BadRegionFinder
This package is for version 3.9 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: 3.9
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("BadRegionFinder")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BadRegionFinder")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BadRegionFinder")| Using BadRegionFinder | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Classification, Coverage, Sequencing, Software, WholeGenome |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | LGPL-3 |
| Depends | |
| Imports | VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics |
| System Requirements | |
| URL |
See More
| Suggests | BSgenome.Hsapiens.UCSC.hg19 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BadRegionFinder_1.12.0.tar.gz |
| Windows Binary | BadRegionFinder_1.12.0.zip |
| Mac OS X 10.11 (El Capitan) | BadRegionFinder_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BadRegionFinder |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BadRegionFinder |
| Bioc Package Browser | https://code.bioconductor.org/browse/BadRegionFinder/ |
| Package Short Url | https://bioconductor.org/packages/BadRegionFinder/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |