shinyepico
ShinyÉPICo
Bioconductor version: 3.23 · Package version: 1.20.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("shinyepico")Details
| Maintainer | Octavio Morante-Palacios <octaviompa@gmail.com> |
| Author | Octavio Morante-Palacios [cre, aut] |
| License | AGPL-3 + file LICENSE |
| URL | https://github.com/omorante/shiny_epico |
| Bug Reports | https://github.com/omorante/shiny_epico/issues |
| Downloads rank | 276 |
| Source branch | RELEASE_3_23 |
| biocViews | DNAMethylation, DifferentialMethylation, Microarray, Preprocessing, QualityControl, Software |
Documentation
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Dependencies
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)
Suggests: knitr (>= 1.30.0), mCSEA (>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData, BiocStyle