anndata

anndata: Access and store annotated data matrices - Published in JOSS (2024)

https://github.com/scverse/anndata

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 7 DOI reference(s) in README and JOSS metadata
○
Academic publication links
✓
Committers with academic emails
4 of 55 committers (7.3%) from academic institutions
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords

anndata bioinformatics data-science machine-learning scanpy scverse transcriptomics

Keywords from Contributors

neuroscience human-cell-atlas imaging dimensionality-reduction topological-data-analysis umap closember

Scientific Fields

Engineering Computer Science - 40% confidence

Last synced: 4 months ago · JSON representation

Repository

Annotated data.

Basic Info

Host: GitHub
Owner: scverse
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: http://anndata.readthedocs.io
Size: 5.9 MB

Statistics

Stars: 651
Watchers: 13
Forks: 171
Open Issues: 266
Releases: 95

Topics

anndata bioinformatics data-science machine-learning scanpy scverse transcriptomics

Created over 8 years ago · Last pushed 4 months ago

Metadata Files

Readme Contributing License

anndata - Annotated data

anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray. anndata offers a broad range of computationally efficient features including, among others, sparse data support, lazy operations, and a PyTorch interface.

Discuss development on GitHub.
Read the documentation.
Ask questions on the scverse Discourse.
Install via pip install anndata or conda install anndata -c conda-forge.
See Scanpy's documentation for usage related to single cell data. anndata was initially built for Scanpy.

anndata is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS. If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

Public API

Our public API is documented in the API section of these docs. We cannot guarantee the stability of our internal APIs, whether it's the location of a function, its arguments, or something else. In other words, we do not officially support (or encourage users to do) something like from anndata._core import AnnData as _core is both not documented and contains a leading underscore. However, we are aware that many users do use these internal APIs and thus encourage them to open an issue or migrate to the public API. That is, if something is missing from our public API as documented, for example a feature you wish to be exported publicly, please open an issue.

Citation

If you use anndata in your work, please cite the anndata publication as follows:

anndata: Annotated data

Isaac Virshup, Sergei Rybakov, Fabian J. Theis, Philipp Angerer, F. Alexander Wolf

JOSS 2024 Sep 16. doi: 10.21105/joss.04371.

You can cite the scverse publication as follows:

The scverse project provides a computational ecosystem for single-cell omics data analysis

Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Scverse Community, Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle & Fabian J. Theis

Nat Biotechnol. 2023 Apr 10. doi: 10.1038/s41587-023-01733-8.

Owner

Name: scverse
Login: scverse
Kind: organization

Website: https://scverse.org
Twitter: scverse_team
Repositories: 28
Profile: https://github.com/scverse

Foundational tools for omics data in the life sciences

JOSS Publication

anndata: Access and store annotated data matrices

Published

September 16, 2024

DOI

10.21105/joss.04371

Volume 9, Issue 101, Page 4371

Authors

Isaac Virshup

University of Melbourne, Australia, Helmholtz Munich, Germany

Sergei Rybakov

Helmholtz Munich, Germany

Fabian J. Theis

Helmholtz Munich, Germany, TU Munich, Germany

Philipp Angerer

Helmholtz Munich, Germany

F. Alexander Wolf

Helmholtz Munich, Germany

Editor

Luiz Irber

Papers & Mentions

Total mentions: 1

Rapid single cell evaluation of human disease and disorder targets using REVEAL: SingleCell™

DOI: 10.1186/s12864-020-07300-8
OpenAlex ID: https://openalex.org/W3119441251
Published: January 2021

Last synced: 2 months ago

GitHub Events

Total

Fork event: 16
Create event: 177
Commit comment event: 1
Release event: 9
Issues event: 101
Watch event: 62
Delete event: 146
Member event: 1
Issue comment event: 614
Push event: 902
Pull request review comment event: 414
Pull request event: 464
Pull request review event: 437

Last Year

Fork event: 16
Create event: 177
Commit comment event: 1
Release event: 9
Issues event: 101
Watch event: 62
Delete event: 146
Member event: 1
Issue comment event: 614
Push event: 902
Pull request review comment event: 414
Pull request event: 464
Pull request review event: 437

Committers

Last synced: 5 months ago

All Time

Total Commits: 1,501
Total Committers: 55
Avg Commits per committer: 27.291
Development Distribution Score (DDS): 0.714

Past Year

Commits: 225
Committers: 16
Avg Commits per committer: 14.063
Development Distribution Score (DDS): 0.493

Top Committers

Name	Email	Commits
Isaac Virshup	i**p@g**m	430
Philipp A	f**p@w**e	346
falexwolf	f**f@g**e	283
Ilan Gold	i**d@g**m	145
pre-commit-ci[bot]	6****]	100
Koncopd	k**d@g**m	59
Robrecht Cannoodt	r**d@g**m	12
Gokcen Eraslan	g**n@b**g	9
Selman Özleyen	3****n	8
Severin Dicks	3****7	8
Gökçen Eraslan	g**n@g**m	8
Volker Bergen	3****n	7
ilia-kats	i**s@g**t	6
Tom White	t**e@g**m	6
Lukas Heumos	l**s@p**t	6
Michal Klein	m**n@t**m	5
Gregor Sturm	m**l@g**e	5
Lumberbot (aka Jack)	3****e	5
Matt Weiden	5****n	4
dawe	c**e@g**m	3
Ryan Williams	r**s@g**m	3
Chris Rands	c**0@h**m	2
Eljas Roellin	6****l	2
Jesko Wagner	3****r	2
Joshua Gould	j****d	2
Selman Özleyen	3****n	2
Wouter-Michiel Vierdag	w**v@h**m	2
huidongchen	g**e@g**m	2
michalk8	4****8	2
giovp	g**l@g**m	2
and 25 more...

