Last data update: 2014.03.03

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wateRmelon : Illumina 450 methylation array normalization and metrics

Package: wateRmelon
Type: Package
Title: Illumina 450 methylation array normalization and metrics
Version: 1.16.0
Tue Mar 22 11: 36:58 GMT 2016
Date: 2016-03-22
Author: Leonard C Schalkwyk, Ruth Pidsley, Chloe CY Wong, with functions contributed by Nizar Touleimat, Matthieu Defrance, Andrew Teschendorff, Jovana Maksimovic, Tyler Gorrie-Stone, Louis El Khouri
Maintainer: Leo <lschal@essex.ac.uk>
Description: 15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.
License: GPL-3
Depends: R (>= 2.10), Biobase, limma, methods, matrixStats, methylumi,
lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19,
illuminaio
Imports: Biobase
Enhances: minfi
Suggests: RPMM
LazyLoad: yes
biocViews: DNAMethylation, Microarray, TwoChannel, Preprocessing,
QualityControl
Collate: as.methylumi.R bscon.R bscon_methy.R bscon_minfi.R getAnn.R
oxyscale.R adaptRefQuantiles.R beta1.R Beta2M.R betaqn.R bgeq.R
bgeqot.R bgeqq2.R bgeqqn.R BMIQ_1.1.R combo.R
concatenateMatrices.R coRankedMatrices.R correctI.R correctII.R
dataDetectPval2NA.R db1.R detectionPval.filter.R dfs2.R
dfsfit.R dmrse.R dmrse_col.R dmrse_row.R dyebuy1.R dyebuy2.R
dyebuy3.R dyebuy4.R filterXY.R findAnnotationProbes.R gcoms.R
gcose.R genki.R genkme.R genkus.R genotype.R getMethylumiBeta.R
getQuantiles.R getSamples.R getsnp.R horv.R loadMethylumi2.R
lumiMethyR2.R M2Beta.R melon.R nbBeadsFilter.R
normalize.quantiles2.R normalizeIlluminaMethylation.R ot.R
outlyx.R pasteque.R peak.correction.R pfilter.R
pipelineIlluminaMethylation.batch.R pwod.R readEPIC.R
preprocessIlluminaMethylation.R referenceQuantiles.R
robustQuantileNorm_Illumina450K.probeCategories.R
robustQuantileNorm_Illumina450K.R seabird.R sextest.R summits.R
swan2.R uniqueAnnotationCategory.R qual.R AllGenerics.R
x_methylumi.R y_minfi.R
NeedsCompilation: no
Packaged: 2016-05-04 04:48:25 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: DNAMethylation, Microarray, Preprocessing, QualityControl, TwoChannel
● 2 images, 35 functions, 2 datasets
● Reverse Depends: 1

RnBeads : RnBeads

Package: RnBeads
Title: RnBeads
Description: RnBeads facilitates comprehensive analysis of various types of DNA
methylation data at the genome scale.
Authors@R: c(
person("Yassen", "Assenov", email = "yassen@mpi-inf.mpg.de",
role = c("aut")),
person("Pavlo", "Lutsik", email = "p.lutsik@mx.uni-saarland.de",
role = c("aut")),
person("Fabian", "Mueller", email = "rnbeads@mpi-inf.mpg.de",
role = c("aut", "cre")))
Date: 2016-03-20
Version: 1.4.0
Suggests: Category, GEOquery, GOstats, Gviz,
IlluminaHumanMethylation450kmanifest, RPMM, RefFreeEWAS,
RnBeads.hg19, XML, annotate, biomaRt, foreach, doParallel,
ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db,
org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, sva,
wateRmelon, wordcloud, argparse, glmnet, impute
Depends: R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25),
GenomicRanges, MASS, RColorBrewer, cluster, ff, fields, ggplot2
(>= 0.9.2), gplots, gridExtra, limma, matrixStats, methods,
illuminaio, methylumi, plyr
Imports: IRanges
License: GPL-3
biocViews: DNAMethylation, MethylationArray, MethylSeq, Epigenetics,
QualityControl, Preprocessing, BatchEffect,
DifferentialMethylation, Sequencing, CpGIsland, TwoChannel,
DataImport
Collate: 'CNV.R' 'Report-class.R' 'Report-methods.R'
'ReportPlot-class.R' 'ReportPlot-methods.R'
'RnBDiffMeth-class.R' 'bigFf.R' 'RnBSet-class.R'
'RnBeadSet-class.R' 'RnBeadRawSet-class.R' 'RnBeads-package.R'
'RnBiseqSet-class.R' 'annotations.R' 'batch.R'
'batch.quality.R' 'bmiq.R' 'cellTypeAdjustment.R'
'clusterArchitecture.R' 'clusterArchitectureSGE.R'
'clustering.R' 'computeCluster.R' 'controlPlots.R'
'controlPlotsBiSeq.R' 'dataExport.R' 'dataImport.R'
'differentialMethylation.R' 'enrichment.R' 'filtering.R'
'filteringSummary.R' 'gender.R' 'greedycut.R' 'loading.R'
'logger.R' 'main.R' 'normalization.R' 'options.R'
'parallelProcessing.R' 'plottingUtils.R' 'profiles.R'
'qualityControl.R' 'readGEO.R' 'regionDescription.R'
'regionProfiles.R' 'subSegments.R' 'sva.R' 'utilities.R'
'wbcInference.R' 'agePrediction.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-04 06:18:43 UTC; biocbuild
Author: Yassen Assenov [aut],
Pavlo Lutsik [aut],
Fabian Mueller [aut, cre]
Maintainer: Fabian Mueller <rnbeads@mpi-inf.mpg.de>

● Data Source: BioConductor
● BiocViews: BatchEffect, CpGIsland, DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, MethylSeq, MethylationArray, Preprocessing, QualityControl, Sequencing, TwoChannel
● 10 images, 238 functions, 2 datasets
● Reverse Depends: 0

normalize450K : Preprocessing of Illumina Infinium 450K data

Package: normalize450K
Type: Package
Title: Preprocessing of Illumina Infinium 450K data
Version: 1.0.0
Date: 2015-08-31
Author: Jonathan Alexander Heiss
Maintainer: Jonathan Alexander Heiss <jonathan.heiss@posteo.de>
Description: Precise measurements are important for epigenome-wide studies investigating DNA methylation in whole blood samples, where effect sizes are expected to be small in magnitude. The 450K platform is often affected by batch effects and proper preprocessing is recommended. This package provides functions to read and normalize 450K '.idat' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values.
Depends: R (>= 3.3), Biobase, illuminaio, quadprog
Imports: utils
License: BSD_2_clause + file LICENSE
biocViews: Normalization, DNAMethylation, Microarray, TwoChannel,
Preprocessing, MethylationArray
NeedsCompilation: no
Packaged: 2016-05-04 06:42:17 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: DNAMethylation, MethylationArray, Microarray, Normalization, Preprocessing, TwoChannel
● 0 images, 2 functions, 0 datasets
● Reverse Depends: 0

Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO