Package: BSgenome.Drerio.UCSC.danRer7.masked
Title: Full masked genome sequences for Danio rerio (UCSC version
danRer7)
Description: Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer7, 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.Drerio.UCSC.danRer7
Imports: BSgenome, BSgenome.Drerio.UCSC.danRer7
License: Artistic-2.0
organism: Danio rerio
species: Zebrafish
provider: UCSC
provider_version: danRer7
release_date: Jul. 2010
release_name: Sanger Institute Zv9
source_url: http://hgdownload.cse.ucsc.edu/goldenPath/danRer7/
biocViews: AnnotationData, Genetics, BSgenome, Danio_rerio
Packaged: 2014-01-08 20:13:47 UTC; hpages
Package: cleanUpdTSeq
Type: Package
Title: This package classifies putative polyadenylation sites as true
or false/internally oligodT primed
Version: 1.10.2
Date: 2015-10-02
Author: Sarah Sheppard, Jianhong Ou, Nathan Lawson, Lihua Julie Zhu
Maintainer: Sarah Sheppard <Sarah.Sheppard@umassmed.edu>; Jianhong Ou
<Jianhong.Ou@umassmed.edu>; Lihua Julie Zhu
<Julie.Zhu@umassmed.edu>
Depends: R (>= 2.15), BiocGenerics (>= 0.1.0), methods, BSgenome, BSgenome.Drerio.UCSC.danRer7, GenomicRanges, seqinr, e1071
Suggests: BiocStyle, knitr, RUnit
Description: This package uses the Naive Bayes classifier (from e1071)
to assign probability values to putative polyadenylation sites
(pA sites) based on training data from zebrafish. This will
allow the user to separate true, biologically relevant pA sites
from false, oligodT primed pA sites.
License: GPL-2
biocViews: Sequencing, SequenceMatching, Genetics, GeneRegulation
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-16 03:58:39 UTC; biocbuild
providing 
.