Bioconductor version: Release (3.13)
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")
):
To install this package, start R (version "4.1") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("shinyepico")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("shinyepico")
HTML | R Script | shinyepico |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | DNAMethylation, DifferentialMethylation, Microarray, Preprocessing, QualityControl, Software |
Version | 1.0.0 |
In Bioconductor since | BioC 3.13 (R-4.1) (< 6 months) |
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 |
Follow Installation instructions to use this package in your R session.
Source Package | shinyepico_1.0.0.tar.gz |
Windows Binary | shinyepico_1.0.0.zip |
macOS 10.13 (High Sierra) | shinyepico_1.0.0.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 |
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