epimutacions
This is the development version of epimutacions; for the stable release version, see epimutacions.
Robust outlier identification for DNA methylation data
Bioconductor version: Development (3.24)
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: Dolors Pelegri-Siso [aut, cre]
, Juan R. Gonzalez [aut]
, Carlos Ruiz-Arenas [aut]
, Carles Hernandez-Ferrer [aut]
, Leire Abarrategui [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri at isglobal.org>
citation("epimutacions")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.3.0), epimutacionsData |
| Imports | minfi, bumphunter, isotree, robustbase, ggplot2, GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment, stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt, BiocParallel, GenomeInfoDb, Homo.sapiens, purrr, tibble, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, AnnotationDbi, AnnotationHub, ExperimentHub, reshape2, grid, ensembldb, gridExtra, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, ggrepel |
| System Requirements | |
| URL | https://github.com/isglobal-brge/epimutacions |
| Bug Reports | https://github.com/isglobal-brge/epimutacions/issues |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices |
| 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_1.17.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | epimutacions_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | epimutacions_1.17.0.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 |