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 (3.20)
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 "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 1.33.0 |
In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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_1.33.0.tar.gz |
Windows Binary | BadRegionFinder_1.33.0.zip |
macOS Binary (x86_64) | BadRegionFinder_1.33.0.tgz |
macOS Binary (arm64) | BadRegionFinder_1.33.0.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 |