Package: snapCGH
Title: Segmentation, normalisation and processing of aCGH data.
Version: 1.42.0
Date: 2009-10-08
Author: Mike L. Smith, John C. Marioni, Steven McKinney, Thomas
Hardcastle, Natalie P. Thorne
Description: Methods for segmenting, normalising and processing aCGH
data; including plotting functions for visualising raw and
segmented data for individual and multiple arrays.
Maintainer: John Marioni <marioni@uchicago.edu>
Depends: limma, DNAcopy, methods
Imports: aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma, methods, stats, tilingArray, utils
License: GPL
biocViews: Microarray, CopyNumberVariation, TwoChannel, Preprocessing
NeedsCompilation: yes
Packaged: 2016-05-04 02:49:21 UTC; biocbuild
Package: PureCN
Type: Package
Title: Estimating tumor purity, ploidy, LOH, and SNV status using
hybrid capture NGS data
Version: 1.0.3
Date: 2016-06-04
Author: Markus Riester
Maintainer: Markus Riester <markus.riester@novartis.com>
Description: This package estimates tumor purity, copy number, loss of
heterozygosity (LOH), and status of single nucleotide variants (SNVs).
PureCN is designed for hybrid capture sequencing data, integrates
well with standard somatic variant detection pipelines,
and has support for tumor samples without matching normal samples.
Depends: R (>= 3.3), DNAcopy, VariantAnnotation (>= 1.14.1)
Imports: GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer, S4Vectors, data.table, grDevices, graphics, stats, utils, SummarizedExperiment, GenomeInfoDb
Suggests: PSCBS, RUnit, BiocStyle, BiocGenerics, knitr
VignetteBuilder: knitr
License: Artistic-2.0
biocViews: CopyNumberVariation, Software, Sequencing,
VariantAnnotation, VariantDetection
NeedsCompilation: no
Packaged: 2016-06-06 06:04:50 UTC; biocbuild
Package: SomatiCA
Type: Package
Title: SomatiCA: identifying, characterizing, and quantifying somatic
copy number aberrations from cancer genome sequencing
Version: 2.2.0
Date: 2016-04-15
Author: Mengjie Chen <mengjie.chen@yale.edu>, Hongyu Zhao
<hongyu.zhao@yale.edu>
Maintainer: Mengjie Chen <mengjie.chen@yale.edu>
Imports: foreach, lars, sn, DNAcopy, methods, rebmix, GenomicRanges, IRanges
Depends: R (>= 2.14.0), lars, DNAcopy, foreach, methods, rebmix, GenomicRanges, IRanges, doParallel
Enhances: sn, SomatiCAData
Description: SomatiCA is a software suite that is capable of
identifying, characterizing, and quantifying somatic CNAs from
cancer genome sequencing. First, it uses read depths and lesser
allele frequencies (LAF) from mapped short sequence reads to
segment the genome and identify candidate CNAs. Second,
SomatiCA estimates the admixture rate from the relative
copy-number profile of tumor-normal pair by a Bayesian finite
mixture model. Third, SomatiCA quantifies absolute somatic
copy-number and subclonality for each genomic segment to guide
its characterization. Results from SomatiCA can be further
integrated with single nucleotide variations (SNVs) to get a
better understanding of the tumor evolution.
License: GPL (>=2)
biocViews: Sequencing, CopyNumberVariation
PackageStatus: Deprecated
NeedsCompilation: no
Packaged: 2016-05-04 04:51:18 UTC; biocbuild
Package: cghMCR
Version: 1.30.0
Title: Find chromosome regions showing common gains/losses
Author: J. Zhang and B. Feng
Maintainer: J. Zhang <jzhang@jimmy.harvard.edu>
Depends: methods, DNAcopy, CNTools, limma
Imports: BiocGenerics (>= 0.1.6), stats4
Description: This package provides functions to identify genomic
regions of interests based on segmented copy number data from
multiple samples.
Keyword: arrayCGH
License: LGPL
LazyLoad: yes
biocViews: Microarray, CopyNumberVariation
NeedsCompilation: no
Packaged: 2016-05-04 02:52:38 UTC; biocbuild
Package: CGHcall
Type: Package
Title: Calling aberrations for array CGH tumor profiles.
Version: 2.34.0
Date: 2014-02-25
Author: Mark van de Wiel, Sjoerd Vosse
Maintainer: Mark van de Wiel <mark.vdwiel@vumc.nl>
Depends: R (>= 2.0.0), impute (>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall
Description: Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.
License: GPL (http://www.gnu.org/copyleft/gpl.html)
biocViews: Microarray,Preprocessing,Visualization
NeedsCompilation: no
Packaged: 2016-05-04 03:02:20 UTC; biocbuild
providing 
.