:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-hermes' .. highlight: bash bioconductor-hermes =================== .. conda:recipe:: bioconductor-hermes :replaces_section_title: :noindex: Preprocessing\, analyzing\, and reporting of RNA\-seq data :homepage: https://bioconductor.org/packages/3.18/bioc/html/hermes.html :license: Apache License 2.0 | file LICENSE :recipe: /`bioconductor-hermes `_/`meta.yaml `_ Provides classes and functions for quality control\, filtering\, normalization and differential expression analysis of pre\-processed RNA\-seq data. Data can be imported from \`SummarizedExperiment\` as well as \`matrix\` objects and can be annotated from BioMart. Filtering for genes without too low expression or containing required annotations\, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including \`cpm\`\, \`rpkm\` and \`tpm\` can be used\, and \`DESeq2\` as well as \`voom\` differential expression analyses are available. .. conda:package:: bioconductor-hermes |downloads_bioconductor-hermes| |docker_bioconductor-hermes| :versions: ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-0`` :depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biomart: ``>=2.58.0,<2.59.0`` :depends bioconductor-complexheatmap: ``>=2.18.0,<2.19.0`` :depends bioconductor-deseq2: ``>=1.42.0,<1.43.0`` :depends bioconductor-edger: ``>=4.0.0,<4.1.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-multiassayexperiment: ``>=1.28.0,<1.29.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-assertthat: :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-checkmate: ``>=2.1`` :depends r-circlize: :depends r-dplyr: :depends r-envstats: :depends r-forcats: :depends r-ggfortify: :depends r-ggplot2: :depends r-ggrepel: ``>=0.9`` :depends r-lifecycle: :depends r-magrittr: :depends r-matrixstats: :depends r-purrr: :depends r-r6: :depends r-rdpack: :depends r-rlang: :depends r-tidyr: :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-hermes and update with:: mamba update bioconductor-hermes To create a new environment, run:: mamba create --name myenvname bioconductor-hermes 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-hermes: (see `bioconductor-hermes/tags`_ for valid values for ````) .. |downloads_bioconductor-hermes| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-hermes.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-hermes :alt: (downloads) .. |docker_bioconductor-hermes| image:: https://quay.io/repository/biocontainers/bioconductor-hermes/status :target: https://quay.io/repository/biocontainers/bioconductor-hermes .. _`bioconductor-hermes/tags`: https://quay.io/repository/biocontainers/bioconductor-hermes?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-hermes/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-hermes/README.html