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:

/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:

1.0.0-0

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

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