To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("BSgenome.Ptroglodytes.UCSC.panTro3.masked")

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

BSgenome.Ptroglodytes.UCSC.panTro3.masked

Full masked genome sequences for Pan troglodytes (UCSC version panTro3)

Bioconductor version: Release (2.14)

Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro3, Oct. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ptroglodytes.UCSC.panTro3, 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.Ptroglodytes.UCSC.panTro3.masked")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("BSgenome.Ptroglodytes.UCSC.panTro3.masked")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BSgenome.Ptroglodytes.UCSC.panTro3.masked")

 

PDF   Reference Manual

Details

biocViews AnnotationData, BSgenome, Genetics, Pan_troglodytes
Version 1.3.99
License Artistic-2.0
Depends BSgenome(>= 1.31.8), BSgenome.Ptroglodytes.UCSC.panTro3
Imports BSgenome, BSgenome.Ptroglodytes.UCSC.panTro3
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.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tar.gz
Windows Binary BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tgz
Mac OS X 10.9 (Mavericks) BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tgz
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