:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-rgreat' .. highlight: bash bioconductor-rgreat =================== .. conda:recipe:: bioconductor-rgreat :replaces_section_title: :noindex: GREAT Analysis \- Functional Enrichment on Genomic Regions :homepage: https://bioconductor.org/packages/3.18/bioc/html/rGREAT.html :license: MIT + file LICENSE :recipe: /`bioconductor-rgreat `_/`meta.yaml `_ :links: biotools: :biotools:`rgreat`, doi: :doi:`10.1038/nmeth.3252` GREAT \(Genomic Regions Enrichment of Annotations Tool\) is a type of functional enrichment analysis directly performed on genomic regions. This package implements the GREAT algorithm \(the local GREAT analysis\)\, also it supports directly interacting with the GREAT web service \(the online GREAT analysis\). Both analysis can be viewed by a Shiny application. rGREAT by default supports more than 600 organisms and a large number of gene set collections\, as well as self\-provided gene sets and organisms from users. Additionally\, it implements a general method for dealing with background regions. .. conda:package:: bioconductor-rgreat |downloads_bioconductor-rgreat| |docker_bioconductor-rgreat| :versions: .. raw:: html
2.4.0-02.2.0-02.0.0-12.0.0-01.26.0-01.24.0-01.22.0-11.22.0-01.20.0-0 ``2.4.0-0``,  ``2.2.0-0``,  ``2.0.0-1``,  ``2.0.0-0``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-1``,  ``1.14.0-0``,  ``1.12.1-0``,  ``1.11.1-0``,  ``1.8.0-0`` .. raw:: html
:depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0`` :depends bioconductor-annotationdbi: ``>=1.64.1,<1.65.0a0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomeinfodb: ``>=1.38.1,<1.39.0a0`` :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicfeatures: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicranges: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-go.db: ``>=3.18.0,<3.19.0`` :depends bioconductor-go.db: ``>=3.18.0,<3.19.0a0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0`` :depends bioconductor-org.hs.eg.db: ``>=3.18.0,<3.19.0`` :depends bioconductor-org.hs.eg.db: ``>=3.18.0,<3.19.0a0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-s4vectors: ``>=0.40.2,<0.41.0a0`` :depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene: ``>=3.2.0,<3.3.0`` :depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene: ``>=3.2.2,<3.3.0a0`` :depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene: ``>=3.18.0,<3.19.0`` :depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene: ``>=3.18.0,<3.19.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends libstdcxx-ng: ``>=12`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-circlize: :depends r-digest: :depends r-doparallel: :depends r-dt: :depends r-foreach: :depends r-getoptlong: ``>=0.0.9`` :depends r-globaloptions: :depends r-progress: :depends r-rcolorbrewer: :depends r-rcpp: :depends r-rcurl: :depends r-rjson: :depends r-shiny: :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-rgreat and update with:: mamba update bioconductor-rgreat To create a new environment, run:: mamba create --name myenvname bioconductor-rgreat 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-rgreat: (see `bioconductor-rgreat/tags`_ for valid values for ````) .. |downloads_bioconductor-rgreat| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-rgreat.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-rgreat :alt: (downloads) .. |docker_bioconductor-rgreat| image:: https://quay.io/repository/biocontainers/bioconductor-rgreat/status :target: https://quay.io/repository/biocontainers/bioconductor-rgreat .. _`bioconductor-rgreat/tags`: https://quay.io/repository/biocontainers/bioconductor-rgreat?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-rgreat/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-rgreat/README.html