Package: shinyepico 1.21.0

Octavio Morante-Palacios

shinyepico: ShinyÉPICo

ShinyÉPICo is a graphical pipeline to analyze Illumina DNA methylation arrays (450k or EPIC). It allows to calculate differentially methylated positions and differentially methylated regions in a user-friendly interface. Moreover, it includes several options to export the results and obtain files to perform downstream analysis.

Authors:Octavio Morante-Palacios [cre, aut]

shinyepico_1.21.0.tar.gz
shinyepico_1.21.0.zip(r-4.7)shinyepico_1.21.0.zip(r-4.6)shinyepico_1.21.0.zip(r-4.5)
shinyepico_1.21.0.tgz(r-4.6-any)shinyepico_1.21.0.tgz(r-4.5-any)
shinyepico_1.21.0.tar.gz(r-4.7-any)shinyepico_1.21.0.tar.gz(r-4.6-any)
shinyepico_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
shinyepico/json (API)

# Install 'shinyepico' in R:

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

Bug tracker:https://github.com/omorante/shiny_epico/issues

On BioConductor:shinyepico-1.21.0(bioc 3.24)shinyepico-1.20.0(bioc 3.23)

differentialmethylation dnamethylation microarray preprocessing qualitycontrol

5.08 score 6 stars 2 scripts 1 exports 203 dependencies

Last updated from:f44c2c2304. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	649
linux-devel-x86_64	OK	722
source / vignettes	OK	736
linux-release-x86_64	OK	731
macos-release-arm64	OK	358
macos-oldrel-arm64	OK	317
windows-devel	OK	649
windows-release	OK	634
windows-oldrel	OK	581
wasm-release	OK	673

Exports:run_shinyepico

Dependencies:abind annotate AnnotationDbi askpass assertthat base64 base64enc beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocParallel Biostrings bit bit64 bitops blob bslib bumphunter ca cachem callr caTools cigarillo cli clipr cluster codetools colorspace commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats dendextend digest dir.expiry doParallel doRNG dplyr DT egg evaluate farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options gclus genefilter generics GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gplots gridExtra gtable gtools h5mread HDF5Array heatmaply highr hms htmltools htmlwidgets httpuv httr httr2 illuminaio IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mgcv mime minfi multtest nlme nor1mix openssl otel permute pillar pkgconfig plotly plyr png preprocessCore prettyunits processx progress promises ps purrr qap quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr registry rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rngtools Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors S7 sass scales scrime selectr Seqinfo seriation shiny shinycssloaders shinyjs shinythemes shinyWidgets siggenes snow sourcetools SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex TSP tzdb utf8 vctrs vegan viridis viridisLite vroom webshot withr xfun XML xml2 xtable XVector yaml zip

shinyÉPICo: the user's guide

Rendered fromshiny_epico.Rmdusingknitr::rmarkdown

Last update: 2020-11-20
Started: 2020-03-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
shinyÉPICo: a graphical and interactive pipeline to analyze Illumina DNA Methylation Arrays	shinyepico-package shinyepico
Run Shiny ÉPICo!	run_shinyepico