Package: regioneR
Type: Package
Title: Association analysis of genomic regions based on permutation
tests
Version: 1.4.2
Date: 2016-04-06
Author: Anna Diez-Villanueva <adiez@imppc.org>, Roberto Malinverni
<rmalinverni@carrerasresearch.org> and Bernat Gel <bgel@imppc.org>
Maintainer: Bernat Gel <bgel@imppc.org>
Description: regioneR offers a statistical framework based on
customizable permutation tests to assess the association
between genomic region sets and other genomic features.
License: Artistic-2.0
Depends: memoise, GenomicRanges, BSgenome, rtracklayer, parallel
Imports: memoise, GenomicRanges, BSgenome, rtracklayer, parallel, graphics, stats, utils, GenomeInfoDb, IRanges
Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19.masked, testthat
VignetteBuilder: knitr
biocViews: Genetics, ChIPSeq, DNASeq, MethylSeq, CopyNumberVariation
NeedsCompilation: no
RoxygenNote: 5.0.1
Packaged: 2016-05-16 05:22:11 UTC; biocbuild
Package: rGADEM
Type: Package
Title: de novo motif discovery
Version: 2.20.0
Date: 2014-04-01
Author: Arnaud Droit, Raphael Gottardo, Gordon Robertson and Leiping Li
Maintainer: Arnaud Droit <arnaud.droit@crchuq.ulaval.ca>
Depends: R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo
Imports: Biostrings, IRanges, methods, graphics, seqLogo
Suggests: BSgenome.Hsapiens.UCSC.hg19
Description: rGADEM is an efficient de novo motif discovery tool for
large-scale genomic sequence data. It is an open-source R
package, which is based on the GADEM software.
License: Artistic-2.0
biocViews: Microarray, ChIPchip, Sequencing, ChIPSeq, MotifDiscovery
NeedsCompilation: yes
Packaged: 2016-05-04 03:26:38 UTC; biocbuild
Package: BSgenome.Amellifera.UCSC.apiMel2.masked
Title: Full masked genome sequences for Apis mellifera (UCSC version
apiMel2)
Description: Full genome sequences for Apis mellifera (Honey Bee) as provided by UCSC (apiMel2, Jan. 2005) and stored in Biostrings objects. The sequences are the same as in BSgenome.Amellifera.UCSC.apiMel2, except that each of them has the 3 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), and (3) the mask of repeats from RepeatMasker (RM mask). Only the AGAPS and AMB masks are "active" by default.
Version: 1.3.99
Author: The Bioconductor Dev Team
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
Depends: BSgenome (>= 1.31.8), BSgenome.Amellifera.UCSC.apiMel2
Imports: BSgenome, BSgenome.Amellifera.UCSC.apiMel2
License: Artistic-2.0
organism: Apis mellifera
species: Honey Bee
provider: UCSC
provider_version: apiMel2
release_date: Jan. 2005
release_name: Baylor College of Medicine HGSC v.Amel_2.0
source_url: http://hgdownload.cse.ucsc.edu/goldenPath/apiMel2/bigZips/
biocViews: AnnotationData, Genetics, BSgenome, Apis_mellifera
Packaged: 2014-01-08 20:13:38 UTC; hpages
Package: BSgenome.Athaliana.TAIR.04232008
Title: Full genome sequences for Arabidopsis thaliana (TAIR version
from April 23, 2008)
Description: Full genome sequences for Arabidopsis thaliana as provided by TAIR (snapshot from April 23, 2008) and stored in Biostrings objects.
Version: 1.3.1000
Author: The Bioconductor Dev Team
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
Depends: BSgenome (>= 1.33.5)
Imports: BSgenome
Suggests:
License: Artistic-2.0
organism: Arabidopsis thaliana
species: Arabidopsis
provider: TAIR
provider_version: 04232008
release_date: NA
release_name: dumped from ADB: Mar/14/08
source_url:
ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/
biocViews: AnnotationData, Genetics, BSgenome, Arabidopsis_thaliana
Packaged: 2014-05-13 21:24:57 UTC; hpages
Package: BSgenome.Athaliana.TAIR.TAIR9
Title: Full genome sequences for Arabidopsis thaliana (TAIR9)
Description: Full genome sequences for Arabidopsis thaliana as provided by TAIR (TAIR9 Genome Release) and stored in Biostrings objects. Note that TAIR10 is an "annotation release" based on the same genome assembly as TAIR9.
Version: 1.3.1000
Author: The Bioconductor Dev Team
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
Depends: BSgenome (>= 1.33.5)
Imports: BSgenome
Suggests:
License: Artistic-2.0
organism: Arabidopsis thaliana
species: Arabidopsis
provider: TAIR
provider_version: TAIR9
release_date: June 9, 2009
release_name: TAIR9 Genome Release
source_url:
ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR9_genome_release/
biocViews: AnnotationData, Genetics, BSgenome, Arabidopsis_thaliana
Packaged: 2014-05-13 21:24:59 UTC; hpages
Package: BSgenome.Btaurus.UCSC.bosTau3.masked
Title: Full masked genome sequences for Bos taurus (UCSC version
bosTau3)
Description: Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
Version: 1.3.99
Author: The Bioconductor Dev Team
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
Depends: BSgenome (>= 1.31.8), BSgenome.Btaurus.UCSC.bosTau3
Imports: BSgenome, BSgenome.Btaurus.UCSC.bosTau3
License: Artistic-2.0
organism: Bos taurus
species: Cow
provider: UCSC
provider_version: bosTau3
release_date: Aug. 2006
release_name: Baylor College of Medicine HGSC Btau_3.1
source_url: http://hgdownload.cse.ucsc.edu/goldenPath/bosTau3/bigZips/
biocViews: AnnotationData, Genetics, BSgenome, Bos_taurus
Packaged: 2014-01-08 20:13:39 UTC; hpages
providing 
.