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Bioconductor - crumblr

crumblr

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

Count ratio uncertainty modeling base linear regression

Bioconductor version: Release (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: 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")
Details biocViews BatchEffect, Clustering, DifferentialExpression, DimensionReduction, Epigenetics, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, QualityControl, RNASeq, Regression, SingleCell, Software, Transcriptomics Version 1.0.0 In Bioconductor since BioC 3.21 (R-4.5) (< 6 months) 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 Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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