https://github.com/bioconductor-source/scddboost
Science Score: 36.0%
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 2 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (5.6%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- Language: C++
- Default Branch: devel
- Size: 5.73 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
About
scDDboost is an R package to analyze changes in the distribution of single-cell expression data between two experimental conditions. Compared to other methods that assess differential expression, scDDboost benefits uniquely from information conveyed by the clustering of cells into cellular subtypes. Through a novel empirical Bayesian formulation it calculates gene-specific posterior probabilities that the marginal expression distribution is the same (or different) between the two conditions. The implementation in scDDboost treats gene-level expression data within each condition as a mixture of negative binomial distributions.
Installation
To install the R package: ```R
install.packages("devtools")
devtools::install_github("wiscstatman/scDDboost") ``` A tutorial and examples can be found at Rpackage/vignette/
Paper
Ma, X., Korthauer, K., Kendziorski, C., and Newton, M. A. (2019). A Compositional Model To Assess Expression Changes From Single-Cell RNA-Seq Data. The Annals of Applied Statistics 15, no. 2 (2021): 880-901. DOI: 10.1214/20-AOAS1423. Formerly, bioRxiv 655795
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
- R >= 4.2 depends
- ggplot2 * depends
- BiocParallel * imports
- EBSeq * imports
- Oscope * imports
- Rcpp >= 0.12.11 imports
- RcppEigen >= 0.3.2.9.0 imports
- SingleCellExperiment * imports
- SummarizedExperiment * imports
- cluster * imports
- mclust * imports
- methods * imports
- stats * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests