- recipe bioconductor-katdetectr
Detection, Characterization and Visualization of Kataegis in Sequencing Data
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/katdetectr.html
- License:
GPL-3 + file LICENSE
- Recipe:
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.
- package bioconductor-katdetectr¶
-
- Versions:
1.0.0-0
- Depends:
bioconductor-biobase
>=2.58.0,<2.59.0
bioconductor-biocparallel
>=1.32.0,<1.33.0
bioconductor-bsgenome
>=1.66.0,<1.67.0
bioconductor-bsgenome.hsapiens.ucsc.hg19
>=1.4.0,<1.5.0
bioconductor-bsgenome.hsapiens.ucsc.hg38
>=1.4.0,<1.5.0
bioconductor-genomeinfodb
>=1.34.0,<1.35.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-iranges
>=2.32.0,<2.33.0
bioconductor-maftools
>=2.14.0,<2.15.0
bioconductor-plyranges
>=1.18.0,<1.19.0
bioconductor-s4vectors
>=0.36.0,<0.37.0
bioconductor-variantannotation
>=1.44.0,<1.45.0
r-base
>=4.2,<4.3.0a0
r-changepoint
>=2.2.3
r-changepoint.np
>=1.0.3
r-checkmate
>=2.0.0
r-dplyr
>=1.0.8
r-ggplot2
>=3.3.5
r-ggtext
>=0.1.1
r-rdpack
>=2.3.1
r-rlang
>=1.0.2
r-tibble
>=3.1.6
r-tidyr
>=1.2.0
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install bioconductor-katdetectr
and update with:
conda update bioconductor-katdetectr
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-katdetectr:<tag>
(see bioconductor-katdetectr/tags for valid values for
<tag>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-katdetectr/README.html)