To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("BSgenome.Drerio.UCSC.danRer7.masked")

In most cases, you don't need to download the package archive at all.

BSgenome.Drerio.UCSC.danRer7.masked

Full masked genome sequences for Danio rerio (UCSC version danRer7)

Bioconductor version: Release (2.14)

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.

Author: The Bioconductor Dev Team

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("BSgenome.Drerio.UCSC.danRer7.masked")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("BSgenome.Drerio.UCSC.danRer7.masked")

Documentation

PDF   Reference Manual

Details

biocViews AnnotationData, BSgenome, Danio_rerio, Genetics
Version 1.3.99
License Artistic-2.0
Depends BSgenome(>= 1.31.8), BSgenome.Drerio.UCSC.danRer7
Imports BSgenome, BSgenome.Drerio.UCSC.danRer7
Suggests
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tar.gz
Windows Binary BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tgz
Mac OS X 10.9 (Mavericks) BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tgz
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