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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

shinyMethyl : Interactive visualization for Illumina's 450k methylation arrays

Package: shinyMethyl
Title: Interactive visualization for Illumina's 450k methylation arrays
Version: 1.6.2
Authors@R: c(person("Jean-Philippe", "Fortin", role = c("cre", "aut"),
email = "jfortin@jhsph.edu"),
person(c("Kasper", "Daniel"), "Hansen", role = "aut"))
Depends: methods, BiocGenerics (>= 0.3.2), shiny (>= 0.9.1), minfi (>=
1.6.0), IlluminaHumanMethylation450kmanifest, matrixStats, R
(>= 3.0.0)
Imports: RColorBrewer
Suggests: shinyMethylData, minfiData, BiocStyle, RUnit, digest, knitr
Description: Interactive tool for visualizing Illumina's 450k array data
Url: https://github.com/Jfortin1/shinyMethyl
VignetteBuilder: knitr
License: Artistic-2.0
biocViews: DNAMethylation, Microarray, TwoChannel, Preprocessing,
QualityControl
NeedsCompilation: no
Packaged: 2016-05-16 04:41:07 UTC; biocbuild
Author: Jean-Philippe Fortin [cre, aut],
Kasper Daniel Hansen [aut]
Maintainer: Jean-Philippe Fortin <jfortin@jhsph.edu>

● Data Source: BioConductor
● BiocViews: DNAMethylation, Microarray, Preprocessing, QualityControl, TwoChannel
● 0 images, 4 functions, 0 datasets
● Reverse Depends: 0

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

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

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