katdetectr
This is the development version of katdetectr; for the stable release version, see katdetectr.
Detection, Characterization and Visualization of Kataegis in Sequencing Data
Bioconductor version: Development (3.24)
Kataegis refers to the occurrence of regional hypermutation and is a phenomenon observed in a wide range of malignancies. Using changepoint detection katdetectr aims to identify putative kataegis foci from common data-formats housing genomic variants. Katdetectr has shown to be a robust package for the detection, characterization and visualization of kataegis.
Author: Daan Hazelaar [aut, cre]
, Job van Riet [aut]
, Harmen van de Werken [ths]
Maintainer: Daan Hazelaar <daanhazelaar at gmail.com>
citation("katdetectr")):
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("katdetectr")
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("katdetectr")| Overview_katdetectr | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, SNP, Sequencing, Software, VariantAnnotation, WholeGenome |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.2) |
| Imports | Biobase(>= 2.54.0), BiocParallel(>= 1.26.2), BSgenome(>= 1.62.0), BSgenome.Hsapiens.UCSC.hg19(>= 1.4.3), BSgenome.Hsapiens.UCSC.hg38(>= 1.4.4), changepoint (>= 2.2.3), changepoint.np (>= 1.0.3), checkmate (>= 2.0.0), dplyr (>= 1.0.8), GenomeInfoDb(>= 1.28.4), GenomicRanges(>= 1.44.0), ggplot2 (>= 3.3.5), ggtext (>= 0.1.1), IRanges(>= 2.26.0), maftools(>= 2.10.5), methods (>= 4.1.3), plyranges(>= 1.17.0), Rdpack (>= 2.3.1), rlang (>= 1.0.2), S4Vectors(>= 0.30.2), scales (>= 1.2.0), tibble (>= 3.1.6), tidyr (>= 1.2.0), tools, utils, VariantAnnotation(>= 1.38.0) |
| System Requirements | |
| URL | https://doi.org/doi:10.18129/B9.bioc.katdetectr |
| Bug Reports | https://github.com/ErasmusMC-CCBC/katdetectr/issues |
See More
| Suggests | BiocStyle(>= 2.26.0), knitr (>= 1.37), rmarkdown (>= 2.13), stats, testthat (>= 3.0.0) |
| 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 | katdetectr_1.15.0.tar.gz |
| Windows Binary (x86_64) | katdetectr_1.15.0.zip |
| macOS Binary (big-sur-x86_64) | katdetectr_1.15.0.tgz |
| macOS Binary (sonoma-arm64) | katdetectr_1.15.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/katdetectr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/katdetectr |
| Bioc Package Browser | https://code.bioconductor.org/browse/katdetectr/ |
| Package Short Url | https://bioconductor.org/packages/katdetectr/ |
| Package Downloads Report | Download Stats |