Last data update: 2014.03.03

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 Results 1 - 3 of 3 found.
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skewr : Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip

Package: skewr
Title: Visualize Intensities Produced by Illumina's Human Methylation
450k BeadChip
Version: 1.4.2
Authors@R: c(person("Ryan", "Putney", role = c("cre", "aut"), email =
"ryanputney@gmail.com"), person("Steven", "Eschrich", role =
"aut"), person("Anders", "Berglund", role = "aut"))
Description: The skewr package is a tool for visualizing the output of
the Illumina Human Methylation 450k BeadChip to aid in quality
control. It creates a panel of nine plots. Six of the plots
represent the density of either the methylated intensity or the
unmethylated intensity given by one of three subsets of the
485,577 total probes. These subsets include Type I-red, Type
I-green, and Type II.The remaining three distributions give the
density of the Beta-values for these same three subsets. Each
of the nine plots optionally displays the distributions of the
"rs" SNP probes and the probes associated with imprinted genes
as series of 'tick' marks located above the x-axis.
Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn,
IlluminaHumanMethylation450kmanifest
Imports: minfi, IRanges, RColorBrewer
Suggests: GEOquery, knitr, minfiData
VignetteBuilder: knitr
License: GPL-2
LazyData: true
biocViews: DNAMethylation, TwoChannel, Preprocessing, QualityControl
Author: Ryan Putney [cre, aut], Steven Eschrich [aut], Anders Berglund
[aut]
Maintainer: Ryan Putney <ryanputney@gmail.com>
NeedsCompilation: no
Packaged: 2016-05-16 05:15:24 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: DNAMethylation, Preprocessing, QualityControl, TwoChannel
● 3 images, 6 functions, 0 datasets
● Reverse Depends: 0

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

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