnData` Zarr store, similar to `HDF5AnnData`.
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- An `AnnDataView` is returned when subsetting an `AnnData` object and provides access to a subset of the data in the referenced object.
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