R Observatory: Metrics for anndata version 0.8.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

anndata

0.8.0Package record

'anndata' for R

0packages dependsuggested by 1

37.3Kdownloads / year

54.9%test coverage

13/13flavors OK

Overview

About

Maintained by Robrecht CannoodtCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 0.8.0

FUNCTIONALITY: Added support for read_zarr() and write_zarr() (PR #33).
BUG FIX: Use the right interface for the all.equal() function (PR #32).
BUG FIX: Add py_to_r converter for anndata.abc._AbstractCSDataset (PR #34).
MINOR CHANGES: Ignore python warnings when running tests (PR #34).
MAJOR CHANGES: Update reticulate package dependency management (PR #36).
MINOR CHANGES: Clean up roxygen code (PR #36).
MINOR CHANGES: Use cli for generating errors (PR #36).

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("anndata", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("dynverse/anndata")

Development version from dynverse/anndata. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-anndata

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-anndata

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-anndata

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.8.0

READMEYes · 446 wordsVignettesYes · 2 · staticNEWSYes · 100% structured · mentions 0.8.0Citation fileNoWebsiteYes · pkgdown

Help pages: 24includes a package overview page
Examples that run: 0%22 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 0%
Help pages citing references: 0%

Vignettes (2)

Demo with scanpy HTML
Getting started HTML

How these are measured

Downloads

37.3K

CRAN downloads in the past year

Rank #2,476 · ~102/day · ~3.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.8K30 days

6.6K90 days

37.3K1 year

Compare downloads with other packages →

Also on5.1K r2u24 autocran6.1K bioconda

How downloads are counted

Repository

dynverse/anndata ↗Organization: dynverse

54Stars

4Forks

2Open issues

0Open PRs

5Releases

155Commits

2Commit identities

155 commits · Last activity 2026-04-01 · +1.9% stars, 30d · Default branch at 0.9.0, ahead of CRAN 0.8.0 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 215
Median days to close, 50 most recently updated closed PRs: 8

Stars over time

2025-07-28 · 502026-10-09 · 54

How these are measured

PracticesBeta

13 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/dynverse/anndata on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (3)

Code of conductContributing guideFunding

Funding links: data-intuitive.com

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-04-01 · The repository has a site deploy workflow

pkgdown site last built 2026-04-01

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdrevdep/

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing anndata adds 14 packages (8 with compiled code, 6.3 MB of source tarballs). Heaviest: Rcpp 1.8 MB, reticulate 1.6 MB, jsonlite 1.0 MB.

Depends (1)

R >= 3.5.0

Imports (7)

assertthat cli lifecycleMatrixmethodsR6 reticulate

LinkingTo (0)

none

Suggests (4)

statstestthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

laminr

How these are counted

Code & Tests

People & History

People (5)

ccp

ccp

ccp

ccp

Releases (9)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.8.0Latest
record
2025-05-27 · current release · diff ↗ ·
added 2 exports
read_zarr, write_zarr
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.7.5.6
record
2023-03-17 · diff ↗
0.7.5.5
record
2022-09-23 · diff ↗
0.7.5.4
record
2022-08-23 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.7.5.3
record
2021-09-10 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.7.5.2
record
2021-03-28 · diff ↗
0.7.5.1
record
2021-02-02 · diff ↗ ·
added 4 exports
Layers, LayersR6, Raw, RawR6
0.7.5
record
2020-11-19 · diff ↗
0.7.4
record
2020-11-04
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-11-04
Total releases: 9 / 6 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Download size: 202 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("anndata")

Format

Cannoodt, R., Angerer, P., Rybakov, S., Virshup, I., & Wolf, A. (2025). anndata: 'anndata' for R (Version 0.8.0) [Computer software]. https://doi.org/10.32614/CRAN.package.anndata

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for anndata version 0.8.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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