Signac
R toolkit for the analysis of single-cell chromatin data
Science Score: 59.0%
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 -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: nature.com -
✓Committers with academic emails
5 of 16 committers (31.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (17.0%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
R toolkit for the analysis of single-cell chromatin data
Basic Info
- Host: GitHub
- Owner: stuart-lab
- License: other
- Language: R
- Default Branch: master
- Homepage: https://stuartlab.org/signac/
- Size: 13.4 MB
Statistics
- Stars: 385
- Watchers: 5
- Forks: 100
- Open Issues: 22
- Releases: 21
Topics
Metadata Files
README.md
Signac 
Overview
Signac is a comprehensive R package for the analysis of single-cell chromatin data. Signac includes functions for quality control, normalization, dimension reduction, clustering, differential activity, and more.
Documentation and tutorials can be found at https://stuartlab.org/signac/
Installation
To install the latest release of Signac from CRAN:
r
setRepositories(ind=1:3) # needed to automatically install Bioconductor dependencies
install.packages("Signac")
To release the latest develop version from GitHub:
r
if (!requireNamespace("remotes", quietly = TRUE))
install.packages("remotes")
remotes::install_github("stuart-lab/signac", ref = "develop")
Release notes
For a changelog please see the NEWS file, also available on the Signac website.
Contributing
We welcome contributions to the Signac package. Please see the contribution guide for more information.
Getting help
If you encounter a bug or have a feature request, please open an issue.
If you would like to discuss questions related to single-cell analysis, you can open a discussion.
Citing Signac
If you use the Signac package in your work please cite Stuart et al. 2021
@ARTICLE{signac,
title = "Single-cell chromatin state analysis with Signac",
author = "Stuart, Tim and Srivastava, Avi and Madad, Shaista and Lareau,
Caleb A and Satija, Rahul",
journal = "Nat. Methods",
publisher = "Nature Publishing Group",
pages = "1--9",
month = nov,
year = 2021,
url = "https://www.nature.com/articles/s41592-021-01282-5",
language = "en"
}
Related packages
Owner
- Name: Stuart Lab
- Login: stuart-lab
- Kind: organization
- Website: https://stuartlab.org
- Twitter: timoast
- Repositories: 2
- Profile: https://github.com/stuart-lab
GitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 127
- Watch event: 57
- Issue comment event: 190
- Push event: 14
- Pull request event: 12
- Fork event: 13
Last Year
- Create event: 1
- Release event: 1
- Issues event: 127
- Watch event: 57
- Issue comment event: 190
- Push event: 14
- Pull request event: 12
- Fork event: 13
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| timoast | 4****t | 1,742 |
| Saket Choudhary | s****c@g****m | 11 |
| Avi Srivastava | a****a@c****u | 6 |
| Avi Srivastava | k****i | 5 |
| yyan7 | y****n@u****u | 5 |
| Gesmira | g****a@g****m | 4 |
| kmwinkley | k****y@g****m | 4 |
| kmwinkley | k****y@h****l | 3 |
| Thomas Wayne McCarthy | t****y@b****m | 2 |
| caleblareau | c****u@g****u | 2 |
| Caleb Lareau | c****u@s****u | 2 |
| Nicole Rockweiler | n****r@g****m | 1 |
| Federico Marini | m****f@u****e | 1 |
| maxim-h | m****v@g****m | 1 |
| Ian Driver | i****n@g****o | 1 |
| Donghoon Lee | h****y | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 469
- Total pull requests: 23
- Average time to close issues: 15 days
- Average time to close pull requests: 4 months
- Total issue authors: 335
- Total pull request authors: 11
- Average comments per issue: 2.49
- Average comments per pull request: 2.13
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 97
- Pull requests: 13
- Average time to close issues: 29 days
- Average time to close pull requests: 2 months
- Issue authors: 75
- Pull request authors: 4
- Average comments per issue: 0.95
- Average comments per pull request: 0.92
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- KshitijDeoghar (6)
- kryptonitecircuit2002 (6)
- emanuelavilla (6)
- mossconfuse (5)
- sylestiel (5)
- linzhangTuesday (5)
- jgarces02 (4)
- zgb963 (4)
- jenellewallace (4)
- sabrinacamp2 (4)
- danielcgingerich (4)
- superSXB (4)
- yamihn (4)
- BartBryant (4)
- Dragonmasterx87 (4)
Pull Request Authors
- lldelisle (8)
- cmf1997 (2)
- Baboon61 (2)
- jeroen (2)
- yuanlizhanshi (2)
- twmccart (2)
- dstyaaaaaa (1)
- nrockweiler (1)
- federicomarini (1)
- bschilder (1)
- Gesmira (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- cran 5,996 last-month
- Total docker downloads: 1,690
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Total dependent packages: 1
(may contain duplicates) -
Total dependent repositories: 17
(may contain duplicates) - Total versions: 24
- Total maintainers: 1
proxy.golang.org: github.com/stuart-lab/signac
- Documentation: https://pkg.go.dev/github.com/stuart-lab/signac#section-documentation
- License: other
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Latest release: v0.2.5
published almost 6 years ago
Rankings
cran.r-project.org: Signac
Analysis of Single-Cell Chromatin Data
- Homepage: https://github.com/stuart-lab/signac
- Documentation: http://cran.r-project.org/web/packages/Signac/Signac.pdf
- License: MIT + file LICENSE
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Latest release: 1.15.0
published 6 months ago
Rankings
Maintainers (1)
Dependencies
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- r-lib/actions/setup-r v2 composite
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- satijalab/seurat latest build