variancePartition
Quantify and interpret divers of variation in multilevel gene expression experiments
Science Score: 23.0%
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 6 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
3 of 22 committers (13.6%) 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
Quantify and interpret divers of variation in multilevel gene expression experiments
Basic Info
- Host: GitHub
- Owner: DiseaseNeuroGenomics
- Language: R
- Default Branch: master
- Homepage: http://DiseaseNeurogenomics.github.io/variancePartition/
- Size: 81.8 MB
Statistics
- Stars: 8
- Watchers: 0
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
variancePartition quantifies and interprets multiple sources of biological and technical variation in gene expression experiments. The package a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. The dream() function performs differential expression analysis for datasets with repeated measures or high dimensional batch effects.
Update
variancePartition 1.31.1 includes a major rewrite of the backend for better error handling. See Changelog. Importantly, the new version is compatible with emprical Bayes moderated t-statistics for linear mixed models using eBayes().
Installation
Latest features from GitHub
r
devtools::install_github("DiseaseNeuroGenomics/variancePartition")
Stable release from Bioconductor
r
BiocManager::install("variancePartition")
Notes
This is a developmental version. For stable release see Bioconductor version.
For questions about specifying contrasts with dream, see examples here.
See frequently asked questions.
See repo of examples from the paper.
Reporting bugs
Please help speed up bug fixes by providing a 'minimal reproducible example' that starts with a new R session. I recommend the reprex package to produce a GitHub-ready example that is reproducable from a fresh R session.
References
Describes extensions of dream including empirical Bayes moderated t-statistics for linear mixed models and applications to single cell data
Describes dream for differential expression:
Describes the variancePartition package:
Owner
- Name: Center for Disease Neurogenomics @ Mount Sinai
- Login: DiseaseNeuroGenomics
- Kind: organization
- Location: United States of America
- Website: DiseaseNeuroGenomics.github.io
- Repositories: 2
- Profile: https://github.com/DiseaseNeuroGenomics
Open source software, documentation and applications for analysis of functional genomics datasets
GitHub Events
Total
- Issues event: 1
- Watch event: 6
- Push event: 3
Last Year
- Issues event: 1
- Watch event: 6
- Push event: 3
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Gabriel Hoffman | g****n@g****m | 153 |
| Gabriel Hoffman | g****n@g****l | 79 |
| GabrielHoffman | g****n@t****g | 51 |
| GabrielHoffman | g****n@t****e | 36 |
| Gabriel Hoffman | g****n@m****u | 34 |
| GabrielHoffman | g****n@t****e | 28 |
| GabrielHoffman | g****n@t****l | 17 |
| Ryan C. Thompson | r****2@m****u | 16 |
| Nitesh Turaga | n****a@g****m | 14 |
| GabrielHoffman | g****n@t****g | 7 |
| Dan Tenenbaum | d****a@f****g | 6 |
| Herve Pages | h****s@f****g | 4 |
| Ryan C. Thompson | r****t@t****g | 3 |
| Gabriel Hoffman | g****n@g****n | 3 |
| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****a@g****m | 2 |
| vobencha | v****n@r****g | 2 |
| J Wokaty | j****y | 2 |
| J Wokaty | j****y@s****u | 2 |
| Kayla-Morrell | k****l@r****g | 1 |
| Gabriel Hoffman | g****n@g****e | 1 |
| Sonali Arora | s****a@f****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 3
- Total pull requests: 1
- Average time to close issues: 7 months
- Average time to close pull requests: 1 minute
- Total issue authors: 3
- Total pull request authors: 1
- Average comments per issue: 0.33
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: 5 months
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Peiyao-Z (1)
- HenrikBengtsson (1)
- tim-meese (1)
Pull Request Authors
- GabrielHoffman (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 85,968 total
- Total dependent packages: 4
- Total dependent repositories: 0
- Total versions: 9
- Total maintainers: 1
bioconductor.org: variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experiments
- Homepage: http://bioconductor.org/packages/variancePartition https://DiseaseNeuroGenomics.github.io/variancePartition
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/variancePartition/inst/doc/variancePartition.pdf
- License: GPL-2
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Latest release: 1.38.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- BiocParallel * depends
- R >= 4.0.0 depends
- ggplot2 * depends
- limma * depends
- Biobase * imports
- MASS * imports
- Matrix >= 1.4.0 imports
- Rdpack * imports
- RhpcBLASctl * imports
- aod * imports
- doParallel * imports
- foreach * imports
- gplots * imports
- grDevices * imports
- graphics * imports
- iterators * imports
- lme4 >= 1.1 imports
- lmerTest * imports
- methods * imports
- pbkrtest >= 0.4 imports
- progress * imports
- remaCor >= 0.0.11 imports
- reshape2 * imports
- rlang * imports
- scales * imports
- stats * imports
- utils * imports
- BiocGenerics * suggests
- BiocStyle * suggests
- DESeq2 * suggests
- RUnit * suggests
- ballgown * suggests
- dendextend * suggests
- edgeR * suggests
- knitr * suggests
- pander * suggests
- r2glmm * suggests
- readr * suggests
- rmarkdown * suggests
- tximport * suggests
- tximportData * suggests