cellxgene

An interactive explorer for single-cell transcriptomics data

https://github.com/chanzuckerberg/cellxgene

Science Score: 46.0%

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

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
2 of 48 committers (4.2%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.9%) to scientific vocabulary

Keywords

dataviz scientific scrna-seq transcriptomics visualization

Keywords from Contributors

bioinformatics imaging genomics sequences scverse anndata scanpy interactive single-cell clade

Last synced: 6 months ago · JSON representation

Repository

An interactive explorer for single-cell transcriptomics data

Basic Info

Host: GitHub
Owner: chanzuckerberg
License: mit
Language: JavaScript
Default Branch: main
Homepage: https://chanzuckerberg.github.io/cellxgene/
Size: 239 MB

Statistics

Stars: 710
Watchers: 38
Forks: 140
Open Issues: 132
Releases: 47

Topics

dataviz scientific scrna-seq transcriptomics visualization

Created over 8 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License

README.md

an interactive explorer for single-cell transcriptomics data

CZ CELLxGENE Annotate (pronounced "cell-by-gene") is an interactive data explorer for single-cell datasets, such as those coming from the Human Cell Atlas. Leveraging modern web development techniques to enable fast visualizations of at least 1 million cells, we hope to enable biologists and computational researchers to explore their data.

Whether you need to visualize one thousand cells or one million, CELLxGENE Annotate helps you gain insight into your single-cell data.

Getting started

The comprehensive guide to CZ CELLxGENE Annotate

The CZ CELLxGENE Annotate documentation is your one-stop-shop for information about CELLxGENE Annotate! You may be particularly interested in:

Seeing what Annotate can do
Learning more about Annotate installation and usage
Preparing your own data for use in Annotate
Checking out our roadmap for future development
Contributing to Annotate

Quick start

To install CELLxGENE Annotate you need Python 3.10+. We recommend installing Annotate into a conda or virtual environment.

Install the package.

bash pip install cellxgene

Launch Annotate with an example anndata file

bash cellxgene launch https://cellxgene-example-data.czi.technology/pbmc3k.h5ad

To explore more datasets already formatted for Annotate, check out the Demo data or see Preparing your data to learn more about formatting your own data for CELLxGENE Annotate.

Supported browsers

CELLxGENE Annotate currently supports the following browsers:

Google Chrome 61+
Edge 15+
Firefox 60+

Please file an issue if you would like us to add support for an unsupported browser.

Finding help

We'd love to hear from you! For questions, suggestions, or accolades, join the #cellxgene-users channel on the CZI Science Community Slack and say "hi!".

For any errors, report bugs on Github.

Developing with CZ CELLxGENE Annotate

Contributing

We warmly welcome contributions from the community! Please see our contributing guide and don't hesitate to open an issue or send a pull request to improve CELLxGENE Annotate. Please see the dev_docs for pull request suggestions, unit test details, local documentation preview, and other development specifics.

This project adheres to the Contributor Covenant code of conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to opensource@chanzuckerberg.com.

Reuse

This project was started with the sole goal of empowering the scientific community to explore and understand their data. As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from this project. All code is freely available for reuse under the MIT license.

Before extending CELLxGENE Annotate, we encourage you to reach out to us with ideas or questions. It might be possible that an extension could be directly contributed, which would make it available for a wider audience, or that it's on our roadmap and under active development.

See the CELLxGENE extensions section of our documentation for examples of community use and CELLxGENE extensions.

Trademarks

Use, reuse, modification, and re-distribution of the source code in this repository is subject to the terms of the applicable open source license. However, that license does not grant permission to use the trademarks without separate, express permission from the Chan Zuckerberg Initiative.

Security

If you believe you have found a security issue, we would appreciate notification. Please send email to security@chanzuckerberg.com.

Inspiration

We've been heavily inspired by several other related single-cell visualization projects, including the UCSC Cell Browser, Cytoscape, Xena, ASAP, GenePattern, and many others. We hope to explore collaborations where useful as this community works together on improving interactive visualization for single-cell data.

We were inspired by Mike Bostock and the crossfilter team for the design of our filtering implementation.

We have been working closely with the scanpy team to integrate with their awesome analysis tools. Special thanks to Alex Wolf, Fabian Theis, and the rest of the team for their help during development and for providing an example dataset.

We are eager to explore integrations with other computational backends such as Seurat or Bioconductor

Owner

Name: Chan Zuckerberg Initiative
Login: chanzuckerberg
Kind: organization
Email: opensource@chanzuckerberg.com
Location: United States of America

Website: https://chanzuckerberg.com/
Repositories: 258
Profile: https://github.com/chanzuckerberg

Finding new ways to leverage technology, community-driven solutions, and collaboration to accelerate progress in science and education.

