Package: SOMNiBUS 1.20.0

Kathleen Klein

SOMNiBUS: Smooth modeling of bisulfite sequencing

This package aims to analyse count-based methylation data on predefined genomic regions, such as those obtained by targeted sequencing, and thus to identify differentially methylated regions (DMRs) that are associated with phenotypes or traits. The method is built a rich flexible model that allows for the effects, on the methylation levels, of multiple covariates to vary smoothly along genomic regions. At the same time, this method also allows for sequencing errors and can adjust for variability in cell type mixture.

Authors:Kaiqiong Zhao [aut], Kathleen Klein [cre], Audrey Lemaçon [ctb, ctr], Simon Laurin-Lemay [ctb, ctr], My Intelligent Machines Inc. [ctr], Celia Greenwood [ths, aut]

SOMNiBUS_1.20.0.tar.gz
SOMNiBUS_1.20.0.zip(r-4.7)SOMNiBUS_1.20.0.zip(r-4.6)SOMNiBUS_1.20.0.zip(r-4.5)
SOMNiBUS_1.20.0.tgz(r-4.6-any)SOMNiBUS_1.20.0.tgz(r-4.5-any)
SOMNiBUS_1.20.0.tar.gz(r-4.7-any)SOMNiBUS_1.20.0.tar.gz(r-4.6-any)
SOMNiBUS_1.20.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SOMNiBUS/json (API)
NEWS

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

Bug tracker:https://github.com/kaiqiong/somnibus/issues

Datasets:
  • RAdat - A simulated methylation dataset based on a real data.
  • RAdat2 - A simulated methylation dataset based on a real data.

On BioConductor:SOMNiBUS-1.21.0(bioc 3.24)SOMNiBUS-1.20.0(bioc 3.23)

dnamethylationregressionepigeneticsdifferentialmethylationsequencingfunctionalprediction

4.00 score 1 stars 5 scripts 258 downloads 1 mentions 14 exports 134 dependencies

Last updated from:63ad257fc1 (on RELEASE_3_23). Checks:2 ERROR, 8 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR277
linux-devel-x86_64OK801
source / vignettesOK508
linux-release-x86_64OK728
macos-release-arm64OK804
macos-oldrel-arm64OK676
windows-develOK951
windows-releaseOK939
windows-oldrelERROR894
wasm-releaseOK257

Exports:binomRegMethModelbinomRegMethModelPlotbinomRegMethModelPredbinomRegMethModelSimbinomRegMethPredPlotformatFromBismarkformatFromBSseqrunSOMNiBUSsplitDataByBedsplitDataByChromatinsplitDataByDensitysplitDataByGenesplitDataByGRangessplitDataByRegion

Dependencies:abindAnnotationDbiAnnotationHubannotatraskpassassortheadbeachmatBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomebsseqcachemcigarilloclicliprcodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdir.expirydplyrfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablegtoolsh5mreadHDF5Arrayhmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpermutepillarpkgconfigplyrpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrregioneRreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsVGAMviridisLitevroomwithrXMLXVectoryaml

Analyzing Targeted Bisulfite Sequencing data with SOMNiBUS

Kaiqiong Zhao

Rendered fromSOMNiBUS.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2023-07-17
Started: 2019-01-24