Package: shinyMethyl 1.41.0

Jean-Philippe Fortin

shinyMethyl: Interactive visualization for Illumina methylation arrays

Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.

Authors:Jean-Philippe Fortin [cre, aut], Kasper Daniel Hansen [aut]

shinyMethyl_1.41.0.tar.gz
shinyMethyl_1.41.0.zip(r-4.5)shinyMethyl_1.41.0.zip(r-4.4)shinyMethyl_1.41.0.zip(r-4.3)
shinyMethyl_1.41.0.tgz(r-4.4-any)shinyMethyl_1.41.0.tgz(r-4.3-any)
shinyMethyl_1.41.0.tar.gz(r-4.5-noble)shinyMethyl_1.41.0.tar.gz(r-4.4-noble)
shinyMethyl_1.41.0.tgz(r-4.4-emscripten)shinyMethyl_1.41.0.tgz(r-4.3-emscripten)
shinyMethyl.pdf |shinyMethyl.html✨
shinyMethyl/json (API)
NEWS

# Install 'shinyMethyl' in R:

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

Bug tracker:https://github.com/jfortin1/shinymethyl/issues

On BioConductor:shinyMethyl-1.41.0(bioc 3.20)shinyMethyl-1.40.0(bioc 3.19)

bioconductor-package

16 exports 1.08 score 144 dependencies 18 mentions

Last updated 2 months agofrom:43d63c902e

Exports:combine getBeta getCN getGreenControls getM getMeth getPCA getRedControls getUnmeth orderByName pData runShinyMethyl sampleNames shinyMethylSet shinySummarize show

Dependencies:abind annotate AnnotationDbi askpass base64 base64enc beanplot BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bslib bumphunter cachem cli clipr codetools commonmark cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest doRNG dplyr fansi fastmap fontawesome foreach formatR fs futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery glue HDF5Array hms htmltools httpuv httr illuminaio IRanges iterators jquerylib jsonlite KEGGREST lambda.r later lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime minfi multtest nlme nor1mix openssl pillar pkgconfig plogr plyr png preprocessCore prettyunits progress promises purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr reshape restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scrime shiny siggenes snow sourcetools SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs vroom withr XML xml2 xtable XVector yaml zlibbioc

shinyMethyl: interactive visualization of Illumina 450K methylation arrays

Jean-Philippe Fortin, Kasper Daniel Hansen

Rendered fromshinyMethyl.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-11-27
Started: 2022-11-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Run the interactive shinyMethyl session	runShinyMethyl
shinyMethylSet instances	combine combine,shinyMethylSet,shinyMethylSet-method getBeta getBeta,shinyMethylSet-method getCN getCN,shinyMethylSet-method getGreenControls getM getM,shinyMethylSet-method getMeth getMeth,shinyMethylSet-method getPCA getRedControls getUnmeth getUnmeth,shinyMethylSet-method orderByName pData pData,shinyMethylSet-method sampleNames sampleNames,shinyMethylSet-method shinyMethylSet shinyMethylSet-class show,shinyMethylSet-method
Summarizing a large 450K experiment into a shinyMethylSet	shinySummarize shinySummarize,GenomicRatioSet-method shinySummarize,RGChannelSet-method shinySummarize-methods

Usage by other packages (reverse dependencies)