Last data update: 2014.03.03

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 Results 1 - 5 of 5 found.
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conumee : Enhanced copy-number variation analysis using Illumina 450k methylation arrays

Package: conumee
Title: Enhanced copy-number variation analysis using Illumina 450k
methylation arrays
Version: 1.4.2
Author: Volker Hovestadt, Marc Zapatka
Maintainer: Volker Hovestadt <conumee@hovestadt.bio>
Address: Division of Molecular Genetics, German Cancer Research Center
(DKFZ), Heidelberg, Germany
Description: This package contains a set of processing and plotting
methods for performing copy-number variation (CNV) analysis
using Illumina 450k methylation arrays.
Imports: methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges,
GenomeInfoDb
Depends: R (>= 3.0), minfi, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
Suggests: BiocStyle, knitr, rmarkdown, minfiData, CopyNumber450kData,
RCurl
License: GPL (>= 2)
LazyData: false
Collate: classes.R annotation.R load.R process.R output.R data.R
biocViews: CopyNumberVariation, DNAMethylation, MethylationArray,
Microarray, Normalization, Preprocessing, QualityControl,
Software
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-16 05:29:05 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: CopyNumberVariation, DNAMethylation, MethylationArray, Microarray, Normalization, Preprocessing, QualityControl, Software
● 18 images, 21 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

CopyNumber450kData : Example data for the Illumina Methylation 450k array

Package: CopyNumber450kData
Version: 1.8.0
Date: 2014-01-22
Title: Example data for the Illumina Methylation 450k array
Description: Data from 52 control samples from 450k methylation arrays
Author: Simon Papillon-Cavanagh, Jean-Philippe Fortin, Nicolas De Jay
Maintainer: Simon Papillon-Cavanagh
<simon.papillon-cavanagh@mail.mcgill.ca>
License: Artistic-2.0
Depends: R (>= 2.13.0), minfi, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
LazyData: yes
biocViews: Tissue, Homo_sapiens_Data, MicroarrayData,
MethylationArrayData, TissueMicroarrayData
NeedsCompilation: no
Packaged: 2016-05-07 20:47:17 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData, Tissue, TissueMicroarrayData
● 0 images, 0 functions, 1 datasets
● Reverse Depends: 0

ELMER : Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Package: ELMER
Title: Inferring Regulatory Element Landscapes and Transcription Factor
Networks Using Cancer Methylomes
Version: 1.4.2
Authors@R: c(person("Lijing", "Yao", role = c("cre", "aut"),
email = "lijingya@usc.edu"),
person("Ben", "Berman", role = "aut"),
person("Peggy", "Farnham", role = "aut"),
person("Hui", "Shen", role = "ctb"),
person("Peter", "Laird", role = "ctb"),
person("Simon","Coetzee", role = "ctb"))
Description:
ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.
Depends: R (>= 3.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19,
Homo.sapiens, ELMER.data
License: GPL-3
LazyData: true
VignetteBuilder: knitr
Imports:
methods,BiocGenerics,S4Vectors,IRanges,GenomeInfoDb,GenomicRanges,ggplot2,reshape,grid,gridExtra,minfi,GenomicFeatures
Suggests: parallel, snow, BiocStyle, knitr, R.utils, downloader
biocViews: DNAMethylation, GeneExpression, MotifAnnotation, Software,
GeneRegulation
NeedsCompilation: no
Packaged: 2016-05-16 05:29:23 UTC; biocbuild
Author: Lijing Yao [cre, aut],
Ben Berman [aut],
Peggy Farnham [aut],
Hui Shen [ctb],
Peter Laird [ctb],
Simon Coetzee [ctb]
Maintainer: Lijing Yao <lijingya@usc.edu>

● Data Source: BioConductor
● BiocViews: DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Software
● 6 images, 30 functions, 0 datasets
● Reverse Depends: 0

minfiData : Example data for the Illumina Methylation 450k array

Package: minfiData
Version: 0.14.0
Title: Example data for the Illumina Methylation 450k array
Description: Data from 6 samples across 2 groups from 450k methylation arrays
Author: Kasper Daniel Hansen, Martin Aryee, Winston Timp
Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
License: Artistic-2.0
Depends: R (>= 2.13.0), minfi, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
LazyData: yes
biocViews: Homo_sapiens_Data, MethylationArrayData
NeedsCompilation: no
Packaged: 2016-05-07 20:20:20 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Homo_sapiens_Data, MethylationArrayData
● 0 images, 0 functions, 2 datasets
● Reverse Depends: 0

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