Package: crumblr 1.5.0
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:
crumblr_1.5.0.tar.gz
crumblr_1.5.0.zip(r-4.7)crumblr_1.5.0.zip(r-4.6)crumblr_1.5.0.zip(r-4.5)
crumblr_1.5.0.tgz(r-4.6-any)crumblr_1.5.0.tgz(r-4.5-any)
crumblr_1.5.0.tar.gz(r-4.7-any)crumblr_1.5.0.tar.gz(r-4.6-any)
crumblr_1.5.0.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
- df_cellCounts - Cell counts following interferon treatment
- hcl - Cell counts following interferon treatment
- info - Cell counts following interferon treatment
On BioConductor:crumblr-1.5.0(bioc 3.24)crumblr-1.4.0(bioc 3.23)
rnaseqgeneexpressiondifferentialexpressionbatcheffectqualitycontrolsinglecellregressionepigeneticsfunctionalgenomicstranscriptomicsnormalizationclusteringdimensionreductionpreprocessingsoftware
Last updated from:e19e122585. Checks:1 NOTE, 1 WARNING, 7 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 290 | ||
| linux-devel-x86_64 | WARNING | 472 | ||
| source / vignettes | ERROR | 388 | ||
| linux-release-x86_64 | ERROR | 438 | ||
| macos-release-arm64 | ERROR | 209 | ||
| macos-oldrel-arm64 | ERROR | 258 | ||
| windows-devel | ERROR | 326 | ||
| windows-release | ERROR | 293 | ||
| windows-oldrel | ERROR | 358 | ||
| wasm-release | OK | 237 |
Exports:buildClusterTreeclrclrInvcrumblrdiffTreedmn_mlelogFracmeanSdPlotplotForestplotScatterDensityplotTreeTestplotTreeTestBetastandardizetreeTest
Dependencies:abindaodapeaplotbackportsbase64encBHBiobaseBiocGenericsBiocParallelbitopsbootbroombslibcachemcaToolsclicodetoolscolorspacecorpcorcowplotcpp11DelayedArrayDerivdigestdoBydplyrEnvStatsevaluatefANCOVAfarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforecastformatRfracdifffsfutile.loggerfutile.optionsgdtoolsgenericsGenomicRangesggfunggiraphggplot2ggplotifyggtreegluegplotsgridExtragridGraphicsgtablegtoolshighrhtmltoolshtmlwidgetsIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlatticelazyevallifecyclelimmalme4lmerTestlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemicrobenchmarkmimeminqamodelrmvtnormnlmenloptrnnetnortestnumDerivpatchworkpbkrtestpillarpkgconfigplyrpurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreformulasremaCorreshape2RfastRhpcBLASctlrlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoSingleCellExperimentsnowSparseArraystatmodstringistringrSummarizedExperimentsystemfontstibbletidyrtidyselecttidytreetimeDatetinytextreeiourcautf8variancePartitionvctrsviridisviridisLitewithrxfunXVectoryamlyulab.utilsziggzoo
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 |
