Package: crumblr 1.5.3

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_1.5.3.tar.gz
crumblr_1.5.3.zip(r-4.7-any)crumblr_1.5.3.zip(r-4.6-any)crumblr_1.5.3.zip(r-4.5-any)
crumblr_1.5.3.tgz(r-4.6-any)crumblr_1.5.3.tgz(r-4.5-any)
crumblr_1.5.3.tar.gz(r-4.7-any)crumblr_1.5.3.tar.gz(r-4.6-any)
crumblr_1.5.3.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.r-universe.dev', 'https://cloud.r-project.org'))

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

Pkgdown/docs site:https://diseaseneurogenomics.github.io

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-1.4.5(bioc 3.23)

rnaseqgeneexpressiondifferentialexpressionbatcheffectqualitycontrolsinglecellregressionepigeneticsfunctionalgenomicstranscriptomicsnormalizationclusteringdimensionreductionpreprocessingsoftware

5.43 score 8 stars 75 scripts 290 downloads 15 exports 147 dependencies

Last updated from:f891b20ef4. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE257
linux-develWARNING520
source / vignettesERROR460
linux-releaseWARNING383
macos-releaseWARNING381
macos-oldrelWARNING314
windows-develWARNING354
windows-releaseWARNING378
windows-oldrelWARNING371
wasm-releaseOK233

Exports:buildClusterTreeclrclrInvcrumblrdiffTreeDirichlet.multinomialdmn_mlelogFracmeanSdPlotplotForestplotScatterDensityplotTreeTestplotTreeTestBetastandardizetreeTest

Dependencies:abindaodapeaplotbackportsbase64encBHBiobaseBiocGenericsBiocParallelbitopsbootbroombslibcachemcaToolsclicodetoolscolorspacecorpcorcowplotcpp11DelayedArrayDerivdigestdirmultdoBydplyrEnvStatsevaluatefANCOVAfarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforecastformatRfracdifffsfutile.loggerfutile.optionsgdtoolsgenericsGenomicRangesggfunggiraphggplot2ggplotifyggtreegluegplotsgridExtragridGraphicsgtablegtoolshighrhtmltoolshtmlwidgetsIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlatticelazyevallifecyclelimmalme4lmerTestlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminqamodelrmvtnormnlmenloptrnnetnortestnumDerivpatchworkpbkrtestpillarpkgconfigplyrpurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreformulasremaCorreshape2RfastRhpcBLASctlrlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoSingleCellExperimentsnowSparseArraystatmodstringistringrSummarizedExperimentsystemfontstibbletidyrtidyselecttidytreetimeDatetinytextreeiourcautf8variancePartitionvctrsviridisviridisLitewithrxfunXVectoryamlyulab.utilsziggzoo