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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BadRegionFinder")
In most cases, you don't need to download the package archive at all.
BadRegionFinder
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see BadRegionFinder.
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
Bioconductor version: 3.3
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("https://bioconductor.org/biocLite.R")
biocLite("BadRegionFinder")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BadRegionFinder")
| R Script | Using BadRegionFinder | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, Classification, Coverage, Sequencing, Software, WholeGenome |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (< 6 months) |
| 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.
| Package Source | BadRegionFinder_1.0.0.tar.gz |
| Windows Binary | BadRegionFinder_1.0.0.zip |
| Mac OS X 10.9 (Mavericks) | BadRegionFinder_1.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/BadRegionFinder/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/BadRegionFinder/ |
| Package Downloads Report | Download Stats |
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