Package: intansv
Title: Integrative analysis of structural variations
Description: This package provides efficient tools to read and integrate
structural variations predicted by popular softwares. Annotation and
visulation of structural variations are also implemented in the
package.
Version: 1.10.0
Author: Wen Yao <ywhzau@gmail.com>
Maintainer: Wen Yao <ywhzau@gmail.com>
biocViews: Genetics, Annotation, Sequencing, Software
Depends: R (>= 2.14.0), plyr, ggbio, GenomicRanges
Imports: BiocGenerics, IRanges
License: Artistic-2.0
NeedsCompilation: no
Packaged: 2016-05-04 05:02:23 UTC; biocbuild
Package: cnvGSA
Type: Package
Title: Gene Set Analysis of (Rare) Copy Number Variants
Version: 1.16.0
Date: 2015-03-02
Author: Daniele Merico <daniele.merico@gmail.com>, Robert Ziman <rziman@gmail.com>; packaged by Joseph Lugo <joseph.r.lugo@gmail.com>
Maintainer: Joseph Lugo <joseph.r.lugo@gmail.com>
Description: This package is intended to facilitate gene-set association with rare CNVs in case-control studies.
License: LGPL
LazyLoad: yes
Depends: brglm, doParallel, foreach, GenomicRanges, methods, splitstackshape
Suggests: cnvGSAdata, org.Hs.eg.db
biocViews: MultipleComparison
NeedsCompilation: no
Packaged: 2016-05-04 04:30:02 UTC; biocbuild
Package: consensusSeekeR
Version: 1.0.2
Date: 2015-05-01
Title: Detection of consensus regions inside a group of experiences
using genomic positions and genomic ranges
Description: This package compares genomic positions and genomic ranges from
multiple experiments to extract common regions. The size of the analyzed region
is adjustable as well as the number of experiences in which a feature must be
present in a potential region to tag this region as a consensus region.
Author: Astrid Deschenes [cre, aut], Fabien Claude Lamaze [ctb], Pascal Belleau
[aut], Arnaud Droit [aut]
Author@R: c(person("Astrid", "Deschenes", email="Astrid-
Louise.Deschenes@crchudequebec.ulaval.ca",
role=c("cre","aut")), person("Fabien Claude", "Lamaze",
email="fabien.lamaze.1@ulaval.ca", role=c("ctb")),
person("Pascal", "Belleau",
email="pascal.belleau@crchuq.ulaval.ca", role=c("aut")),
person("Arnaud", "Droit",
email="arnaud.droit@crchuq.ulaval.ca", role=c("aut")))
Depends: R (>= 2.10), BiocGenerics, IRanges, GenomicRanges, BiocParallel
Imports: GenomeInfoDb, rtracklayer, stringr, S4Vectors
Suggests: BiocStyle, ggplot2, knitr, RUnit
License: Artistic-2.0
URL: https://github.com/ArnaudDroitLab/consensusSeekeR
BugReports: https://github.com/ArnaudDroitLab/consensusSeekeR/issues
VignetteBuilder: knitr
NeedsCompilation: no
biocViews: BiologicalQuestion, ChIPSeq, Genetics, MultipleComparison,
Transcription, PeakDetection, Sequencing, Coverage
Maintainer: Astrid Louise Deschenes <Astrid-Louise.Deschenes@crchudequebec.ulaval.ca>
RoxygenNote: 5.0.1
Packaged: 2016-05-16 05:51:37 UTC; biocbuild
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: ensembldb
Type: Package
Title: Utilities to create and use an Ensembl based annotation database
Version: 1.4.6
Author: Johannes Rainer <johannes.rainer@eurac.edu>,
Tim Triche <tim.triche@usc.edu>
Maintainer: Johannes Rainer <johannes.rainer@eurac.edu>
URL: https://github.com/jotsetung/ensembldb
BugReports: https://github.com/jotsetung/ensembldb/issues
Imports: methods, RSQLite, DBI, Biobase, GenomeInfoDb, AnnotationDbi
(>= 1.31.19), rtracklayer, S4Vectors, AnnotationHub, Rsamtools, IRanges
Depends: BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.23.21), GenomicFeatures (>= 1.23.18)
Suggests: BiocStyle, knitr, rmarkdown, EnsDb.Hsapiens.v75 (>= 0.99.7), RUnit, shiny, Gviz, BSgenome.Hsapiens.UCSC.hg19
VignetteBuilder: knitr
Description: The package provides functions to create and use
transcript centric annotation databases/packages. The
annotation for the databases are directly fetched from Ensembl
using their Perl API. The functionality and data is similar to
that of the TxDb packages from the GenomicFeatures package,
but, in addition to retrieve all gene/transcript models and
annotations from the database, the ensembldb package provides
also a filter framework allowing to retrieve annotations for
specific entries like genes encoded on a chromosome region or
transcript models of lincRNA genes.
Collate: Classes.R Generics.R dbhelpers.R Methods.R Methods-Filter.R
loadEnsDb.R makeEnsemblDbPackage.R EnsDbFromGTF.R runEnsDbApp.R
select-methods.R seqname-utils.R zzz.R
biocViews: Genetics, AnnotationData, Sequencing, Coverage
License: LGPL
NeedsCompilation: no
Packaged: 2016-06-07 05:12:18 UTC; biocbuild
providing 
.