Package: RNAmodR.RiboMethSeq 1.21.0

Felix G.M. Ernst

RNAmodR.RiboMethSeq: Detection of 2'-O methylations by RiboMethSeq

RNAmodR.RiboMethSeq implements the detection of 2'-O methylations on RNA from experimental data generated with the RiboMethSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data.

Authors:Felix G.M. Ernst [aut, cre], Denis L.J. Lafontaine [ctb, fnd]

# Install 'RNAmodR.RiboMethSeq' in R:

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

Bug tracker:https://github.com/felixernst/rnamodr.ribomethseq/issues

Datasets:

msrms - Example data in the RNAmodR.RiboMethSeq package

On BioConductor:RNAmodR.RiboMethSeq-1.21.0(bioc 3.21)RNAmodR.RiboMethSeq-1.20.0(bioc 3.20)

software workflowstep visualization sequencing bioconductor modifications ribomethseq rna rnamodr

4.00 score 1 stars 4 scripts 194 downloads 8 exports 158 dependencies

Last updated 23 days agofrom:e2f22fe894. Checks:OK: 1 NOTE: 4 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	WARNING	Oct 31 2024
R-4.3-win	NOTE	Oct 31 2024
R-4.3-mac	WARNING	Oct 31 2024

Exports:aggregateData findMod getDataTrack ModRiboMethSeq ModSetRiboMethSeq plotData plotDataByCoord settings<-

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem caTools checkmate cli cluster codetools colorRamps colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gplots gridExtra gtable gtools Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime Modstrings munsell nlme nnet openssl pillar pkgconfig plogr plyr png prettyunits progress ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown RNAmodR ROCR rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

RNAmodR: RiboMethSeq

Felix G.M. Ernst and Denis L.J. Lafontaine

Rendered fromRNAmodR.RiboMethSeq.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-01-09
Started: 2019-01-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ModRiboMethSeq class to analyze RiboMethSeq data	ModRiboMethSeq ModRiboMethSeq-class ModSetRiboMethSeq ModSetRiboMethSeq-class RiboMethSeq
Functions for ModRiboMethSeq	aggregate aggregateData,ModRiboMethSeq-method findMod,ModRiboMethSeq-method getDataTrack,ModRiboMethSeq-method modify ModRiboMethSeq-functions plotData plotData,ModRiboMethSeq-method plotData,ModSetRiboMethSeq-method plotDataByCoord plotDataByCoord,ModRiboMethSeq,GRanges-method plotDataByCoord,ModSetRiboMethSeq,GRanges-method settings settings<-,ModRiboMethSeq-method
RNAmodR.RiboMethSeq	RNAmodR.RiboMethSeq
Example data in the RNAmodR.RiboMethSeq package	msrms RNAmodR.RiboMethSeq-datasets