Last data update: 2014.03.03

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 Results 1 - 10 of 18 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

IlluminaHumanMethylation27kmanifest : Annotation for Illumina's 27k methylation arrays

Package: IlluminaHumanMethylation27kmanifest
Version: 0.4.0
Title: Annotation for Illumina's 27k methylation arrays
Description: Manifest for Illumina's 27k array data
Author: Kasper Daniel Hansen
Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
License: Artistic-2.0
Depends: R (>= 2.13.0), minfi
LazyData: yes
biocViews: IlluminaChip, Homo_sapiens, DNAMethylation
Packaged: 2012-09-08 21:54:09 UTC; khansen

● Data Source: BioConductor
● BiocViews: DNAMethylation, Homo_sapiens, IlluminaChip
● 0 images, 0 functions, 1 datasets
● Reverse Depends: 0

IlluminaHumanMethylation450kanno.ilmn12.hg19 : Annotation for Illumina's 450k methylation arrays

Package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Version: 0.2.1
Title: Annotation for Illumina's 450k methylation arrays
Description: Manifests and annotation for Illumina's 450k array data
Author: Kasper Daniel Hansen
Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
License: Artistic-2.0
Depends: R (>= 2.10.0), minfi
LazyData: yes
Packaged: 2013-11-08 23:12:18 UTC; mcarlson

● Data Source: BioConductor
● 0 images, 0 functions, 1 datasets
● Reverse Depends: 5

IlluminaHumanMethylation450kmanifest : Annotation for Illumina's 450k methylation arrays

Package: IlluminaHumanMethylation450kmanifest
Version: 0.4.0
Title: Annotation for Illumina's 450k methylation arrays
Description: Manifest for Illumina's 450k array data
Author: Kasper Daniel Hansen, Martin Aryee
Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
License: Artistic-2.0
Depends: R (>= 2.13.0), minfi
LazyData: yes
biocViews: IlluminaChip, Homo_sapiens, DNAMethylation
Packaged: 2012-09-08 21:57:39 UTC; khansen

● Data Source: BioConductor
● BiocViews: DNAMethylation, Homo_sapiens, IlluminaChip
● 0 images, 0 functions, 1 datasets
● Reverse Depends: 5

IlluminaHumanMethylationEPICanno.ilm10b2.hg19 : Annotation for Illumina's EPIC methylation arrays

Package: IlluminaHumanMethylationEPICanno.ilm10b2.hg19
Version: 0.3.0
Title: Annotation for Illumina's EPIC methylation arrays
Description: An annotation package for Illumina's EPIC methylation arrays.
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("cre", "aut"),
email = "kasperdanielhansen@gmail.com"))
License: Artistic-2.0
URL: https://bitbucket.com/kasperdanielhansen/Illumina_EPIC
BugReports:
https://bitbucket.com/kasperdanielhansen/Illumina_EPIC/issues
Depends: R (>= 3.2.0), minfi
LazyData: yes
biocViews: IlluminaChip, Homo_sapiens, DNAMethylation
NeedsCompilation: no
Packaged: 2016-03-21 01:24:30 UTC; khansen
Author: Kasper Daniel Hansen [cre, aut]
Maintainer: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>

● Data Source: BioConductor
● BiocViews: DNAMethylation, Homo_sapiens, IlluminaChip
● 0 images, 0 functions, 1 datasets
● Reverse Depends: 0

IlluminaHumanMethylationEPICmanifest : Manifest for Illumina's EPIC methylation arrays

Package: IlluminaHumanMethylationEPICmanifest
Version: 0.3.0
Title: Manifest for Illumina's EPIC methylation arrays
Description: A manifest package for Illumina's EPIC methylation arrays.
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("cre", "aut"),
email = "kasperdanielhansen@gmail.com"))
License: Artistic-2.0
URL: https://bitbucket.com/kasperdanielhansen/Illumina_EPIC
BugReports:
https://bitbucket.com/kasperdanielhansen/Illumina_EPIC/issues
Depends: R (>= 3.2.0), minfi
LazyData: yes
biocViews: IlluminaChip, Homo_sapiens, DNAMethylation
NeedsCompilation: no
Packaged: 2016-03-20 19:46:38 UTC; khansen
Author: Kasper Daniel Hansen [cre, aut]
Maintainer: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>

● Data Source: BioConductor
● BiocViews: DNAMethylation, Homo_sapiens, IlluminaChip
● 0 images, 0 functions, 1 datasets
● Reverse Depends: 0

ChAMP : Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Package: ChAMP
Type: Package
Title: Chip Analysis Methylation Pipeline for Illumina
HumanMethylation450 and EPIC
Version: 1.10.0
Date: 2016-04-25
Description: The package includes quality control metrics, a selection
of normalization methods and novel methods to identify
differentially methylated regions and to highlight copy number
alterations. In addition there is a method to help calculate hmC using BS and oxBS samples.
Authors@R: c(person("Tiffany", "Morris", role = c("cre", "aut"),
email = "champ450k@gmail.com"),
person("Tian","Yuan",role = "aut"),
person("Lee", "Stirling", role = "ctb"),
person("Andrew", "Feber", role = "ctb"),
person("Andrew", "Teschendorff", role = "ctb"),
person("Ankur", "Chakravarthy", role = "ctb"))
License: GPL-3
Depends: R (>= 3.2), minfi, ChAMPdata, Illumina450ProbeVariants.db
Imports: sva, IlluminaHumanMethylation450kmanifest, limma, RPMM,
DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr,
GenomicRanges, RefFreeEWAS, qvalue, isva, doParallel, bumphunter, quadprog
biocViews: Microarray, MethylationArray, Normalization, TwoChannel,
CopyNumber, DNAMethylation
Author: Tiffany Morris [cre, aut],
Yuan Tian [aut],
Lee Stirling [ctb],
Andrew Feber [ctb],
Andrew Teschendorff [ctb],
Ankur Chakravarthy [ctb]
Maintainer: Yuan Tian, Tiffany Morris <champ450k@gmail.com>
NeedsCompilation: no
Packaged: 2016-05-04 05:15:29 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, TwoChannel
● 0 images, 12 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

CopyNumber450k : R package for calling CNV from Illumina 450k methylation microarrays

Package: CopyNumber450k
Title: R package for calling CNV from Illumina 450k methylation
microarrays
Version: 1.8.0
Date: 2014-02-04
Author: Simon Papillon-Cavanagh, Jean-Philippe Fortin, Nicolas De Jay
Maintainer: Simon Papillon-Cavanagh
<simon.papillon-cavanagh@mail.mcgill.ca>
Description: This package contains a set of functions that allow CNV
calling from Illumina 450k methylation microarrays.
License: Artistic-2.0
Imports: methods
Depends: Biobase, minfi, DNAcopy, preprocessCore, BiocGenerics
Suggests: CopyNumber450kData, minfiData
LinkingTo:
LazyData: yes
Collate: AllClasses.R AllGenerics.R CNV450kSet-accessors.R
CNV450kSet-actions.R CNV450kSet-comparison.R
CNV450kSet-initialize.R CNV450kSet-plot.R extract.R
normalization.functional.R normalization.quantile.R
biocViews: DNAMethylation, Microarray, Preprocessing, QualityControl,
CopyNumberVariation
NeedsCompilation: no
Packaged: 2016-05-04 05:20:08 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: CopyNumberVariation, DNAMethylation, Microarray, Preprocessing, QualityControl
● 4 images, 1 functions, 0 datasets
● Reverse Depends: 0

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