recipe bioconductor-signer

Empirical Bayesian approach to mutational signature discovery

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-signer/meta.yaml

Links:

biotools: signer

The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variation (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.

package bioconductor-signer

(downloads) docker_bioconductor-signer

versions:
2.4.0-02.2.1-02.0.0-12.0.0-01.20.0-21.20.0-11.20.0-01.18.0-01.16.0-1

2.4.0-02.2.1-02.0.0-12.0.0-01.20.0-21.20.0-11.20.0-01.18.0-01.16.0-11.16.0-01.14.0-01.12.0-01.10.0-11.8.0-01.6.1-01.4.0-01.2.2-01.0.1-0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-biocfilecache:

>=2.10.1,<2.11.0a0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocgenerics:

>=0.48.1,<0.49.0a0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-biostrings:

>=2.70.1,<2.71.0a0

depends bioconductor-bsgenome:

>=1.70.0,<1.71.0

depends bioconductor-bsgenome:

>=1.70.1,<1.71.0a0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomeinfodb:

>=1.38.1,<1.39.0a0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.1,<1.55.0a0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0a0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0a0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

depends bioconductor-variantannotation:

>=1.48.1,<1.49.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-ada:

depends r-base:

>=4.3,<4.4.0a0

depends r-bsplus:

depends r-class:

depends r-clue:

depends r-cowplot:

depends r-dplyr:

depends r-dt:

depends r-e1071:

depends r-future:

depends r-future.apply:

depends r-ggplot2:

depends r-ggpubr:

depends r-glmnet:

depends r-kknn:

depends r-listenv:

depends r-magrittr:

depends r-mass:

depends r-maxstat:

depends r-nloptr:

depends r-nmf:

depends r-pheatmap:

depends r-pmcmrplus:

depends r-ppclust:

depends r-proc:

depends r-proxy:

depends r-pvclust:

depends r-randomforest:

depends r-rcolorbrewer:

depends r-rcpp:

depends r-rcpparmadillo:

>=0.7.100

depends r-readr:

depends r-reshape2:

depends r-scales:

depends r-shiny:

depends r-shinycssloaders:

depends r-shinydashboard:

depends r-shinywidgets:

depends r-survival:

depends r-survivalanalysis:

depends r-survminer:

depends r-tibble:

depends r-tidyr:

depends r-vgam:

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-signer

and update with::

   mamba update bioconductor-signer

To create a new environment, run:

mamba create --name myenvname bioconductor-signer

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-signer:<tag>

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

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