Package: msgbsR 1.37.0

Benjamin Mayne

msgbsR: msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions

Pipeline for the anaysis of a MS-GBS experiment.

Authors:Benjamin Mayne

msgbsR_1.37.0.tar.gz
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msgbsR_1.37.0.tgz(r-4.6-any)msgbsR_1.37.0.tgz(r-4.5-any)
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msgbsR_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
msgbsR/json (API)

# Install 'msgbsR' in R:

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

Datasets:

cuts - A GRanges object of differentially methylated MspI cut sites on chromosome 20 in Rat from a MS-GBS experiment.
ratdata - Read counts of potential MspI cut sites from a MS-GBS experiment of prostates from rats
ratdata2 - Read counts of correct MspI cut sites from a MS-GBS experiment of prostates from rats

On BioConductor:msgbsR-1.37.0(bioc 3.24)msgbsR-1.36.0(bioc 3.23)

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

immunooncology differentialmethylation dataimport epigenetics methylseq

4.65 score 2 scripts 3 mentions 5 exports 163 dependencies

Last updated from:9f01b78a20. Checks:3 ERROR, 2 OK, 5 NOTE. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	ERROR	280
linux-devel-x86_64	ERROR	553
source / vignettes	OK	431
linux-release-x86_64	NOTE	560
macos-release-arm64	NOTE	479
macos-oldrel-arm64	NOTE	394
windows-devel	ERROR	469
windows-release	NOTE	452
windows-oldrel	NOTE	455
wasm-release	OK	264

Exports:checkCuts diffMeth plotCircos plotCounts rawCounts

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr easyRNASeq edgeR ensembldb evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb genomeIntervals GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 glue graph gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 hwriter interp intervals IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle limma locfit LSD magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nnet openssl OrganismDbi pillar pkgconfig plyr png prettyunits progress ProtGenerics purrr pwalign R.methodsS3 R.oo R.utils R6 rappdirs RBGL RColorBrewer Rcpp RcppEigen RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo ShortRead snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr xfun XML xml2 XVector yaml

Introduction | Reading data into R | Confirmation of correct cut sites | Visualization of read counts | Differential methylation analysis | Visualization of cut site locations | Session Information | References

Rendered frommsgbsR_Vignette.Rnwusingutils::Sweave

Last update: 2017-04-24
Started: 2017-04-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
checkCuts	checkCuts
A GRanges object of differentially methylated MspI cut sites on chromosome 20 in Rat from a MS-GBS experiment.	cuts
diffMeth	diffMeth
msgbsR	msgbsR-package msgbsR
plotCircos	plotCircos
plotCounts	plotCounts
Read counts of potential MspI cut sites from a MS-GBS experiment of prostates from rats	ratdata
Read counts of correct MspI cut sites from a MS-GBS experiment of prostates from rats	ratdata2
rawCounts	rawCounts

Usage by other packages (reverse dependencies)