shinyepico
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see shinyepico.
ShinyÉPICo
Bioconductor version: 3.19
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("shinyepico")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, DifferentialMethylation, Microarray, Preprocessing, QualityControl, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | shinyepico_1.12.0.tar.gz |
| Windows Binary (x86_64) | shinyepico_1.12.0.zip |
| macOS Binary (x86_64) | shinyepico_1.12.0.tgz |
| macOS Binary (arm64) | shinyepico_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/shinyepico |
| Source Repository (Developer Access) | git clone [email protected]:packages/shinyepico |
| Bioc Package Browser | https://code.bioconductor.org/browse/shinyepico/ |
| Package Short Url | https://bioconductor.org/packages/shinyepico/ |
| Package Downloads Report | Download Stats |