- recipe bioconductor-katdetectr
Detection, Characterization and Visualization of Kataegis in Sequencing Data
- Homepage:
https://bioconductor.org/packages/3.17/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:
1.2.0-0,1.0.0-0- depends bioconductor-biobase:
>=2.60.0,<2.61.0- depends bioconductor-biocparallel:
>=1.34.0,<1.35.0- depends bioconductor-bsgenome:
>=1.68.0,<1.69.0- depends bioconductor-bsgenome.hsapiens.ucsc.hg19:
>=1.4.0,<1.5.0- depends bioconductor-bsgenome.hsapiens.ucsc.hg38:
>=1.4.0,<1.5.0- depends bioconductor-genomeinfodb:
>=1.36.0,<1.37.0- depends bioconductor-genomicranges:
>=1.52.0,<1.53.0- depends bioconductor-iranges:
>=2.34.0,<2.35.0- depends bioconductor-maftools:
>=2.16.0,<2.17.0- depends bioconductor-plyranges:
>=1.20.0,<1.21.0- depends bioconductor-s4vectors:
>=0.38.0,<0.39.0- depends bioconductor-variantannotation:
>=1.46.0,<1.47.0- depends r-base:
>=4.3,<4.4.0a0- depends r-changepoint:
>=2.2.3- depends r-changepoint.np:
>=1.0.3- depends r-checkmate:
>=2.0.0- depends r-dplyr:
>=1.0.8- depends r-ggplot2:
>=3.3.5- depends r-ggtext:
>=0.1.1- depends r-rdpack:
>=2.3.1- depends r-rlang:
>=1.0.2- depends r-tibble:
>=3.1.6- depends r-tidyr:
>=1.2.0- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-katdetectr and update with:: mamba update bioconductor-katdetectr
To create a new environment, run:
mamba create --name myenvname bioconductor-katdetectr
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, 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)
