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 (3.21)
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] (ORCID:
Maintainer: Daan Hazelaar <daanhazelaar at gmail.com>
citation("katdetectr")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 | 1.9.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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_1.9.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |