recipe r-sigminer

Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Macintyre, Geoff, et al. (2018) <DOI:10.1038/s41588-018-0179-8>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.

Homepage:

https://github.com/ShixiangWang/sigminer

License:

MIT / MIT

Recipe:

/r-sigminer/meta.yaml

package r-sigminer

versions:

2.3.1-1,  2.3.1-0,  2.3.0-0,  2.2.2-0,  2.2.0-2,  2.2.0-1,  2.2.0-0,  2.1.9-2,  2.1.9-1, 

2.3.1-1,  2.3.1-0,  2.3.0-0,  2.2.2-0,  2.2.0-2,  2.2.0-1,  2.2.0-0,  2.1.9-2,  2.1.9-1,  2.1.9-0,  2.1.8-1,  2.1.8-0,  2.1.7-1,  2.1.7-0,  2.1.6-1,  2.1.6-0,  2.1.5-1,  2.1.5-0,  2.1.4-0,  2.1.3-1,  2.1.3-0,  2.1.2-1,  2.1.2-0,  2.1.1-0,  2.1.0-0,  2.0.5-0,  2.0.4-0,  2.0.3-0,  2.0.2-0,  2.0.1-1,  2.0.1-0,  2.0.0-1,  2.0.0-0,  1.2.5-1,  1.2.5-0,  1.2.4-0,  1.2.1-0

depends bioconductor-maftools:

>=2.18.0,<2.19.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-cli:

>=2.0.0

depends r-cowplot:

depends r-data.table:

depends r-dplyr:

depends r-furrr:

>=0.2.0

depends r-future:

depends r-ggplot2:

>=3.3.0

depends r-ggpubr:

depends r-magrittr:

depends r-nmf:

depends r-purrr:

depends r-rcpp:

depends r-rlang:

>=0.1.2

depends r-tidyr:

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-sigminer

and update with::

   mamba update r-sigminer

To create a new environment, run:

mamba create --name myenvname r-sigminer

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-sigminer:<tag>

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

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