recipe bioconductor-genomicozone

Delineate outstanding genomic zones of differential gene activity

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/GenomicOZone.html

License:

LGPL (>=3)

Recipe:

/bioconductor-genomicozone/meta.yaml

The package clusters gene activity along chromosome into zones, detects differential zones as outstanding, and visualizes maps of outstanding zones across the genome. It enables characterization of effects on multiple genes within adaptive genomic neighborhoods, which could arise from genome reorganization, structural variation, or epigenome alteration. It guarantees cluster optimality, linear runtime to sample size, and reproducibility. One can apply it on genome-wide activity measurements such as copy number, transcriptomic, proteomic, and methylation data.

package bioconductor-genomicozone

versions:

1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-ggbio:

>=1.50.0,<1.51.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ckmeans.1d.dp:

>=4.3.0

depends r-ggplot2:

depends r-gridextra:

depends r-lsr:

depends r-plyr:

depends r-rdpack:

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-genomicozone

and update with::

   mamba update bioconductor-genomicozone

To create a new environment, run:

mamba create --name myenvname bioconductor-genomicozone

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-genomicozone:<tag>

(see `bioconductor-genomicozone/tags`_ for valid values for ``<tag>``)

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