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✨
DESCRIPTION |NEWS
card.svg |card.png
SOMNiBUS/json (API)

# 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)

dnamethylation regression epigenetics differentialmethylation sequencing functionalprediction

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

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

Target	Result	Time
bioc-checks	ERROR	328
linux-devel-x86_64	OK	777
source / vignettes	OK	474
linux-release-x86_64	OK	754
macos-release-arm64	OK	646
macos-oldrel-arm64	OK	784
windows-devel	OK	795
windows-release	OK	911
windows-oldrel	OK	835
wasm-release	OK	291

Exports:binomRegMethModel binomRegMethModelPlot binomRegMethModelPred binomRegMethModelSim binomRegMethPredPlot formatFromBismark formatFromBSseq runSOMNiBUS splitDataByBed splitDataByChromatin splitDataByDensity splitDataByGene splitDataByGRanges splitDataByRegion

Dependencies:abind AnnotationDbi AnnotationHub annotatr askpass assorthead beachmat BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob BSgenome bsseq cachem cigarillo cli clipr codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats dir.expiry dplyr farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable gtools h5mread HDF5Array hms httr httr2 IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl permute pillar pkgconfig plyr png prettyunits progress purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr regioneR reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs VGAM viridisLite vroom withr XML XVector yaml

Analyzing Targeted Bisulfite Sequencing data with SOMNiBUS

Rendered fromSOMNiBUS.Rmdusingknitr::rmarkdown

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

Help page	Topics
A smoothed-EM algorithm to estimate covariate effects and test regional association in Bisulfite Sequencing-derived methylation data	binomRegMethModel
Plot the smooth covariate effect	binomRegMethModelPlot
A smoothed-EM algorithm to estimate covariate effects and test regional association in Bisulfite Sequencing-derived methylation data	binomRegMethModelPred
Simulate Bisulfite sequencing data from specified smooth covariate effects	binomRegMethModelSim
Plot the predicted methylation levels	binomRegMethPredPlot
Parsing output from the Bismark alignment suite	formatFromBismark
Parsing output from the BSseq package	formatFromBSseq
A simulated methylation dataset based on a real data.	RAdat
A simulated methylation dataset based on a real data.	RAdat2
Wrapper function running the smoothed-EM algorithm to estimate covariate effects and test regional association in Bisulfite Sequencing-derived methylation data	runSOMNiBUS
Split methylation data into regions based on the genomic annotations	splitDataByBed
Split methylation data into regions based on the chromatin states	splitDataByChromatin
Split methylation data into regions based on the density of CpGs	splitDataByDensity
Split methylation data into regions based on the genes annotations	splitDataByGene
Split methylation data into regions based on the genomic annotations	splitDataByGRanges
Split methylation data into regions based on the spacing of CpGs	splitDataByRegion

Package: SOMNiBUS 1.21.0

SOMNiBUS: Smooth modeling of bisulfite sequencing

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)