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SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

https://github.com/hemberg-lab/sc3

Science Score: 23.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 18 committers (16.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.8%) to scientific vocabulary

Keywords

bioconductor-package human-cell-atlas single-cell-rna-seq

Keywords from Contributors

hdf5 rhdf5 bioconductor derfinder rnaseq bioinformatics image-analysis mirror pathway-analysis reproducibility
Last synced: 11 months ago · JSON representation

Repository

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

Basic Info
Statistics
  • Stars: 128
  • Watchers: 10
  • Forks: 55
  • Open Issues: 19
  • Releases: 0
Topics
bioconductor-package human-cell-atlas single-cell-rna-seq
Created over 10 years ago · Last pushed about 5 years ago
Metadata Files
Readme License

README.md

Q: What is this?
A: SC3 is a tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 main page is on BioConductor.

Q: How to install/run SC3?
A: Please follow the SC3 manual from its BioConductor page.

If you would like to install the latest development version of SC3 please install it from the GitHub repository: install.packages("devtools") devtools::install_github("hemberg-lab/SC3")

Q: Where can I report bugs, comments, issues or suggestions?
A: Please use this page.

Q: Where can I ask questions about SC3?
A: Please use this page.

Q: Is SC3 published?
A: Yes, SC3 is published in Nature Methods.

Q: What is SC3 licence?
A: GPL-3

Owner

  • Name: Hemberg Lab
  • Login: hemberg-lab
  • Kind: organization
  • Location: United States of America

GitHub Events

Total
  • Watch event: 7
Last Year
  • Watch event: 7

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 339
  • Total Committers: 18
  • Avg Commits per committer: 18.833
  • Development Distribution Score (DDS): 0.265
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Vladimir Kiselev v****v@g****m 249
v.kiselev v****v@b****8 21
Andrew Yin a****2@i****k 18
wikiselev v****6@s****k 16
Dan Tenenbaum d****a@f****g 7
Herve Pages h****s@f****g 5
Nitesh Turaga n****a@g****m 4
nh3 n****3 3
d.tenenbaum d****m@b****8 3
Hervé Pagès h****s@f****g 2
Shians r****u@g****m 2
vobencha v****a@g****m 2
vobencha v****n@r****g 2
tallulandrews t****s@g****m 1
j.java j****a@b****8 1
Nikos Patikas n****3@s****k 1
Jim Java j****a@r****g 1
Kayla-Morrell k****l@r****g 1
Committer Domains (Top 20 + Academic)
roswellpark.org: 3 fhcrc.org: 2 sanger.ac.uk: 2 fredhutch.org: 1 internal.sanger.ac.uk: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 157
  • Total pull requests: 27
  • Average time to close issues: 2 months
  • Average time to close pull requests: 10 days
  • Total issue authors: 60
  • Total pull request authors: 7
  • Average comments per issue: 3.43
  • Average comments per pull request: 0.56
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • wikiselev (15)
  • yicheinchang (4)
  • LuyiTian (3)
  • kieranrcampbell (2)
  • dsimps1993 (2)
  • hkarakurt8742 (2)
  • dkoppstein (2)
  • bsamal20 (2)
  • Shians (2)
  • ghost (1)
  • eshraaqsaeed (1)
  • biosyssun (1)
  • makimenkova (1)
  • yuqiyuqitan (1)
  • galib36 (1)
Pull Request Authors
  • ay2sanger (7)
  • tallulandrews (2)
  • pati-ni (2)
  • Shians (1)
  • nh3 (1)
  • gorgitko (1)
  • zhangguy (1)
Top Labels
Issue Labels
enhancement (8)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 74,287 total
  • Total dependent packages: 4
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: SC3

Single-Cell Consensus Clustering

  • Versions: 5
  • Dependent Packages: 4
  • Dependent Repositories: 0
  • Downloads: 74,287 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 4.4%
Downloads: 13.1%
Maintainers (1)
vladimir.yu.kiselev@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.3 depends
  • BiocGenerics * imports
  • ROCR * imports
  • Rcpp >= 0.11.1 imports
  • S4Vectors * imports
  • SingleCellExperiment * imports
  • SummarizedExperiment * imports
  • WriteXLS * imports
  • cluster * imports
  • doParallel * imports
  • doRNG * imports
  • e1071 * imports
  • foreach * imports
  • ggplot2 * imports
  • graphics * imports
  • methods * imports
  • parallel * imports
  • pheatmap >= 1.0.8 imports
  • robustbase * imports
  • rrcov * imports
  • shiny * imports
  • stats * imports
  • utils * imports
  • knitr * suggests
  • mclust * suggests
  • rmarkdown * suggests
  • scater * suggests