Package: deepSNV
Maintainer: Moritz Gerstung <mg14@sanger.ac.uk>
License: GPL-3
Title: Detection of subclonal SNVs in deep sequencing data.
biocViews: GeneticVariability, SNP, Sequencing, Genetics, DataImport
LinkingTo: Rhtslib
Type: Package
LazyLoad: yes
Authors@R: c( person("Niko","Beerenwinkel", role="ths"),
person("David", "Jones", role = "ctb"),
person("Inigo", "Martincorena", role = "ctb"),
person("Moritz","Gerstung",
email = "mg14@sanger.ac.uk", role= c("aut","cre")) )
Description: This package provides provides quantitative variant callers for
detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing
experiments. The deepSNV algorithm is used for a comparative setup with a
control experiment of the same loci and uses a beta-binomial model and a
likelihood ratio test to discriminate sequencing errors and subclonal SNVs.
The shearwater algorithm computes a Bayes classifier based on a
beta-binomial model for variant calling with multiple samples for
precisely estimating model parameters such as local error rates and
dispersion and prior knowledge, e.g. from variation data bases such as
COSMIC.
Version: 1.18.1
URL: http://github.com/mg14/deepSNV
Depends: R (>= 2.13.0), methods, graphics, parallel, Rhtslib, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.13.44),
Imports: Rhtslib
Suggests: RColorBrewer, knitr
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-05-12 03:17:01 UTC; biocbuild
Author: Niko Beerenwinkel [ths],
David Jones [ctb],
Inigo Martincorena [ctb],
Moritz Gerstung [aut, cre]
Package: ensemblVEP
Version: 1.12.0
Title: R Interface to Ensembl Variant Effect Predictor
Author: Valerie Obenchain
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
Depends: methods, BiocGenerics, GenomicRanges, VariantAnnotation
Imports: S4Vectors (>= 0.9.25), Biostrings, SummarizedExperiment
Suggests: RUnit
Description: Query the Ensembl Variant Effect Predictor via the perl API
SystemRequirements: Ensembl VEP (API version 84) and the Perl package
DBD::mysql must be installed. See the package README and
Ensembl web site,
http://www.ensembl.org/info/docs/tools/vep/index.html for
installation instructions.
License: Artistic-2.0
LazyLoad: yes
biocViews: Annotation, VariantAnnotation, SNP
NeedsCompilation: no
Packaged: 2016-05-04 04:49:45 UTC; biocbuild
Package: DOQTL
Version: 1.8.0
Date: 2012-12-07
Title: Genotyping and QTL Mapping in DO Mice
Author: Daniel Gatti, Karl Broman, Andrey Shabalin, Petr Simecek
Maintainer: Daniel Gatti <Dan.Gatti@jax.org>
Depends: R (>= 3.0.0), BSgenome.Mmusculus.UCSC.mm10, GenomicRanges, VariantAnnotation
Imports: annotate, annotationTools, biomaRt, Biobase, BiocGenerics, corpcor, doParallel, foreach, fpc, hwriter, IRanges, iterators, mclust, QTLRel, regress, rhdf5, Rsamtools, RUnit, XML
Suggests: MUGAExampleData, doMPI
Description: DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, DOQTL can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.
biocViews: GeneticVariability, SNP, Genetics, HiddenMarkovModel
License: GPL-3
LazyData: true
ByteCompile: yes
URL: http://do.jax.org
NeedsCompilation: yes
Packaged: 2016-05-04 05:39:30 UTC; biocbuild
Package: RareVariantVis
Type: Package
Title: Visualization of rare variants in whole genome sequencing data
Version: 1.6.2
Date: 2016-04-23
Author: Tomasz Stokowy
Maintainer: Tomasz Stokowy <tomasz.stokowy@k2.uib.no>
Description: Genomic variants can be analyzed and visualized using many
tools. Unfortunately, number of tools for global interrogation
of variants is limited. Package RareVariantVis aims to present
genomic variants (especially rare ones) in a global, per
chromosome way. Visualization is performed in two ways -
standard that outputs png figures and interactive that uses
JavaScript d3 package. Interactive visualization allows to
analyze trio/family data, for example in search for causative
variants in rare Mendelian diseases.
License: Artistic-2.0
LazyData: TRUE
Depends: BiocGenerics, VariantAnnotation, googleVis
Imports: S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
Suggests: knitr, AshkenazimSonChr21
VignetteBuilder: knitr
biocViews: GenomicVariation, Sequencing, WholeGenome
NeedsCompilation: no
Packaged: 2016-05-16 05:29:45 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
providing 
.