GitHub Events

Total

Issues event: 15
Watch event: 75
Delete event: 8
Issue comment event: 29
Push event: 1
Pull request review event: 2
Pull request event: 21
Fork event: 22
Create event: 10

Last Year

Issues event: 15
Watch event: 75
Delete event: 8
Issue comment event: 29
Push event: 1
Pull request review event: 2
Pull request event: 21
Fork event: 22
Create event: 10

Committers

Last synced: 6 months ago

All Time

Total Commits: 1,489
Total Committers: 48
Avg Commits per committer: 31.021
Development Distribution Score (DDS): 0.717

Past Year

Commits: 7
Committers: 3
Avg Commits per committer: 2.333
Development Distribution Score (DDS): 0.429

Top Committers

Name	Email	Commits
Colin Megill	c**l@g**m	421
Bruce Martin	b**e@c**m	335
Charlotte Weaver	c**r@g**m	204
Severiano Badajoz	s**z@c**m	118
bmccandless	b**s@c**m	86
Matt Weiden	5****n	58
maniarathi	m**i@g**m	42
Sidney Bell	s**l@g**m	40
Madison Dunitz	m**z@c**m	27
Timmy Huang	t****n	20
Justin Kiggins	j**s@g**m	14
Andrew Tolopko	a****i	13
dependabot[bot]	4****]	13
Marcus Kinsella	m****l	12
Jeremy Freeman	t**b@g**m	9
Ben MR	b**s@c**m	8
fionagriffin	4****n	8
atarashansky	a**y@c**m	6
Emanuele Bezzi	e**i@c**m	5
maniarathi	a**i@c**m	4
Ronen	k****r	4
ashin-czi	1****i	4
Mim Hastie	m**m@c**m	3
Ambrose J Carr	a****r	3
Leslie	h**g@g**m	2
Isaiah Norton	i****n	2
Prete	m**e@s**k	2
Rohan Agarwal	4****a	2
Trent Smith	1****7	2
Snyk bot	s**t@s**o	2
and 18 more...

Committer Domains (Top 20 + Academic)

chanzuckerberg.com: 10 uber.com: 1 gruenings.eu: 1 gmx.de: 1 jamestaylor.org: 1 uw.edu: 1 snyk.io: 1 sanger.ac.uk: 1 clevercanary.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 115
Total pull requests: 146
Average time to close issues: 6 months
Average time to close pull requests: about 1 month
Total issue authors: 82
Total pull request authors: 27
Average comments per issue: 2.23
Average comments per pull request: 2.03
Merged pull requests: 42
Bot issues: 1
Bot pull requests: 66

Past Year

Issues: 17
Pull requests: 49
Average time to close issues: 6 days
Average time to close pull requests: 6 days
Issue authors: 17
Pull request authors: 8
Average comments per issue: 0.18
Average comments per pull request: 1.22
Merged pull requests: 10
Bot issues: 1
Bot pull requests: 23

View more stats

Top Authors

Issue Authors

MaximilianLombardo (13)
atolopko-czi (10)
seve (5)
colinmegill (3)
lijinbio (3)
bkmartinjr (2)
dsadgat (2)
neuromusic (2)
slinnarsson (2)
royfrancis (1)
aopisco (1)
ambrosejcarr (1)
dependabot[bot] (1)
ivirshup (1)
Pointillomic (1)

Pull Request Authors

dependabot[bot] (66)
atolopko-czi (14)
kaloster (12)
atarashansky (8)
wontonst (5)
tihuan (4)
ebezzi (4)
seve (4)
Neah-Ko (2)
moritzschaefer (2)
NetoRutes (2)
ashin-czi (2)
roaga (2)
smoe (2)
neuromusic (2)

Top Labels

Issue Labels

bug (29) question (22) user request (19) frontend (6) tech debt (4) epic (4) P3 (3) backend (3) enhancement (2) on-call (2) P1 (2) cleanup (2) P4 (2) injected (1) security (1) P2 (1) conversation (1) docs (1) tech (1) dependencies (1) javascript (1)

Pull Request Labels

dependencies (66) stale (59) autoclosed (58) javascript (39) python (17) question (1)

Packages

Total packages: 2
Total downloads:
- pypi 954 last-month
Total docker downloads: 559

Total dependent packages: 1
(may contain duplicates)
Total dependent repositories: 6
(may contain duplicates)
Total versions: 45
Total maintainers: 5

pypi.org: cellxgene

Web application for exploration of large scale scRNA-seq datasets

Homepage: https://github.com/chanzuckerberg/cellxgene
Documentation: https://cellxgene.readthedocs.io/
License: MIT
Latest release: 1.3.0
published over 1 year ago

Versions: 42
Dependent Packages: 1
Dependent Repositories: 6
Downloads: 954 Last month
Docker Downloads: 559

Rankings

Docker downloads count: 2.3%

Stargazers count: 2.7%

Forks count: 4.5%

Dependent packages count: 4.8%

Average: 4.8%

Dependent repos count: 6.0%

Downloads: 8.4%

Maintainers (5)

tarashan atolopko-czi kuni-czi colinmegill dsadgat

Last synced: 6 months ago

proxy.golang.org: github.com/chanzuckerberg/cellxgene

Documentation: https://pkg.go.dev/github.com/chanzuckerberg/cellxgene#section-documentation
License: mit
Latest release: v1.2.0
published about 2 years ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 6.5%

Average: 6.7%

Dependent repos count: 7.0%

Last synced: 6 months ago

Dependencies

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