shinyepico

DOI: 10.18129/B9.bioc.shinyepico    

ShinyÉPICo

Bioconductor version: Release (3.14)

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>

Installation

To install this package, start R (version "4.1") 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")

 

HTML	R Script	shinyepico
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DNAMethylation, DifferentialMethylation, Microarray, Preprocessing, QualityControl, Software
Version	1.2.0
In Bioconductor since	BioC 3.13 (R-4.1) (1 year)
License	AGPL-3 + file LICENSE
Depends	R (>= 4.0.0)
Imports	DT (>= 0.15.0), data.table (>= 1.13.0), doParallel (>= 1.0.0), dplyr (>= 1.0.0), 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 (>= 0.4.0), 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 (>= 1.1.0), zip (>= 2.1.0)
LinkingTo
Suggests	knitr (>= 1.30.0), mCSEA(>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData
SystemRequirements
Enhances
URL	https://github.com/omorante/shiny_epico
BugReports	https://github.com/omorante/shiny_epico/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	shinyepico_1.2.0.tar.gz
Windows Binary	shinyepico_1.2.0.zip
macOS 10.13 (High Sierra)	shinyepico_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/shinyepico
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/shinyepico
Package Short Url	https://bioconductor.org/packages/shinyepico/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive