Package: zenith 1.15.0

Gabriel Hoffman

zenith: Gene set analysis following differential expression using linear (mixed) modeling with dream

Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream by considering the correlation between gene expression traits. This package implements the camera method from the limma package proposed by Wu and Smyth (2012). Zenith is a simple extension of camera to be compatible with linear mixed models implemented in variancePartition::dream().

Authors:Gabriel Hoffman [aut, cre]

zenith_1.15.0.tar.gz
zenith_1.15.0.zip(r-4.7)zenith_1.15.0.zip(r-4.6)zenith_1.15.0.zip(r-4.5)
zenith_1.15.0.tgz(r-4.6-any)zenith_1.15.0.tgz(r-4.5-any)
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zenith_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
zenith/json (API)

# Install 'zenith' in R:
install.packages('zenith', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

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

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

On BioConductor:zenith-1.15.0(bioc 3.24)zenith-1.14.0(bioc 3.23)

rnaseqgeneexpressiongenesetenrichmentdifferentialexpressionbatcheffectqualitycontrolregressionepigeneticsfunctionalgenomicstranscriptomicsnormalizationpreprocessingmicroarrayimmunooncologysoftware

6.55 score 1 packages 197 scripts 6 exports 156 dependencies

Last updated from:a5f57fabb9. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE225
linux-devel-x86_64WARNING437
source / vignettesOK341
linux-release-x86_64WARNING432
macos-release-arm64WARNING253
macos-oldrel-arm64WARNING210
windows-develWARNING317
windows-releaseWARNING340
windows-oldrelWARNING355
wasm-releaseOK236

Exports:get_GeneOntologyget_MSigDBplotZenithResultszenithzenith_gsazenithPR_gsa

Dependencies:abindannotateAnnotationDbiaodaskpassassertthatbabelgenebackportsBHBiobaseBiocFileCacheBiocGenericsBiocManagerBiocParallelBiostringsbitbit64bitopsblobbootbroomcachemcaToolsclicodetoolscolorspacecorpcorcowplotcpp11crayoncurlDBIdbplyrDelayedArrayDerivdir.expirydoBydplyredgeREnrichmentBrowserEnvStatsfANCOVAfarverfastmapfilelockforecastformatRfracdifffutile.loggerfutile.optionsgenericsGenomicRangesggplot2glueGO.dbgplotsgraphgraphiteGSEABasegtablegtoolshmshttrhttr2hwriterIRangesisobanditeratorsjsonliteKEGGgraphKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalme4lmerTestlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminqamodelrmsigdbrmvtnormnlmenloptrnnetnortestnumDerivopensslorg.Hs.eg.dbpathviewpbkrtestpillarpkgconfigplyrpngprettyunitsprogresspurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRCurlRdpackreformulasremaCorreshape2RfastRgraphvizRhpcBLASctlrlangRSQLiteS4ArraysS4VectorsS7safescalesSeqinfosnowSparseArraySparseMSPIAstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttimeDateurcautf8variancePartitionvctrsviridisLitewithrXMLxtableXVectorziggzoo

Loading gene sets
Easy loading of gene set databases | Other databases | Custom gene sets | Session Info
Rendered fromloading_genesets.Rmdusingknitr::rmarkdown

Last update: 2025-03-19
Started: 2022-05-13

Zenith gene set testing after dream analysis
Standard workflow | Session Info
Rendered fromzenith.Rmdusingknitr::rmarkdown

Last update: 2022-07-06
Started: 2022-04-08