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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.41.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 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_1.41.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | BadRegionFinder_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | BadRegionFinder_1.41.0.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 |