To install this package, start R and enter:

## try http if https is not available
source("https://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: 3.1

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:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("BSgenome.Ptroglodytes.UCSC.panTro3.masked")

Documentation


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
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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
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Package Short Url	http://bioconductor.org/packages/BSgenome.Ptroglodytes.UCSC.panTro3.masked/
Package Downloads Report	Download Stats

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