clusterexperiment
R package of techniques for comparing clusterings of single-cell sequencing data
Science Score: 33.0%
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
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○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: plos.org -
✓Committers with academic emails
4 of 17 committers (23.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.8%) to scientific vocabulary
Keywords from Contributors
Repository
R package of techniques for comparing clusterings of single-cell sequencing data
Basic Info
- Host: GitHub
- Owner: epurdom
- Language: R
- Default Branch: master
- Size: 179 MB
Statistics
- Stars: 38
- Watchers: 3
- Forks: 13
- Open Issues: 58
- Releases: 0
Metadata Files
README.md
R package: clusterExperiment
Functions for running and comparing many different clusterings of single-cell sequencing data.
News and Updates
Version 2.3.0 is on Bioconductor (development version) with many new changes. Checkout out a brief description of the major changes. For complete details, see the NEWS file.
Summary of changes from previous versions:
- Version 2.0.0 brief description
Publications
The paper acompanying this package can be found at:
Risso D, Purvis L, Fletcher R, Das D, Ngai J, Dudoit S, Purdom E (2018) "clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets" PLoS Comput Biol. 2018 Sep 4;14(9):e1006378 link
There is a github repository (epurdom/RSECPaper for this paper that gives the code for reproducing the analysis in that manuscript.
A F1000 workflow demonstrating the use of RSEC for clustering as part of trajectory estimation with the package
slingshotand normalization withzinbwavePerraudeau F, Risso D, Street K, Purdom E, and Dudoit S (2017) "Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference" F1000Research 6:1158.
A compiled version of the vignette (i.e. tutorial) of the github version of
clusterExperiment(corresponding to themasterbranch) can be found (here)[http://bioconductor.org/packages/devel/bioc/vignettes/clusterExperiment/inst/doc/clusterExperimentTutorial.html]The compiled version of the vignette corresponding to the version of
clusterExperimentavailable with the latest release of Bioconductor can be found (here)[http://bioconductor.org/packages/release/bioc/vignettes/clusterExperiment/inst/doc/clusterExperimentTutorial.html]
Installation instructions
Installation From Bioconductor
We recommend installation of the package via bioconductor.
r
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("clusterExperiment")
To install the most recent version of the package available on the development branch of bioconductor, follow the above instructions, after downloading the development version of bioconductor (see here for instructions).
If you are having problems installing/updating the package gsl from source because your gsl installation is not found, this answer (and the comment following it) on stackoverflow may be of help.
Installation of Github Version:
We generally try to keep the bioconductor devel version up-to-date with the master branch of this git repository. But since this can require installing R and/or bioconductor development version, it can be convenient to be able to get just the most recent version from github.
You can install the github version via
r
library(devtools)
install_github("epurdom/clusterExperiment")
Development branch:
The develop branch is our development branch where we are actively updating features, and may contain bugs or be in the process of being updated. You should not use the develop branch unless it passes TravisCI checks (see below) and you want to be using a very beta version.
The development branch can be installed via the install_github command above, but indicating the develop branch:
r
library(devtools)
install_github("epurdom/clusterExperiment", ref="develop")
Status Checks
Below are status checks for the package. Note that occassionally errors do not appear here immediately. Clicking on the link will give you the most up-to-date status.
| Resource: | Status |
| ------------- | ------------ |
| Bioc Release | 
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| Bioc Development | 
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| Travis CI master | 
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| Travis CI develop | 
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| Appveyor master | |
| Appveyor develop |
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Issues and bug reports
Please use https://github.com/epurdom/clusterExperiment/issues to submit issues, bug reports, and comments.
Owner
- Name: Elizabeth Purdom
- Login: epurdom
- Kind: user
- Website: http://www.stat.berkeley.edu/~epurdom
- Repositories: 11
- Profile: https://github.com/epurdom
GitHub Events
Total
- Issues event: 3
- Watch event: 5
- Issue comment event: 1
Last Year
- Issues event: 3
- Watch event: 5
- Issue comment event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Elizabeth Purdom | e****m@s****u | 1,808 |
| Davide Risso | r****e@g****m | 151 |
| Davide Risso | d****2@m****u | 56 |
| Elizabeth Purdom | e****m@s****u | 47 |
| Nitesh Turaga | n****a@g****m | 14 |
| Herve Pages | h****s@f****g | 5 |
| kevinbenac | 3****c | 3 |
| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****a@g****m | 2 |
| vobencha | v****n@r****g | 2 |
| Davide Risso | d****e@D****n | 2 |
| lshep | l****d@r****g | 1 |
| LiNk-NY | m****9@g****m | 1 |
| Elizabeth Purdom | e****m@s****U | 1 |
| Martin Morgan | m****n@f****g | 1 |
| mtmorgan@fhcrc.org | m****n@f****g@b****8 | 1 |
| d.risso | d****o@b****8 | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 9 months ago
All Time
- Total issues: 185
- Total pull requests: 6
- Average time to close issues: 4 months
- Average time to close pull requests: 16 days
- Total issue authors: 20
- Total pull request authors: 4
- Average comments per issue: 1.52
- Average comments per pull request: 0.67
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 0.25
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- epurdom (131)
- drisso (28)
- diyadas (6)
- bd4everyone (2)
- allonw (2)
- fperraudeau (1)
- JensFGG (1)
- koenvandenberge (1)
- rufletch (1)
- siyao-liu (1)
- spholmes (1)
- SaskiaFreytag (1)
- flde (1)
- pshukla63 (1)
- legeinei123 (1)
Pull Request Authors
- kevinbenac (2)
- drisso (2)
- kant (1)
- csoneson (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
- Total downloads: unknown
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 0
(may contain duplicates) - Total versions: 6
proxy.golang.org: github.com/epurdom/clusterexperiment
- Documentation: https://pkg.go.dev/github.com/epurdom/clusterexperiment#section-documentation
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Latest release: v1.99.1
published about 8 years ago
Rankings
proxy.golang.org: github.com/epurdom/clusterExperiment
- Documentation: https://pkg.go.dev/github.com/epurdom/clusterExperiment#section-documentation
-
Latest release: v1.99.1
published about 8 years ago
Rankings
Dependencies
- BiocGenerics * depends
- R >= 3.6.0 depends
- SingleCellExperiment * depends
- SummarizedExperiment >= 1.15.4 depends
- BiocSingular * imports
- DelayedArray >= 0.7.48 imports
- HDF5Array >= 1.7.10 imports
- Matrix * imports
- NMF * imports
- RColorBrewer * imports
- Rcpp * imports
- S4Vectors * imports
- ape >= 5.0 imports
- cluster * imports
- edgeR * imports
- grDevices * imports
- graphics * imports
- howmany * imports
- kernlab * imports
- limma * imports
- locfdr * imports
- matrixStats * imports
- mbkmeans * imports
- methods * imports
- parallel * imports
- phylobase * imports
- pracma * imports
- scales * imports
- stats * imports
- stringr * imports
- zinbwave * imports
- BiocStyle * suggests
- MAST * suggests
- Rtsne * suggests
- igraph * suggests
- knitr * suggests
- rmarkdown * suggests
- scran * suggests
- testthat * suggests