Package: SOMNiBUS 1.21.0

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_1.21.0.tar.gz
SOMNiBUS_1.21.0.zip(r-4.7)SOMNiBUS_1.21.0.zip(r-4.6)SOMNiBUS_1.21.0.zip(r-4.5)
SOMNiBUS_1.21.0.tgz(r-4.6-any)SOMNiBUS_1.21.0.tgz(r-4.5-any)
SOMNiBUS_1.21.0.tar.gz(r-4.7-any)SOMNiBUS_1.21.0.tar.gz(r-4.6-any)
SOMNiBUS_1.21.0.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.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 278 downloads 1 mentions 14 exports 134 dependencies

Last updated from:8ae13398ae. Checks:1 ERROR, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR343
linux-devel-x86_64OK744
source / vignettesOK482
linux-release-x86_64OK764
macos-release-arm64OK681
macos-oldrel-arm64OK647
windows-develOK898
windows-releaseOK857
windows-oldrelOK890
wasm-releaseOK244

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 May 26 2026.

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