Package index • anndata

Package documentation

anndata-package anndata: anndata - Annotated Data

Creating an AnnData object

AnnData(): Create an Annotated Data Matrix

Concatenating two or more AnnData objects

concat(): concat

Reading an AnnData object from a file

read_csv(): read_csv

read_excel(): read_excel

read_h5ad(): read_h5ad

read_hdf(): read_hdf

read_loom(): read_loom

read_mtx(): read_mtx

read_text(): read_text

read_umi_tools(): read_umi_tools

read_zarr(): Read from a hierarchical Zarr array store.

Writing an AnnData object to a file

write_csvs(): Write annotation to .csv files.

write_h5ad(): Write .h5ad-formatted hdf5 file.

write_loom(): Write .loom-formatted hdf5 file.

write_zarr(): Write a hierarchical Zarr array store.

Installer

Helper function for installing the anndata Python package

install_anndata() deprecated: Install anndata

Helper functions / sugar syntax

Layers(): Create a Layers object

Raw(): Create a Raw object

dimnames(<AnnDataR6>) `dimnames<-`(<AnnDataR6>) dim(<AnnDataR6>) as.data.frame(<AnnDataR6>) as.matrix(<AnnDataR6>) r_to_py(<AnnDataR6>) py_to_r(<anndata._core.anndata.AnnData>) `[`(<AnnDataR6>) t(<AnnDataR6>) py_to_r(<anndata._core.sparse_dataset.SparseDataset>) py_to_r(<h5py._hl.dataset.Dataset>): AnnData Helpers

dimnames(<RawR6>) dim(<RawR6>) as.matrix(<RawR6>) r_to_py(<RawR6>) py_to_r(<anndata._core.raw.Raw>) `[`(<RawR6>): Raw Helpers

all.equal(<AnnDataR6>) all.equal(<LayersR6>) all.equal(<RawR6>): Test if two objects objects are equal

names(<LayersR6>) length(<LayersR6>) r_to_py(<LayersR6>) py_to_r(<anndata._core.aligned_mapping.LayersBase>) `[`(<LayersR6>) `[<-`(<LayersR6>) `[[`(<LayersR6>) `[[<-`(<LayersR6>): Layers Helpers

`[[<-`(<collections.abc.MutableMapping>) `[[`(<collections.abc.Mapping>) `[<-`(<collections.abc.MutableMapping>) `[`(<collections.abc.Mapping>) names(<collections.abc.Mapping>) py_to_r(<collections.abc.Set>) py_to_r(<pandas.core.indexes.base.Index>) py_to_r(<collections.abc.KeysView>) py_to_r(<collections.abc.Mapping>) py_to_r(<anndata.abc._AbstractCSDataset>): Convert between Python and R objects