recipe r-pscbs

Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

Homepage:

https://github.com/HenrikBengtsson/PSCBS

License:

GPL3 / GPL-2.0-or-later

Recipe:

/r-pscbs/meta.yaml

package r-pscbs

(downloads) docker_r-pscbs

versions:
0.67.0-0,  0.66.0-2,  0.66.0-1,  0.66.0-0,  0.65.0-5,  0.65.0-4,  0.65.0-3,  0.65.0-2,  0.65.0-1, 

0.67.0-0,  0.66.0-2,  0.66.0-1,  0.66.0-0,  0.65.0-5,  0.65.0-4,  0.65.0-3,  0.65.0-2,  0.65.0-1,  0.65.0-0,  0.64.0-2,  0.64.0-1,  0.64.0-0,  0.63.0-0,  0.61.0-0,  0.60.3-0,  0.60.0-2,  0.60.0-0

depends bioconductor-aroma.light:

>=2.4.0

depends bioconductor-dnacopy:

>=1.42.0

depends r-base:

>=4.3,<4.4.0a0

depends r-future:

>=1.28.0

depends r-listenv:

>=0.8.0

depends r-matrixstats:

>=0.62.0

depends r-r.cache:

>=0.16.0

depends r-r.methodss3:

>=1.8.2

depends r-r.oo:

>=1.25.0

depends r-r.utils:

>=2.12.0

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 r-pscbs

and update with::

   mamba update r-pscbs

To create a new environment, run:

mamba create --name myenvname r-pscbs

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/r-pscbs:<tag>

(see `r-pscbs/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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