Package: cpvSNP
Type: Package
Title: Gene set analysis methods for SNP association p-values that lie
in genes in given gene sets
Version: 1.4.0
Date: 2015-04-09
Author: Caitlin McHugh, Jessica Larson, and Jason Hackney
Maintainer: Caitlin McHugh <mchughc@uw.edu>
Imports: methods, corpcor, BiocParallel, ggplot2, plyr
Depends: R (>= 2.10), GenomicFeatures, GSEABase (>= 1.24.0)
Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle
Description: Gene set analysis methods exist to combine SNP-level
association p-values into gene sets, calculating a single
association p-value for each gene set. This package implements
two such methods that require only the calculated SNP p-values,
the gene set(s) of interest, and a correlation matrix (if
desired). One method (GLOSSI) requires independent SNPs and the
other (VEGAS) can take into account correlation (LD) among the
SNPs. Built-in plotting functions are available to help users
visualize results.
License: Artistic-2.0
biocViews: Genetics, StatisticalMethod, Pathways, GeneSetEnrichment,
GenomicVariation
NeedsCompilation: no
Packaged: 2016-05-04 05:57:21 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
Package: InPAS
Type: Package
Title: Identification of Novel alternative PolyAdenylation Sites (PAS)
Version: 1.4.4
Date: 2016-06-20
Authors@R: c(person("Jianhong Ou", "Developer", role = c("aut", "cre"),
email = "jianhong.ou@umassmed.edu"), person("Lihua Julie Zhu",
"Developer", role = "aut", email = "Julie.Zhu@umassmed.edu"))
Author: Jianhong Ou, Sung Mi Park, Michael R. Green and Lihua Julie Zhu
Maintainer: Jianhong Ou <jianhong.ou@umassmed.edu>
Description: Alternative polyadenylation (APA) is one of the important
post-transcriptional regulation mechanisms which occurs in
most human genes. InPAS facilitates the discovery of novel
APA sites from RNAseq data. It leverages cleanUpdTSeq to fine
tune identified APA sites.
biocViews: RNASeq, Sequencing, AlternativeSplicing, Coverage,
DifferentialSplicing, GeneRegulation, Transcription
License: GPL (>= 2)
Lazyload: yes
Imports: AnnotationDbi, BSgenome, cleanUpdTSeq, Gviz, seqinr, preprocessCore, IRanges, GenomeInfoDb, depmixS4, limma, BiocParallel
Depends: R (>= 3.1), methods, Biobase, GenomicRanges, GenomicFeatures, S4Vectors
Suggests: RUnit, BiocGenerics, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, org.Hs.eg.db, org.Mm.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, rtracklayer, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-21 05:10:44 UTC; biocbuild
Package: RNAprobR
Title: An R package for analysis of massive parallel sequencing based
RNA structure probing data
Version: 1.4.0
Date: 2015-09-23
Authors@R: c(person("Lukasz Jan", "Kielpinski", role=c("aut"),
email="kielpinski@bio.ku.dk"), person("Nikos", "Sidiropoulos",
role=c("cre", "aut"), email="nikos.sidiro@gmail.com"), person("Jeppe",
"Vinther", role="aut", email="jvinther@bio.ku.dk"))
Description: This package facilitates analysis of Next Generation Sequencing
data for which positional information with a single nucleotide resolution
is a key. It allows for applying different types of relevant
normalizations, data visualization and export in a table or UCSC
compatible bedgraph file.
Depends: R (>= 3.1.1), GenomicFeatures (>= 1.16.3), plyr (>= 1.8.1), BiocGenerics (>= 0.10.0)
Imports: Biostrings (>= 2.32.1), GenomicRanges (>= 1.16.4), Rsamtools (>=
1.16.1), rtracklayer (>= 1.24.2), GenomicAlignments (>= 1.5.12)
Suggests: BiocStyle
License: GPL (>=2)
LazyData: true
biocViews: Coverage, Normalization, Sequencing, GenomeAnnotation
NeedsCompilation: no
Packaged: 2016-05-04 06:09:19 UTC; biocbuild
Author: Lukasz Jan Kielpinski [aut],
Nikos Sidiropoulos [cre, aut],
Jeppe Vinther [aut]
Maintainer: Nikos Sidiropoulos <nikos.sidiro@gmail.com>
Package: OrganismDbi
Title: Software to enable the smooth interfacing of different database
packages
Description: The package enables a simple unified interface to several
annotation packages each of which has its own schema by taking
advantage of the fact that each of these packages implements a
select methods.
Version: 1.14.1
Author: Marc Carlson, Herve Pages, Martin Morgan, Valerie Obenchain
Maintainer: Biocore Data Team <maintainer@bioconductor.org>
Depends: R (>= 2.14.0), methods, BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.23.31)
Imports: Biobase, BiocInstaller, GenomicRanges, graph, IRanges, RBGL, RSQLite, S4Vectors (>= 0.9.25), stats
Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, rtracklayer, biomaRt, RUnit
Collate: AllGenerics.R AllClasses.R methods-select.R
methods-transcripts.R createOrganismPackage.R seqinfo.R
test_OrganismDbi_package.R
License: Artistic-2.0
biocViews: Annotation, Infrastructure
NeedsCompilation: no
Packaged: 2016-05-17 03:36:32 UTC; biocbuild
Package: SplicingGraphs
Title: Create, manipulate, visualize splicing graphs, and assign
RNA-seq reads to them
Version: 1.12.0
Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages
License: Artistic-2.0
Description: This package allows the user to create, manipulate, and visualize
splicing graphs and their bubbles based on a gene model for a given
organism. Additionally it allows the user to assign RNA-seq reads to
the edges of a set of splicing graphs, and to summarize them in
different ways.
Maintainer: H. Pages <hpages@fredhutch.org>
Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22), Rgraphviz (>= 2.3.7)
Imports: methods, utils, igraph, BiocGenerics, S4Vectors (>= 0.9.25), IRanges (>= 2.3.21), GenomeInfoDb, GenomicRanges (>= 1.23.21), GenomicFeatures, Rsamtools, GenomicAlignments, graph, Rgraphviz
Suggests: igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit
Collate: utils.R igraph-utils.R SplicingGraphs-class.R
plotTranscripts-methods.R sgedgesByGene-methods.R
txpath-methods.R sgedges-methods.R sgraph-methods.R
rsgedgesByGene-methods.R bubbles-methods.R assignReads.R
countReads-methods.R toy_data.R zzz.R
biocViews: Genetics, Annotation, DataRepresentation, Visualization,
Sequencing, RNASeq, GeneExpression, AlternativeSplicing,
Transcription
NeedsCompilation: no
Packaged: 2016-05-04 04:58:04 UTC; biocbuild
providing 
.