:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-edger' .. highlight: bash bioconductor-edger ================== .. conda:recipe:: bioconductor-edger :replaces_section_title: :noindex: Empirical Analysis of Digital Gene Expression Data in R :homepage: https://bioconductor.org/packages/3.18/bioc/html/edgeR.html :license: GPL (>=2) :recipe: /`bioconductor-edger `_/`meta.yaml `_ :links: biotools: :biotools:`edger`, usegalaxy-eu: :usegalaxy-eu:`edger` Differential expression analysis of RNA\-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions\, including empirical Bayes estimation\, exact tests\, generalized linear models and quasi\-likelihood tests. As well as RNA\-seq\, it be applied to differential signal analysis of other types of genomic data that produce read counts\, including ChIP\-seq\, ATAC\-seq\, Bisulfite\-seq\, SAGE and CAGE. .. conda:package:: bioconductor-edger |downloads_bioconductor-edger| |docker_bioconductor-edger| :versions: .. raw:: html
4.0.2-03.42.4-03.40.0-13.40.0-03.36.0-23.36.0-13.36.0-03.34.0-03.32.1-0 ``4.0.2-0``,  ``3.42.4-0``,  ``3.40.0-1``,  ``3.40.0-0``,  ``3.36.0-2``,  ``3.36.0-1``,  ``3.36.0-0``,  ``3.34.0-0``,  ``3.32.1-0``,  ``3.32.0-0``,  ``3.30.0-0``,  ``3.28.0-1``,  ``3.28.0-0``,  ``3.26.5-0``,  ``3.26.0-0``,  ``3.24.3-0``,  ``3.24.1-0``,  ``3.22.5-0``,  ``3.20.7-0``,  ``3.20.1-0``,  ``3.20.0-0``,  ``3.18.1-0``,  ``3.16.5-0``,  ``3.14.0-1``,  ``3.14.0-0``,  ``3.12.1-1``,  ``3.12.1-0``,  ``3.12.0-0``,  ``3.10.5-0`` .. raw:: html
:depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-limma: ``>=3.58.1,<3.59.0a0`` :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-locfit: :depends r-rcpp: :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-edger and update with:: mamba update bioconductor-edger To create a new environment, run:: mamba create --name myenvname bioconductor-edger 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-edger: (see `bioconductor-edger/tags`_ for valid values for ````) .. |downloads_bioconductor-edger| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-edger.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-edger :alt: (downloads) .. |docker_bioconductor-edger| image:: https://quay.io/repository/biocontainers/bioconductor-edger/status :target: https://quay.io/repository/biocontainers/bioconductor-edger .. _`bioconductor-edger/tags`: https://quay.io/repository/biocontainers/bioconductor-edger?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-edger/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-edger/README.html