minfi
This is the development version of minfi; for the stable release version, see minfi.
Analyze Illumina Infinium DNA methylation arrays
Bioconductor version: Development (3.21)
Tools to analyze & visualize Illumina Infinium methylation arrays.
Author: Kasper Daniel Hansen [cre, aut], Martin Aryee [aut], Rafael A. Irizarry [aut], Andrew E. Jaffe [ctb], Jovana Maksimovic [ctb], E. Andres Houseman [ctb], Jean-Philippe Fortin [ctb], Tim Triche [ctb], Shan V. Andrews [ctb], Peter F. Hickey [ctb]
Maintainer: Kasper Daniel Hansen <kasperdanielhansen at gmail.com>
citation("minfi")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("minfi")
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("minfi")| minfi User's Guide | HTML | R Script |
| Reference Manual |
Details
| biocViews | DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylationArray, Microarray, MultiChannel, Normalization, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 1.53.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (13 years) |
| License | Artistic-2.0 |
| Depends | methods, BiocGenerics(>= 0.15.3), GenomicRanges, SummarizedExperiment(>= 1.1.6), Biostrings, bumphunter(>= 1.1.9) |
| Imports | S4Vectors, GenomeInfoDb, Biobase(>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio(>= 0.23.2), DelayedMatrixStats(>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray(>= 0.15.16), HDF5Array, BiocParallel |
| System Requirements | |
| URL | https://github.com/hansenlab/minfi |
| Bug Reports | https://github.com/hansenlab/minfi/issues |
See More
| Suggests | IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData(>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k(>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools |
| Linking To | |
| Enhances | |
| Depends On Me | ChAMP, REMP, bigmelon, conumee, methylumi, IlluminaHumanMethylation27kanno.ilmn12.hg19, IlluminaHumanMethylation27kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICanno.ilm10b3.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICv2anno.20a1.hg38, IlluminaHumanMethylationEPICv2manifest, BeadSorted.Saliva.EPIC, FlowSorted.Blood.450k, FlowSorted.Blood.EPIC, FlowSorted.CordBlood.450k, FlowSorted.CordBloodCombined.450k, FlowSorted.CordBloodNorway.450k, FlowSorted.DLPFC.450k, minfiData, minfiDataEPIC, methylationArrayAnalysis |
| Imports Me | DMRcate, MEAL, MEAT, MethylAid, deconvR, epimutacions, funtooNorm, iNETgrate, methylCC, methylclock, methylumi, missMethyl, quantro, recountmethylation, shinyMethyl, shinyepico, skewr, HiBED, EMAS |
| Suggests Me | GeoTcgaData, Harman, MultiDataSet, RnBeads, epivizrChart, epivizr, planet, brgedata, epimutacionsData, GSE159526, MLML2R |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | minfi_1.53.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/minfi |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/minfi |
| Bioc Package Browser | https://code.bioconductor.org/browse/minfi/ |
| Package Short Url | https://bioconductor.org/packages/minfi/ |
| Package Downloads Report | Download Stats |