Package: coMET
Type: Package
Title: coMET: visualisation of regional epigenome-wide association scan
(EWAS) results and DNA co-methylation patterns
Version: 1.4.4
Date: 2016-06-12
Author: Tiphaine C. Martin, Thomas Hardiman, Idil Yet, Pei-Chien Tsai, Jordana T. Bell
Maintainer: Tiphaine Martin <tiphaine.martin@kcl.ac.uk>
Description: Visualisation of EWAS results in a genomic region. In addition to phenotype-association P-values, coMET also generates plots of co-methylation patterns and provides a series of annotation tracks. It can be used to other omic-wide association scans as long as the data can be translated to genomic level and for any species.
Depends: R (>= 3.3.0), grid, utils, biomaRt, Gviz, psych
Suggests: knitr, RUnit, BiocGenerics, BiocStyle
Imports: colortools, hash, grDevices, gridExtra, rtracklayer, IRanges, S4Vectors, GenomicRanges, ggbio, ggplot2, trackViewer, stats, corrplot
License: GPL (>= 2)
URL: http://epigen.kcl.ac.uk/comet
biocViews: Software, DifferentialMethylation, Visualization,
Sequencing, Genetics, FunctionalGenomics, Microarray,
MethylationArray, MethylSeq, ChIPSeq, DNASeq, RiboSeq, RNASeq,
ExomeSeq, DNAMethylation, GenomeWideAssociation
VignetteBuilder: knitr
NeedsCompilation: no
Repository: Bioconductor
Packaged: 2016-06-13 05:03:36 UTC; biocbuild
Package: DMRforPairs
Version: 1.8.0
Date: 2014-03-03
Title: DMRforPairs: identifying Differentially Methylated Regions
between unique samples using array based methylation profiles
Authors@R: c(person("Martin", "Rijlaarsdam", role = c("aut", "cre"),
email = "m.a.rijlaarsdam@gmail.com"), person("Yvonne", "vd
Zwan", role = "aut"), person("Lambert", "Dorssers", role =
"aut"), person("Leendert", "Looijenga", role = "aut"))
Depends: R (>= 2.15.2), Gviz (>= 1.2.1), R2HTML (>= 2.2.1), GenomicRanges (>= 1.10.7), parallel
Description: DMRforPairs (formerly DMR2+) allows researchers to compare
n>=2 unique samples with regard to their methylation profile.
The (pairwise) comparison of n unique single samples distinguishes
DMRforPairs from other existing pipelines as these often
compare groups of samples in either single CpG locus or region
based analysis. DMRforPairs defines regions of interest as
genomic ranges with sufficient probes located in close
proximity to each other. Probes in one region are optionally
annotated to the same functional class(es). Differential
methylation is evaluated by comparing the methylation values
within each region between individual samples and (if the
difference is sufficiently large), testing this difference
formally for statistical significance.
License: GPL (>= 2)
URL: http://www.martinrijlaarsdam.nl
http://www.erasmusmc.nl/pathologie/research/lepo/3898639/
biocViews: Microarray, DNAMethylation, DifferentialMethylation,
ReportWriting, Visualization, Annotation
Author: Martin Rijlaarsdam [aut, cre], Yvonne vd Zwan [aut], Lambert
Dorssers [aut], Leendert Looijenga [aut]
Maintainer: Martin Rijlaarsdam <m.a.rijlaarsdam@gmail.com>
NeedsCompilation: no
Packaged: 2016-05-04 05:25:22 UTC; biocbuild
Package: biomvRCNS
Type: Package
Title: Copy Number study and Segmentation for multivariate biological
data
Version: 1.12.0
Date: 2015-06-04
Author: Yang Du
Maintainer: Yang Du <tooyoung@gmail.com>
Description: In this package, a Hidden Semi Markov Model (HSMM) and one
homogeneous segmentation model are designed and implemented for
segmentation genomic data, with the aim of assisting in
transcripts detection using high throughput technology like
RNA-seq or tiling array, and copy number analysis using aCGH or
sequencing.
License: GPL (>= 2)
LazyLoad: yes
Imports: methods, mvtnorm
Depends: IRanges, GenomicRanges, Gviz
Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene
biocViews: aCGH, CopyNumberVariation, Microarray, Sequencing,
Sequencing, Visualization, Genetics
NeedsCompilation: yes
Packaged: 2016-05-04 04:52:36 UTC; biocbuild