To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("BadRegionFinder")

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

BadRegionFinder

DOI: 10.18129/B9.bioc.BadRegionFinder    

This is the development version of BadRegionFinder; for the stable release version, see BadRegionFinder.

BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage

Bioconductor version: Development (3.7)

BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.

Author: Sarah Sandmann

Maintainer: Sarah Sandmann <sarah.sandmann at uni-muenster.de>

Citation (from within R, enter citation("BadRegionFinder")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("BadRegionFinder")

Documentation

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

browseVignettes("BadRegionFinder")

 

PDF R Script Using BadRegionFinder
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, Classification, Coverage, Sequencing, Software, WholeGenome
Version 1.7.0
In Bioconductor since BioC 3.3 (R-3.3) (1.5 years)
License LGPL-3
Depends
Imports VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics
LinkingTo
Suggests BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package BadRegionFinder_1.7.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) BadRegionFinder_1.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BadRegionFinder
Package Short Url http://bioconductor.org/packages/BadRegionFinder/
Package Downloads Report Download Stats

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