Package: anndata 0.7.5.6

Robrecht Cannoodt

anndata: 'anndata' for R

A 'reticulate' wrapper for the Python package 'anndata'. Provides a scalable way of keeping track of data and learned annotations. Used to read from and write to the h5ad file format.

Authors:Philipp Angerer [ccp], Alex Wolf [ccp], Isaac Virshup [ccp], Sergei Rybakov [ccp], Robrecht Cannoodt [aut, cre, cph]

anndata_0.7.5.6.tar.gz
anndata_0.7.5.6.zip(r-4.5)anndata_0.7.5.6.zip(r-4.4)anndata_0.7.5.6.zip(r-4.3)
anndata_0.7.5.6.tgz(r-4.4-any)anndata_0.7.5.6.tgz(r-4.3-any)
anndata_0.7.5.6.tar.gz(r-4.5-noble)anndata_0.7.5.6.tar.gz(r-4.4-noble)
anndata_0.7.5.6.tgz(r-4.4-emscripten)anndata_0.7.5.6.tgz(r-4.3-emscripten)
anndata.pdf |anndata.html
anndata/json (API)
NEWS

# Install 'anndata' in R:
install.packages('anndata', repos = c('https://dynverse.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/dynverse/anndata/issues

On CRAN:

19 exports 41 stars 3.31 score 14 dependencies 4 dependents 1 mentions 486 scripts 1.8k downloads

Last updated 12 days agofrom:f7ff3410d9. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 05 2024
R-4.5-winNOTESep 05 2024
R-4.5-linuxNOTESep 05 2024
R-4.4-winNOTESep 05 2024
R-4.4-macNOTESep 05 2024
R-4.3-winOKSep 05 2024
R-4.3-macOKSep 05 2024

Exports:AnnDataAnnDataR6concatinstall_anndataLayersLayersR6RawRawR6read_csvread_excelread_h5adread_hdfread_loomread_mtxread_textread_umi_toolswrite_csvswrite_h5adwrite_loom

Dependencies:assertthatherejsonlitelatticeMatrixpngR6rappdirsRcppRcppTOMLreticulaterlangrprojrootwithr

Demo with scanpy

Rendered fromscanpy_demo.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2021-03-28
Started: 2021-03-28

Getting started

Rendered fromgetting_started.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2024-09-05
Started: 2021-03-28

Readme and manuals

Help Manual

Help pageTopics
anndata - Annotated Dataanndata-package anndata
Test if two objects objects are equalall.equal.AnnDataR6 all.equal.LayersR6 all.equal.RawR6
Create an Annotated Data MatrixAnnData AnnDataR6
concatconcat
AnnData Helpersas.data.frame.AnnDataR6 as.matrix.AnnDataR6 dim.AnnDataR6 dimnames.AnnDataR6 dimnames<-.AnnDataR6 py_to_r.anndata._core.anndata.AnnData py_to_r.anndata._core.sparse_dataset.SparseDataset py_to_r.h5py._hl.dataset.Dataset r_to_py.AnnDataR6 t.AnnDataR6 [.AnnDataR6
Raw Helpersas.matrix.RawR6 dim.RawR6 dimnames.RawR6 py_to_r.anndata._core.raw.Raw r_to_py.RawR6 [.RawR6
Install anndatainstall_anndata
Create a Layers objectLayers LayersR6
Layers Helperslength.LayersR6 names.LayersR6 py_to_r.anndata._core.aligned_mapping.LayersBase r_to_py.LayersR6 [.LayersR6 [<-.LayersR6 [[.LayersR6 [[<-.LayersR6
Convert between Python and R objectsnames.collections.abc.Mapping py_to_r.collections.abc.KeysView py_to_r.collections.abc.Mapping py_to_r.collections.abc.Set py_to_r.pandas.core.indexes.base.Index r-py-conversion [.collections.abc.Mapping [<-.collections.abc.MutableMapping [[.collections.abc.Mapping [[<-.collections.abc.MutableMapping
Create a Raw objectRaw RawR6
read_csvread_csv
read_excelread_excel
read_h5adread_h5ad
read_hdfread_hdf
read_loomread_loom
read_mtxread_mtx
read_textread_text
read_umi_toolsread_umi_tools
Write annotation to .csv files.write_csvs
Write .h5ad-formatted hdf5 file.write_h5ad
Write .loom-formatted hdf5 file.write_loom