Package: crumblr 1.4.5

Gabriel Hoffman

crumblr: Count ratio uncertainty modeling base linear regression

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.

Authors:Gabriel Hoffman [aut, cre]

crumblr_1.4.5.tar.gz
crumblr_1.4.5.zip(r-4.7-any)crumblr_1.4.5.zip(r-4.6-any)crumblr_1.4.5.zip(r-4.5-any)
crumblr_1.4.5.tgz(r-4.6-any)crumblr_1.4.5.tgz(r-4.5-any)
crumblr_1.4.5.tar.gz(r-4.7-any)crumblr_1.4.5.tar.gz(r-4.6-any)
crumblr_1.4.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
crumblr/json (API)

# Install 'crumblr' in R:

install.packages('crumblr', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/diseaseneurogenomics/crumblr/issues

Datasets:

df_cellCounts - Cell counts following interferon treatment
hcl - Cell counts following interferon treatment
info - Cell counts following interferon treatment

On BioConductor:crumblr-1.5.3(bioc 3.24)crumblr-1.4.0(bioc 3.23)

rnaseq geneexpression differentialexpression batcheffect qualitycontrol singlecell regression epigenetics functionalgenomics transcriptomics normalization clustering dimensionreduction preprocessing software

7.03 score 7 stars 68 scripts 256 downloads 15 exports 147 dependencies

Last updated from:a6f6ed4a1e (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	290
linux-devel-x86_64	OK	535
source / vignettes	OK	427
linux-release-x86_64	OK	545
macos-release-arm64	OK	292
macos-oldrel-arm64	OK	305
windows-devel	OK	399
windows-release	OK	345
windows-oldrel	OK	362
wasm-release	OK	256

Exports:buildClusterTree clr clrInv crumblr diffTree Dirichlet.multinomial dmn_mle logFrac meanSdPlot plotForest plotScatterDensity plotTreeTest plotTreeTestBeta standardize treeTest

Dependencies:abind aod ape aplot backports base64enc BH Biobase BiocGenerics BiocParallel bitops boot broom bslib cachem caTools cli codetools colorspace corpcor cowplot cpp11 DelayedArray Deriv digest dirmult doBy dplyr EnvStats evaluate fANCOVA farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver forecast formatR fracdiff fs futile.logger futile.options gdtools generics GenomicRanges ggfun ggiraph ggplot2 ggplotify ggtree glue gplots gridExtra gridGraphics gtable gtools highr htmltools htmlwidgets IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r lattice lazyeval lifecycle limma lme4 lmerTest lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mime minqa modelr mvtnorm nlme nloptr nnet nortest numDeriv patchwork pbkrtest pillar pkgconfig plyr purrr R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel Rdpack reformulas remaCor reshape2 Rfast RhpcBLASctl rlang rmarkdown S4Arrays S4Vectors S7 sass scales Seqinfo SingleCellExperiment snow SparseArray statmod stringi stringr SummarizedExperiment systemfonts tibble tidyr tidyselect tidytree timeDate tinytex treeio urca utf8 variancePartition vctrs viridis viridisLite withr xfun XVector yaml yulab.utils zigg zoo

Normal approximation vs. empirical simulation

Simulations | D=2 categories | D=15 categories | Consideration of overdispersion | Session Info

Rendered fromcrumblr_theory.Rmdusingknitr::rmarkdown

Last update: 2026-07-15
Started: 2021-10-28

Using crumblr in practice

Rendered fromcrumblr.Rmdusingknitr::rmarkdown

Last update: 2025-02-06
Started: 2022-02-03

Integration with dreamlet / SingleCellExperiment

Load and process single cell data | Aggregate to pseudobulk | Process data | Analysis | Session Info

Rendered fromintegration.Rmdusingknitr::rmarkdown

Last update: 2025-02-06
Started: 2024-06-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
crumblr	crumblr-package
Perform hierarchical clustering on reducedDim	buildClusterTree
Centered log ratio transform	clr
Inverse of Centered log ratio transform	clrInv
Count ratio uncertainty modeling based linear regression	crumblr crumblr,data.frame-method crumblr,matrix-method
Compare difference in estimates between two trees	diffTree
MLE for Dirichlet Multinomial	dmn_mle
Cell counts following interferon treatment	df_cellCounts hcl IFNCellCounts info
Log fractions and precision weights	logFrac
Plot row standard deviations versus rank of row means	meanSdPlot
Forest plot	plotForest plotForest,treedata-method
Scatter plot with 2D density using viridis colors	plotScatterDensity
Plot tree with results from multivariate testing	plotTreeTest
Plot tree coefficients from multivariate testing	plotTreeTestBeta
Standardize observations using precision weights	standardize standardize,EList-method
Perform multivariate testing along a hierarchy	treeTest