:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-epiregulon' .. highlight: bash bioconductor-epiregulon ======================= .. conda:recipe:: bioconductor-epiregulon :replaces_section_title: :noindex: Gene regulatory network inference from single cell epigenomic data :homepage: https://bioconductor.org/packages/3.20/bioc/html/epiregulon.html :license: MIT + file LICENSE :recipe: /`bioconductor-epiregulon `_/`meta.yaml `_ Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network \(regulons\). This is achieved through integration of scATAC\-seq and scRNA\-seq data and incorporation of public bulk TF ChIP\-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions. .. conda:package:: bioconductor-epiregulon |downloads_bioconductor-epiregulon| |docker_bioconductor-epiregulon| :versions: ``1.2.0-0`` :depends bioconductor-annotationhub: ``>=3.14.0,<3.15.0`` :depends bioconductor-annotationhub: ``>=3.14.0,<3.15.0a0`` :depends bioconductor-assorthead: ``>=1.0.0,<1.1.0`` :depends bioconductor-assorthead: ``>=1.0.0,<1.1.0a0`` :depends bioconductor-aucell: ``>=1.28.0,<1.29.0`` :depends bioconductor-aucell: ``>=1.28.0,<1.29.0a0`` :depends bioconductor-beachmat: ``>=2.22.0,<2.23.0`` :depends bioconductor-beachmat: ``>=2.22.0,<2.23.0a0`` :depends bioconductor-biocparallel: ``>=1.40.0,<1.41.0`` :depends bioconductor-biocparallel: ``>=1.40.0,<1.41.0a0`` :depends bioconductor-bluster: ``>=1.16.0,<1.17.0`` :depends bioconductor-bluster: ``>=1.16.0,<1.17.0a0`` :depends bioconductor-bsgenome.hsapiens.ucsc.hg19: ``>=1.4.0,<1.5.0`` :depends bioconductor-bsgenome.hsapiens.ucsc.hg19: ``>=1.4.3,<1.5.0a0`` :depends bioconductor-bsgenome.hsapiens.ucsc.hg38: ``>=1.4.0,<1.5.0`` :depends bioconductor-bsgenome.hsapiens.ucsc.hg38: ``>=1.4.5,<1.5.0a0`` :depends bioconductor-bsgenome.mmusculus.ucsc.mm10: ``>=1.4.0,<1.5.0`` :depends bioconductor-bsgenome.mmusculus.ucsc.mm10: ``>=1.4.3,<1.5.0a0`` :depends bioconductor-experimenthub: ``>=2.14.0,<2.15.0`` :depends bioconductor-experimenthub: ``>=2.14.0,<2.15.0a0`` :depends bioconductor-genomeinfodb: ``>=1.42.0,<1.43.0`` :depends bioconductor-genomeinfodb: ``>=1.42.0,<1.43.0a0`` :depends bioconductor-genomicranges: ``>=1.58.0,<1.59.0`` :depends bioconductor-genomicranges: ``>=1.58.0,<1.59.0a0`` :depends bioconductor-iranges: ``>=2.40.0,<2.41.0`` :depends bioconductor-iranges: ``>=2.40.0,<2.41.0a0`` :depends bioconductor-motifmatchr: ``>=1.28.0,<1.29.0`` :depends bioconductor-motifmatchr: ``>=1.28.0,<1.29.0a0`` :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0`` :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0a0`` :depends bioconductor-scmultiome: ``>=1.6.0,<1.7.0`` :depends bioconductor-scmultiome: ``>=1.6.0,<1.7.0a0`` :depends bioconductor-scran: ``>=1.34.0,<1.35.0`` :depends bioconductor-scran: ``>=1.34.0,<1.35.0a0`` :depends bioconductor-scuttle: ``>=1.16.0,<1.17.0`` :depends bioconductor-scuttle: ``>=1.16.0,<1.17.0a0`` :depends bioconductor-singlecellexperiment: ``>=1.28.0,<1.29.0`` :depends bioconductor-singlecellexperiment: ``>=1.28.0,<1.29.0a0`` :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0`` :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc: ``>=13`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends libstdcxx: ``>=13`` :depends r-base: ``>=4.4,<4.5.0a0`` :depends r-checkmate: :depends r-entropy: :depends r-lifecycle: :depends r-matrix: :depends r-rcpp: :requirements: :additional platforms: .. 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-epiregulon and update with:: mamba update bioconductor-epiregulon To create a new environment, run:: mamba create --name myenvname bioconductor-epiregulon 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-epiregulon: (see `bioconductor-epiregulon/tags`_ for valid values for ````) .. |downloads_bioconductor-epiregulon| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-epiregulon.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-epiregulon :alt: (downloads) .. |docker_bioconductor-epiregulon| image:: https://quay.io/repository/biocontainers/bioconductor-epiregulon/status :target: https://quay.io/repository/biocontainers/bioconductor-epiregulon .. _`bioconductor-epiregulon/tags`: https://quay.io/repository/biocontainers/bioconductor-epiregulon?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-epiregulon/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-epiregulon/README.html