Package index

Package documentation

anndata-package anndata superseded

anndata - Annotated Data

Creating an AnnData object

AnnData()

Create an Annotated Data Matrix

Concatenating two or more AnnData objects

concat() superseded

concat

Reading an AnnData object from a file

read_csv() superseded

read_csv

read_excel() superseded

read_excel

read_h5ad() superseded

read_h5ad

read_hdf() superseded

read_hdf

read_loom() superseded

read_loom

read_mtx() superseded

read_mtx

read_text() superseded

read_text

read_umi_tools() superseded

read_umi_tools

read_zarr() superseded

Read from a hierarchical Zarr array store.

Writing an AnnData object to a file

write_csvs() superseded

Write annotation to .csv files.

write_h5ad() superseded

Write .h5ad-formatted hdf5 file.

write_loom() superseded

Write .loom-formatted hdf5 file.

write_zarr() superseded

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