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shinyepico

ShinyÉPICo


Bioconductor version: Release (3.18)

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.

Author: Octavio Morante-Palacios [cre, aut]

Maintainer: Octavio Morante-Palacios <octaviompa at gmail.com>

Citation (from within R, enter citation("shinyepico")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("shinyepico")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("shinyepico")
shinyepico HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DNAMethylation, DifferentialMethylation, Microarray, Preprocessing, QualityControl, Software
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License AGPL-3 + file LICENSE
Depends R (>= 4.3.0)
Imports DT (>= 0.15.0), data.table (>= 1.13.0), doParallel (>= 1.0.0), dplyr (>= 1.0.9), foreach (>= 1.5.0), GenomicRanges(>= 1.38.0), ggplot2 (>= 3.3.0), gplots (>= 3.0.0), heatmaply (>= 1.1.0), limma(>= 3.42.0), minfi(>= 1.32.0), plotly (>= 4.9.2), reshape2 (>= 1.4.0), rlang (>= 1.0.2), rmarkdown (>= 2.3.0), rtracklayer(>= 1.46.0), shiny (>= 1.5.0), shinyWidgets (>= 0.5.0), shinycssloaders (>= 0.3.0), shinyjs (>= 1.1.0), shinythemes (>= 1.1.0), statmod (>= 1.4.0), tidyr (>= 1.2.0), zip (>= 2.1.0)
System Requirements
URL https://github.com/omorante/shiny_epico
Bug Reports https://github.com/omorante/shiny_epico/issues
See More
Suggests knitr (>= 1.30.0), mCSEA(>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package shinyepico_1.10.0.tar.gz
Windows Binary shinyepico_1.10.0.zip
macOS Binary (x86_64) shinyepico_1.10.0.tgz
macOS Binary (arm64) shinyepico_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/shinyepico
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/shinyepico
Bioc Package Browser https://code.bioconductor.org/browse/shinyepico/
Package Short Url https://bioconductor.org/packages/shinyepico/
Package Downloads Report Download Stats