Package: MethylSeekR 1.47.0

Lukas Burger

MethylSeekR: Segmentation of Bis-seq data

This is a package for the discovery of regulatory regions from Bis-seq data

Authors:Lukas Burger, Dimos Gaidatzis, Dirk Schubeler and Michael Stadler

MethylSeekR_1.47.0.tar.gz
MethylSeekR_1.47.0.zip(r-4.5)MethylSeekR_1.47.0.zip(r-4.4)MethylSeekR_1.47.0.zip(r-4.3)
MethylSeekR_1.47.0.tgz(r-4.4-any)MethylSeekR_1.47.0.tgz(r-4.3-any)
MethylSeekR_1.47.0.tar.gz(r-4.5-noble)MethylSeekR_1.47.0.tar.gz(r-4.4-noble)
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MethylSeekR.pdf |MethylSeekR.html✨
MethylSeekR/json (API)

# Install 'MethylSeekR' in R:

install.packages('MethylSeekR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:MethylSeekR-1.47.0(bioc 3.21)MethylSeekR-1.46.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencing methylseq dnamethylation

4.83 score 34 scripts 395 downloads 33 mentions 11 exports 75 dependencies

Last updated 2 months agofrom:bd272df9a1. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 08 2024
R-4.5-win	NOTE	Dec 08 2024
R-4.5-linux	NOTE	Dec 08 2024
R-4.4-win	NOTE	Dec 08 2024
R-4.4-mac	NOTE	Dec 08 2024
R-4.3-win	NOTE	Dec 08 2024
R-4.3-mac	NOTE	Dec 08 2024

Exports:calculateFDRs plotAlphaDistributionOneChr plotFinalSegmentation plotPMDSegmentation readMethylome readSNPTable removeSNPs savePMDSegments saveUMRLMRSegments segmentPMDs segmentUMRsLMRs

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options geneplotter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mhsmm mime mvtnorm openssl pkgconfig plogr png R6 RColorBrewer RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils vctrs XML xtable XVector yaml zlibbioc

MethylSeekR

Rendered fromMethylSeekR.Rnwusingutils::Sweaveon Dec 08 2024.

Last update: 2021-06-07
Started: 2013-01-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Segmentation of Bis-seq methylation data	MethylSeekR-package MethylSeekR
Determine false discovery rate	calculateFDRs
Calculate and plot alpha distribution.	plotAlphaDistributionOneChr
Plotting final segmentation	plotFinalSegmentation
Plotting the PMD Segmentation	plotPMDSegmentation
Load Bis-seq data	readMethylome
Load SNP table	readSNPTable
Remove CpGs overlapping SNPs	removeSNPs
Save PMD segments	savePMDSegments
Save UMR and LMR segments	saveUMRLMRSegments
PMD segmenter	segmentPMDs
Identify UMRs and LMRs	segmentUMRsLMRs

Usage by other packages (reverse dependencies)