- 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:
- 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¶
- versions:
2.4.0-0,2.2.1-0,2.0.0-1,2.0.0-0,1.20.0-2,1.20.0-1,1.20.0-0,1.18.0-0,1.16.0-1,2.4.0-0,2.2.1-0,2.0.0-1,2.0.0-0,1.20.0-2,1.20.0-1,1.20.0-0,1.18.0-0,1.16.0-1,1.16.0-0,1.14.0-0,1.12.0-0,1.10.0-1,1.8.0-0,1.6.1-0,1.4.0-0,1.2.2-0,1.0.1-0- 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
myenvnamebeing 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>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-signer/README.html)
