Bioconductor - katdetectr

Bioconductor - katdetectr
Bioconductor 3.22
Software Packages
katdetectr
katdetectr
This is the
released
version of katdetectr; for the devel version, see
katdetectr
Detection, Characterization and Visualization of Kataegis in Sequencing Data
DOI:
10.18129/B9.bioc.katdetectr
Bioconductor version:
Release (3.22)
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: 0000-0002-7513-6813
, Job van Riet [aut]
ORCID: 0000-0001-7767-7923
, Harmen van de Werken [ths]
ORCID: 0000-0002-9794-1477
Maintainer:
Daan Hazelaar
Citation (from within R, enter
citation("katdetectr")
):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")

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
PDF
NEWS
Text
LICENSE
Text
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Details
biocViews
Classification
SNP
Sequencing
Software
VariantAnnotation
WholeGenome
Version
1.12.0
In Bioconductor since
BioC 3.16 (R-4.2) (3.5 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
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Suggests
BiocStyle
(>= 2.26.0),
knitr
(>= 1.37),
rmarkdown
(>= 2.13), stats,
testthat
(>= 3.0.0)
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instructions to use this package in your R session.
Source Package
katdetectr_1.12.0.tar.gz
Windows Binary (x86_64)
katdetectr_1.12.0.zip
macOS Binary (x86_64)
katdetectr_1.12.0.tgz
macOS Binary (arm64)
katdetectr_1.12.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/katdetectr
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/katdetectr
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