:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-trena' .. highlight: bash bioconductor-trena ================== .. conda:recipe:: bioconductor-trena :replaces_section_title: :noindex: Fit transcriptional regulatory networks using gene expression\, priors\, machine learning :homepage: https://bioconductor.org/packages/3.17/bioc/html/trena.html :license: GPL-3 :recipe: /`bioconductor-trena `_/`meta.yaml `_ Methods for reconstructing transcriptional regulatory networks\, especially in species for which genome\-wide TF binding site information is available. .. conda:package:: bioconductor-trena |downloads_bioconductor-trena| |docker_bioconductor-trena| :versions: ``1.20.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.11.6-0``,  ``1.8.0-0``,  ``1.6.1-0``,  ``1.4.2-0`` :depends bioconductor-annotationdbi: ``>=1.60.0,<1.61.0`` :depends bioconductor-biomart: ``>=2.54.0,<2.55.0`` :depends bioconductor-biostrings: ``>=2.66.0,<2.67.0`` :depends bioconductor-bsgenome: ``>=1.66.0,<1.67.0`` :depends bioconductor-bsgenome.hsapiens.ucsc.hg19: ``>=1.4.0,<1.5.0`` :depends bioconductor-bsgenome.hsapiens.ucsc.hg38: ``>=1.4.0,<1.5.0`` :depends bioconductor-bsgenome.mmusculus.ucsc.mm10: ``>=1.4.0,<1.5.0`` :depends bioconductor-genomicranges: ``>=1.50.0,<1.51.0`` :depends bioconductor-motifdb: ``>=1.40.0,<1.41.0`` :depends bioconductor-org.hs.eg.db: ``>=3.16.0,<3.17.0`` :depends bioconductor-snplocs.hsapiens.dbsnp150.grch38: ``>=0.99.0,<0.100.0`` :depends r-base: ``>=4.2,<4.3.0a0`` :depends r-dbi: :depends r-glmnet: ``>=2.0.3`` :depends r-lassopv: :depends r-randomforest: :depends r-rmysql: :depends r-rpostgresql: :depends r-rsqlite: :depends r-wgcna: :depends r-xgboost: :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-trena and update with:: mamba update bioconductor-trena To create a new environment, run:: mamba create --name myenvname bioconductor-trena 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-trena: (see `bioconductor-trena/tags`_ for valid values for ````) .. |downloads_bioconductor-trena| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-trena.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-trena :alt: (downloads) .. |docker_bioconductor-trena| image:: https://quay.io/repository/biocontainers/bioconductor-trena/status :target: https://quay.io/repository/biocontainers/bioconductor-trena .. _`bioconductor-trena/tags`: https://quay.io/repository/biocontainers/bioconductor-trena?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-trena/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-trena/README.html