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crumblr

This is the development version of crumblr; to use it, please install the devel version of Bioconductor.

Count ratio uncertainty modeling base linear regression


Bioconductor version: Development (3.21)

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] ORCID iD ORCID: 0000-0002-0957-0224

Maintainer: Gabriel Hoffman <gabriel.hoffman at mssm.edu>

Citation (from within R, enter citation("crumblr")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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 HTML R Script
crumblr_theory HTML R Script
crumblr_treeTest HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, Clustering, DifferentialExpression, DimensionReduction, Epigenetics, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, QualityControl, RNASeq, Regression, SingleCell, Software, Transcriptomics
Version 0.99.21
In Bioconductor since BioC 3.21 (R-4.5)
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
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, HMP, reshape2, glue, tidyverse, BiocGenerics, compositions
Linking To
Enhances
Depends On Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package crumblr_0.99.21.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64) crumblr_0.99.21.tgz
macOS Binary (arm64) crumblr_0.99.21.tgz
Source Repository git clone https://git.bioconductor.org/packages/crumblr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/crumblr
Bioc Package Browser https://code.bioconductor.org/browse/crumblr/
Package Short Url https://bioconductor.org/packages/crumblr/
Package Downloads Report Download Stats