epimutacions
This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see epimutacions.
Robust outlier identification for DNA methylation data
Bioconductor version: 3.15
The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations.
Author: Leire Abarrategui [aut, cre], Juan R. Gonzalez [aut], Carlos Ruiz-Arenas [aut], Carles Hernandez-Ferrer [aut]
Maintainer: Leire Abarrategui <abarrategui.leire at gmail.com>
citation("epimutacions")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("epimutacions")
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("epimutacions")| Detection of epimutations with state of the art methods in methylation data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiologicalQuestion, DNAMethylation, Normalization, Preprocessing, Software, StatisticalMethod |
| Version | 1.0.3 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.2.0), epimutacionsData |
| Imports | minfi, bumphunter, isotree, robustbase, ggplot2, GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment, stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt, BiocParallel |
| System Requirements | |
| URL | https://github.com/isglobal-brge/epimutacions |
| Bug Reports | https://github.com/isglobal-brge/epimutacions/issues |
See More
| Suggests | AnnotationDbi, AnnotationHub, testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, methods, ensembldb, ExperimentHub, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, grid, gridExtra, grDevices, tibble, Gviz, ggrepel, reshape2, purrr, GenomeInfoDb, Homo.sapiens |
| 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 | epimutacions_1.0.3.tar.gz |
| Windows Binary | epimutacions_1.0.3.zip |
| macOS Binary (x86_64) | epimutacions_1.0.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/epimutacions |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/epimutacions |
| Bioc Package Browser | https://code.bioconductor.org/browse/epimutacions/ |
| Package Short Url | https://bioconductor.org/packages/epimutacions/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.15 | Source Archive |