recipe bioconductor-katdetectr

Detection, Characterization and Visualization of Kataegis in Sequencing Data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/katdetectr.html

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-katdetectr/meta.yaml

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:

1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-bsgenome:

>=1.74.0,<1.75.0

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:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-maftools:

>=2.22.0,<2.23.0

depends bioconductor-plyranges:

>=1.26.0,<1.27.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-variantannotation:

>=1.52.0,<1.53.0

depends r-base:

>=4.4,<4.5.0a0

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-scales:

>=1.2.0

depends r-tibble:

>=3.1.6

depends r-tidyr:

>=1.2.0

requirements:

additional platforms:

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 myenvname being 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>``)

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Link to this page

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-katdetectr/README.html)