This package is for version 3.15 of Bioconductor;
for the stable, up-to-date release version, see
minfi.
Analyze Illumina Infinium DNA methylation arrays
Bioconductor version: 3.15
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 (from within R, enter citation("minfi")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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")
Details
biocViews
DNAMethylation,
DataImport,
DifferentialMethylation,
Epigenetics,
ImmunoOncology,
MethylationArray,
Microarray,
MultiChannel,
Normalization,
Preprocessing,
QualityControl,
Software,
TwoChannel
Version
1.42.0
In Bioconductor since
BioC 2.9 (R-2.14) (12.5 years)
License
Artistic-2.0
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
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
BeadSorted.Saliva.EPIC,
bigmelon,
ChAMP,
conumee,
FlowSorted.Blood.450k,
FlowSorted.Blood.EPIC,
FlowSorted.CordBlood.450k,
FlowSorted.CordBloodCombined.450k,
FlowSorted.CordBloodNorway.450k,
FlowSorted.DLPFC.450k,
IlluminaHumanMethylation27kanno.ilmn12.hg19,
IlluminaHumanMethylation27kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
IlluminaHumanMethylationEPICanno.ilm10b3.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
IlluminaHumanMethylationEPICmanifest,
methylationArrayAnalysis,
methylumi,
minfiData,
minfiDataEPIC,
REMP,
shinyMethyl
Imports Me
DMRcate,
ENmix,
epimutacions,
funtooNorm,
MEAL,
MEAT,
MethylAid,
methylCC,
methylclock,
methylumi,
missMethyl,
quantro,
recountmethylation,
shinyepico,
skewr
Suggests Me
brgedata,
CopyNeutralIMA,
EnMCB,
epimutacionsData,
epivizr,
epivizrChart,
GSE159526,
Harman,
mCSEA,
MultiDataSet,
planet,
RnBeads
Links To Me
Package Archives
Follow Installation instructions to use this package in your R session.
Source Repository
git clone https://git.bioconductor.org/packages/minfi
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/minfi