Package: msgbsR 1.31.0

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_1.31.0.tar.gz
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msgbsR_1.31.0.tgz(r-4.4-any)msgbsR_1.31.0.tgz(r-4.3-any)
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msgbsR.pdf |msgbsR.html✨
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-1.31.0(bioc 3.21)msgbsR-1.30.0(bioc 3.20)

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

4.48 score 1 scripts 209 downloads 3 mentions 5 exports 172 dependencies

Last updated 2 months agofrom:c7b70de6ef. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 18 2024
R-4.5-win	NOTE	Dec 18 2024
R-4.5-linux	NOTE	Dec 18 2024
R-4.4-win	NOTE	Dec 18 2024
R-4.4-mac	NOTE	Dec 18 2024
R-4.3-win	NOTE	Dec 18 2024
R-4.3-mac	NOTE	Dec 18 2024

Exports:checkCuts diffMeth plotCircos plotCounts rawCounts

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr easyRNASeq edgeR ensembldb evaluate fansi farver fastmap filelock fontawesome forcats foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData genomeIntervals GenomicAlignments GenomicFeatures GenomicRanges GGally ggbio ggplot2 ggstats 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 mgcv mime munsell nlme nnet openssl OrganismDbi patchwork pillar pkgconfig plogr 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 sass scales ShortRead snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

msgbsR_Example

Rendered frommsgbsR_Vignette.Rnwusingutils::Sweaveon Dec 18 2024.

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)