crumblr
Count ratio uncertainty modeling base linear regression
Bioconductor version: 3.23 · Package version: 1.4.5
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Crumblr enables analysis of count ratio data using precision weighted linear (mixed) models. It uses an asymptotic normal approximation of the variance following the centered log ration transform (CLR) that is widely used in compositional data analysis. Crumblr provides a fast, flexible alternative to GLMs and GLMM's while retaining high power and controlling the false positive rate.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("crumblr")Details
| Maintainer | Gabriel Hoffman <gabriel.hoffman@mssm.edu> |
| Author | Gabriel Hoffman [aut, cre] (ORCID: <https://orcid.org/0000-0002-0957-0224>) |
| License | Artistic-2.0 |
| URL | https://DiseaseNeurogenomics.github.io/crumblr |
| Bug Reports | https://github.com/DiseaseNeurogenomics/crumblr/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | BatchEffect, Clustering, DifferentialExpression, DimensionReduction, Epigenetics, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, QualityControl, RNASeq, Regression, SingleCell, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/crumblr/ |
Citation
From within R, enter citation("crumblr"):
Gabriel Hoffman. crumblr: Count ratio uncertainty modeling base linear regression. doi:10.18129/B9.bioc.crumblr, R package version 1.4.5, https://bioconductor.org/packages/crumblr.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Using crumblr in practice
- Normal approximation vs. empirical simulation
- Integration with dreamlet / SingleCellExperiment
Download
Follow the installation instructions to use this package in your R session.
| Source package | crumblr_1.4.5.tar.gz |
| Windows binary (x86_64) | crumblr_1.4.5.zip |
| macOS binary (arm64) | crumblr_1.4.5.tgz |
| macOS binary (x86_64) | crumblr_1.4.5.tgz |
Dependencies
Depends: R (>= 4.4.0), ggplot2, methods
Imports: Rdpack, viridis, tidytree, variancePartition (>= 1.36.3), SingleCellExperiment, ggtree, dplyr, stats, MASS, Rfast, dirmult
Suggests: BiocStyle, RUnit, knitr, rmarkdown, dreamlet, muscat, ExperimentHub, scater, reshape2, glue, tidyverse, BiocGenerics, compositions