recipe r-cin-signature-quantification

Quantification of copy number signatures in cancer samples from copy number profiles. The signatures are a readout of mutational processes resulting in chromosomal instability (CIN). Methods from Drews et al. (Nature, 2022) and Macintyre et al. (Nature Genetics, 2018) are included.

Homepage:

https://github.com/markowetzlab/CINSignatureQuantification

License:

ASL

Recipe:

/r-cin-signature-quantification/meta.yaml

package r-cin-signature-quantification

versions:

1.2.0-0

depends bioconductor-biobase:

>=2.46.0

depends r-base:

>=4.5,<4.6.0a0

depends r-data.table:

>=1.14

depends r-doparallel:

>=1.0.16

depends r-foreach:

>=1.5.1

depends r-knitr:

depends r-limsolve:

>=1.5.6

depends r-rmarkdown:

depends r-stringr:

>=1.4

depends r-testthat:

>=3.0.0

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 r-cin-signature-quantification

and update with::

   mamba update r-cin-signature-quantification

To create a new environment, run:

mamba create --name myenvname r-cin-signature-quantification

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-cin-signature-quantification:<tag>

(see `r-cin-signature-quantification/tags`_ for valid values for ``<tag>``)

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