crumblr
This is thereleased version of crumblr; for the devel version, seecrumblr.
Count ratio uncertainty modeling base linear regression
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: 0000-0002-0957-0224
Maintainer: Gabriel Hoffman <gabriel.hoffman at mssm.edu>
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 appropriateBioconductor 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 | ||
| NEWS | Text |
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 |
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
FollowInstallation instructions to use this package in your R session.
| Source Package | crumblr_1.2.0.tar.gz |
| Windows Binary (x86_64) | crumblr_1.2.0.zip |
| 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 |