Committer Domains (Top 20 + Academic)

broadinstitute.org: 2 lenail.org: 1 pks.mpg.de: 1 tum.de: 1 chanzuckerberg.com: 1 onerussian.com: 1 gregor-sturm.de: 1 tngtech.com: 1 posteo.net: 1 gmx.net: 1 gmx.de: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 373
Total pull requests: 1,347
Average time to close issues: 9 months
Average time to close pull requests: 24 days
Total issue authors: 167
Total pull request authors: 45
Average comments per issue: 3.29
Average comments per pull request: 1.64
Merged pull requests: 1,097
Bot issues: 0
Bot pull requests: 139

Past Year

Issues: 90
Pull requests: 599
Average time to close issues: 17 days
Average time to close pull requests: 4 days
Issue authors: 50
Pull request authors: 19
Average comments per issue: 1.23
Average comments per pull request: 1.27
Merged pull requests: 462
Bot issues: 0
Bot pull requests: 60

View more stats

Top Authors

Issue Authors

ivirshup (56)
ilan-gold (43)
flying-sheep (30)
WeilerP (8)
grst (7)
LucaMarconato (6)
Zethson (5)
Hrovatin (5)
gtca (4)
Rafael-Silva-Oliveira (4)
joshua-gould (4)
falexwolf (3)
colganwi (3)
LuckyMD (3)
kaizhang (3)

Pull Request Authors

meeseeksmachine (353)
ilan-gold (353)
flying-sheep (262)
pre-commit-ci[bot] (137)
ivirshup (125)
Intron7 (16)
falexwolf (11)
ilia-kats (9)
syelman (6)
Zethson (6)
grst (5)
amalia-k510 (5)
gszep (4)
eroell (4)
selmanozleyen (4)

Top Labels

Issue Labels

Bug 🐛 (145) enhancement (142) Triage 🩺 (48) stale (47) topic: io (42) Needs info❔ (29) topic: api (24) dev process (19) topic: backed (18) docs (16) topic: combining (14) topic: indexing (13) backend: zarr (13) pinned (12) upstream (12) type: sparse 🫥 (12) performance 🐌 (11) type: dask array (9) topic: gpu (8) topic: views 👀 (8) question (8) backend: hdf5 (6) testing (6) type: dataframe 🧮 (6) skip-gpu-ci (6) topic: compatibility (4) topic: cloud ☁️ (4) breaking change ‼️ (4) help wanted 🙏 (3) duplicate (3)

Pull Request Labels

skip-gpu-ci (942) dev process (266) run-gpu-ci (129) Bug 🐛 (66) docs (58) no milestone (41) topic: backed (33) type: sparse 🫥 (26) benchmark (25) backend: zarr (24) enhancement (18) topic: combining (17) topic: api (17) backend: hdf5 (16) performance 🐌 (15) topic: io (13) topic: gpu (11) needs retroactive review (9) type: awkward array 😐 (9) type: dask array (9) testing (8) type: dataframe 🧮 (7) topic: views 👀 (6) topic: indexing (6) upstream (4) DON’T MERGE (2) breaking change ‼️ (2) topic: exported functions (2) topic: error messages 🤬 (1) topic: compatibility (1)

Packages

Total packages: 1
Total downloads:
- pypi 962,749 last-month
Total docker downloads: 36,483

Total dependent packages: 389
Total dependent repositories: 467
Total versions: 100
Total maintainers: 2

pypi.org: anndata

Annotated data.

Documentation: https://anndata.readthedocs.io/
License: bsd-3-clause
Latest release: 0.12.2
published 5 months ago

Versions: 100
Dependent Packages: 389
Dependent Repositories: 467
Downloads: 962,749 Last month
Docker Downloads: 36,483

Rankings

Dependent packages count: 0.1%

Dependent repos count: 0.7%

Downloads: 0.9%

Docker downloads count: 1.4%

Average: 1.7%

Stargazers count: 2.9%

Forks count: 4.1%

Maintainers (2)

falexwolf ivirshup

Last synced: 5 months ago

Dependencies

.github/workflows/benchmark.yml actions

actions/cache v3 composite
actions/checkout v2 composite
mamba-org/setup-micromamba v1 composite

.github/workflows/check-pr-milestoned.yml actions

.github/workflows/close-stale.yml actions

actions/stale v5 composite

.github/workflows/codespell.yml actions

actions/checkout v3 composite
codespell-project/actions-codespell v2 composite

.github/workflows/label-stale.yml actions

actions/stale v5 composite

.github/workflows/test-gpu.yml actions

actions/checkout v3 composite
codecov/codecov-action v3 composite
flying-sheep/check v1 composite
mamba-org/setup-micromamba v1 composite

.github/workflows/publish.yml actions

actions/checkout v4 composite
actions/setup-python v4 composite
pypa/gh-action-pypi-publish release/v1 composite

pyproject.toml pypi

array_api_compat *
exceptiongroup python_version<'3.11'
h5py >=3
natsort *
numpy >=1.16.5
packaging >=20
pandas >=1.1.1, !=2.1.0rc0, !=2.1.2
scipy >1.4

anndata

Science Score: 95.0%

Keywords

Keywords from Contributors

Scientific Fields

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

anndata - Annotated data

Public API

Citation

Owner

JOSS Publication

anndata: Access and store annotated data matrices

Authors

Editor

Tags

Papers & Mentions

Rapid single cell evaluation of human disease and disorder targets using REVEAL: SingleCell™

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: anndata

Rankings

Maintainers (2)

Dependencies