https://github.com/bioconductor-source/variancepartition
Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
-
✓DOI references
Found 6 DOI reference(s) in README -
○Academic publication links
-
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (11.8%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- Language: R
- Default Branch: devel
- Size: 79.4 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- 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: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
GitHub Events
Total
Last Year
Dependencies
- BiocParallel * depends
- R >= 4.3.0 depends
- ggplot2 * depends
- limma * depends
- Biobase * imports
- MASS * imports
- Matrix >= 1.4.0 imports
- Rdpack * imports
- RhpcBLASctl * imports
- aod * imports
- corpcor * imports
- fANCOVA * imports
- gplots * imports
- grDevices * imports
- graphics * imports
- iterators * imports
- lme4 >= 1.1.33 imports
- lmerTest * imports
- matrixStats * imports
- methods * imports
- pbkrtest >= 0.4 imports
- remaCor >= 0.0.15 imports
- reshape2 * imports
- rlang * imports
- scales * imports
- stats * imports
- utils * imports
- BiocGenerics * suggests
- BiocStyle * suggests
- DESeq2 * suggests
- RUnit * suggests
- Rfast * suggests
- ballgown * suggests
- cowplot * suggests
- dendextend * suggests
- edgeR * suggests
- knitr * suggests
- pander * suggests
- r2glmm * suggests
- readr * suggests
- rmarkdown * suggests
- statmod * suggests
- tximport * suggests
- tximportData * suggests
- zenith * suggests