crumblr
This is the development version of crumblr; for the stable release version, see crumblr.
Count ratio uncertainty modeling base linear regression
Bioconductor version: Development (3.24)
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.
Author: Gabriel Hoffman [aut, cre] 
Maintainer: Gabriel Hoffman <gabriel.hoffman at mssm.edu>
citation("crumblr")):Gabriel Hoffman. crumblr: Count ratio uncertainty modeling base linear regression. doi:10.18129/B9.bioc.crumblr, R package version 1.5.3, https://bioconductor.org/packages/crumblr.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("crumblr")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("crumblr")| crumblr_theory | HTML | R Script |
| crumblr | HTML | R Script |
| crumblr_treeTest | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, Clustering, DifferentialExpression, DimensionReduction, Epigenetics, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, QualityControl, RNASeq, Regression, SingleCell, Software, Transcriptomics |
| Version | 1.5.3 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0), ggplot2, methods |
| Imports | Rdpack, viridis, tidytree, variancePartition (>= 1.36.3), SingleCellExperiment, ggtree, dplyr, stats, MASS, Rfast, dirmult |
| System Requirements | |
| URL | https://DiseaseNeurogenomics.github.io/crumblr |
| Bug Reports | https://github.com/DiseaseNeurogenomics/crumblr/issues |
See More
| Suggests | BiocStyle, RUnit, knitr, rmarkdown, dreamlet, muscat, ExperimentHub, scater, reshape2, glue, tidyverse, BiocGenerics, compositions |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | crumblr_1.5.3.tar.gz |
| Windows Binary (x86_64) | crumblr_1.5.3.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | crumblr_1.5.3.tgz |
| macOS Binary (sonoma-arm64) | crumblr_1.5.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/crumblr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/crumblr |
| Package Short Url | https://bioconductor.org/packages/crumblr/ |
| Package Downloads Report | Download Stats |