Package: zenith 1.9.0
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:
zenith_1.9.0.tar.gz
zenith_1.9.0.zip(r-4.5)zenith_1.9.0.zip(r-4.4)zenith_1.9.0.zip(r-4.3)
zenith_1.9.0.tgz(r-4.4-any)zenith_1.9.0.tgz(r-4.3-any)
zenith_1.9.0.tar.gz(r-4.5-noble)zenith_1.9.0.tar.gz(r-4.4-noble)
zenith_1.9.0.tgz(r-4.4-emscripten)zenith_1.9.0.tgz(r-4.3-emscripten)
zenith.pdf |zenith.html✨
zenith/json (API)
NEWS
| # 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:https://gabrielhoffman.github.io
On BioConductor:zenith-1.9.0(bioc 3.21)zenith-1.8.0(bioc 3.20)
rnaseqgeneexpressiongenesetenrichmentdifferentialexpressionbatcheffectqualitycontrolregressionepigeneticsfunctionalgenomicstranscriptomicsnormalizationpreprocessingmicroarrayimmunooncologysoftware
Last updated 2 months agofrom:5422050b36. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 02 2024 |
| R-4.5-win | NOTE | Dec 02 2024 |
| R-4.5-linux | NOTE | Dec 02 2024 |
| R-4.4-win | NOTE | Dec 02 2024 |
| R-4.4-mac | NOTE | Dec 02 2024 |
| R-4.3-win | NOTE | Dec 02 2024 |
| R-4.3-mac | NOTE | Dec 02 2024 |
Exports:get_GeneOntologyget_MSigDBplotZenithResultszenithzenith_gsazenithPR_gsa
Dependencies:abindannotateAnnotationDbiaodaskpassbabelgenebackportsBHBiobaseBiocFileCacheBiocGenericsBiocManagerBiocParallelBiostringsbitbit64bitopsblobbootbroomcachemcaToolsclicodetoolscolorspacecorpcorcowplotcpp11crayoncurlDBIdbplyrDelayedArrayDerivdoBydplyredgeREnrichmentBrowserEnvStatsfANCOVAfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2glueGO.dbgplotsgraphgraphiteGSEABasegtablegtoolshmshttrhwriterIRangesisobanditeratorsjsonliteKEGGgraphKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalme4lmerTestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmsigdbrmunsellmvtnormnlmenloptrnortestnumDerivopensslorg.Hs.eg.dbpathviewpbkrtestpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppGSLRcppParallelRcppZigguratRCurlRdpackremaCorreshape2RfastRgraphvizRhpcBLASctlrlangRSQLiteS4ArraysS4VectorssafescalessnowSparseArraySparseMSPIAstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8variancePartitionvctrsviridisLitewithrXMLxtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For Correlation | .rankSumTestWithCorrelation |
| Evaluate mean correlation between residuals in gene set | corInGeneSet |
| Load Gene Ontology genesets | get_GeneOntology |
| Load MSigDB genesets | get_MSigDB |
| Heatmap of zenith results using ggplot2 | plotZenithResults |
| Gene set analysis following differential expression with dream | zenith |
| Perform gene set analysis using zenith | zenith_gsa zenith_gsa,MArrayLM,GeneSetCollection,ANY-method zenith_gsa,MArrayLM,GeneSetCollection-method |
| Gene set analysis using pre-computed test statistic | zenithPR_gsa |
