crumblr

This is the released version of crumblr; for the devel version, see crumblr.

Count ratio uncertainty modeling base linear regression

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DOI: 10.18129/B9.bioc.crumblr

Bioconductor version: Release (3.22)

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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BatchEffect, Clustering, DifferentialExpression, DimensionReduction, Epigenetics, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, QualityControl, RNASeq, Regression, SingleCell, Software, Transcriptomics

Version 1.2.0

In Bioconductor since BioC 3.21 (R-4.5) (0.5 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

System Requirements

URL https://DiseaseNeurogenomics.github.io/crumblr

Bug Reports https://github.com/DiseaseNeurogenomics/crumblr/issues

Suggests BiocStyle, RUnit, knitr, rmarkdown, dreamlet, muscat, ExperimentHub, scater, HMP, reshape2, glue, tidyverse, BiocGenerics, compositions

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Build Report Build Report

Package Archives

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

Source Package crumblr_1.2.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) crumblr_1.2.0.tgz

macOS Binary (arm64) crumblr_1.2.0.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

Old Source Packages for BioC 3.22 Source Archive