Science Score: 36.0%
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 11 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 6 committers (16.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.9%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: willtownes
- License: lgpl-3.0
- Language: R
- Default Branch: master
- Size: 436 KB
Statistics
- Stars: 95
- Watchers: 9
- Forks: 11
- Open Issues: 19
- Releases: 0
Metadata Files
README.md
R package: glmpca
Generalized PCA for non-normally distributed data. If you find this useful please cite Feature Selection and Dimension Reduction based on a Multinomial Model. (doi:10.1186/s13059-019-1861-6)
A python implementation is also available.
Installation
The glmpca package is available from CRAN. To install the stable release (recommended):
r
install.packages("glmpca")
To install the development version:
r
remotes::install_github("willtownes/glmpca")
Usage
```r library(glmpca)
create a simple dataset with two clusters
mu<-rep(c(.5,3),each=10) mu<-matrix(exp(rnorm(10020)),nrow=100) mu[,1:10]<-mu[,1:10]exp(rnorm(100)) clust<-rep(c("red","black"),each=10) Y<-matrix(rpois(prod(dim(mu)),mu),nrow=nrow(mu))
visualize the latent structure
res<-glmpca(Y, 2) factors<-res$factors plot(factors[,1],factors[,2],col=clust,pch=19) ```
For more details see the vignettes. For compatibility with Bioconductor, see scry. For compatibility with Seurat objects, see Seurat-wrappers.
Alternative implementations
GLM-PCA has been around for awhile and we have not been able to dedicate as much time to its maintenance and ongoing improvement as we would like. Fortunately, there are numerous alternative implementations that improve on our basic idea. Many of them are likely to be faster and more memory-efficient than our version, and some have interesting additional capabilities such as uncertainty quantification. In reverse chronological order, here are some packages to check out.
- fastglmpca. Preprint: Weine, Carbonetto, & Stephens (2024).
- scGBM. Preprint: Nicol & Miller 2023.
- NewWave. Publication: Agostinis et al 2022.
- LDVAE. Publication: Svensson et al 2020.
Issues and bug reports
Please use https://github.com/willtownes/glmpca/issues to submit issues, bug reports, and comments.
Owner
- Name: Will Townes
- Login: willtownes
- Kind: user
- Location: Pittsburgh, PA
- Company: Carnegie Mellon University
- Website: http://willtownes.github.io
- Twitter: will_townes
- Repositories: 12
- Profile: https://github.com/willtownes
Assistant Professor of Statistics and Data Science
GitHub Events
Total
- Watch event: 1
- Fork event: 1
Last Year
- Watch event: 1
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Will Townes | w****s@g****m | 34 |
| Kelly Street | k****t@r****u | 15 |
| Kelly Street | s****y@g****m | 11 |
| Peter Hickey | p****y@g****m | 1 |
| Philipp A | f****p@w****e | 1 |
| rmflight | r****9@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 34
- Total pull requests: 3
- Average time to close issues: 3 months
- Average time to close pull requests: 11 days
- Total issue authors: 23
- Total pull request authors: 3
- Average comments per issue: 2.41
- Average comments per pull request: 1.67
- Merged pull requests: 3
- 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
Top Authors
Issue Authors
- willtownes (9)
- frederikziebell (3)
- leon-seranova (2)
- jeremymsimon (1)
- jakeyeung (1)
- JauntyJJS (1)
- hanbin973 (1)
- venchi9 (1)
- spinkney (1)
- const-ae (1)
- davemcg (1)
- jtheorell (1)
- bc2zb (1)
- ttriche (1)
- seawavevan (1)
Pull Request Authors
- flying-sheep (1)
- PeteHaitch (1)
- rmflight (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- cran 712 last-month
- Total docker downloads: 546
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Total dependent packages: 2
(may contain duplicates) -
Total dependent repositories: 9
(may contain duplicates) - Total versions: 4
- Total maintainers: 1
cran.r-project.org: glmpca
Dimension Reduction of Non-Normally Distributed Data
- Homepage: https://github.com/willtownes/glmpca
- Documentation: http://cran.r-project.org/web/packages/glmpca/glmpca.pdf
- License: LGPL (≥ 3) | file LICENSE
-
Latest release: 0.2.0
published almost 6 years ago
Rankings
Maintainers (1)
conda-forge.org: r-glmpca
- Homepage: https://github.com/willtownes/glmpca
- License: Artistic-2.0
-
Latest release: 0.2.0
published almost 6 years ago
Rankings
Dependencies
- R >= 3.5 depends
- MASS * imports
- methods * imports
- stats * imports
- utils * imports
- Matrix * suggests
- covr * suggests
- ggplot2 * suggests
- knitr * suggests
- logisticPCA * suggests
- markdown * suggests
- testthat * suggests