:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-vulcan' .. highlight: bash bioconductor-vulcan =================== .. conda:recipe:: bioconductor-vulcan :replaces_section_title: :noindex: VirtUaL ChIP\-Seq data Analysis using Networks :homepage: https://bioconductor.org/packages/3.18/bioc/html/vulcan.html :license: LGPL-3 :recipe: /`bioconductor-vulcan `_/`meta.yaml `_ Vulcan \(VirtUaL ChIP\-Seq Analysis through Networks\) is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a differential binding signature coming from ChIP\-Seq data. In order to do so\, our package combines strategies from different BioConductor packages\: DESeq for data normalization\, ChIPpeakAnno and DiffBind for annotation and definition of ChIP\-Seq genomic peaks\, csaw to define optimal peak width and viper for applying a regulatory network over a differential binding signature. .. conda:package:: bioconductor-vulcan |downloads_bioconductor-vulcan| |docker_bioconductor-vulcan| :versions: ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.4.0-0`` :depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-chippeakanno: ``>=3.36.0,<3.37.0`` :depends bioconductor-csaw: ``>=1.36.0,<1.37.0`` :depends bioconductor-deseq2: ``>=1.42.0,<1.43.0`` :depends bioconductor-diffbind: ``>=3.12.0,<3.13.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene: ``>=3.2.0,<3.3.0`` :depends bioconductor-viper: ``>=1.36.0,<1.37.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-catools: :depends r-gplots: :depends r-locfit: :depends r-wordcloud: :depends r-zoo: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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-vulcan and update with:: mamba update bioconductor-vulcan To create a new environment, run:: mamba create --name myenvname bioconductor-vulcan 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-vulcan: (see `bioconductor-vulcan/tags`_ for valid values for ````) .. |downloads_bioconductor-vulcan| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-vulcan.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-vulcan :alt: (downloads) .. |docker_bioconductor-vulcan| image:: https://quay.io/repository/biocontainers/bioconductor-vulcan/status :target: https://quay.io/repository/biocontainers/bioconductor-vulcan .. _`bioconductor-vulcan/tags`: https://quay.io/repository/biocontainers/bioconductor-vulcan?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-vulcan/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-vulcan/README.html