BSgenome.Drerio.UCSC.danRer6.masked

DOI: 10.18129/B9.bioc.BSgenome.Drerio.UCSC.danRer6.masked    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Drerio.UCSC.danRer6.masked.

Full masked genome sequences for Danio rerio (UCSC version danRer6)

Bioconductor version: 3.9

Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer6, Dec. 2008) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer6, 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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BSgenome.Drerio.UCSC.danRer6.masked")

For older versions of R, please refer to the appropriate Bioconductor release.

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.danRer6
Imports	BSgenome, BSgenome.Drerio.UCSC.danRer6
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Package Archives

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

Source Package	BSgenome.Drerio.UCSC.danRer6.masked_1.3.99.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Package Short Url	https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer6.masked/
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