:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-outrider' .. highlight: bash bioconductor-outrider ===================== .. conda:recipe:: bioconductor-outrider :replaces_section_title: :noindex: OUTRIDER \- OUTlier in RNA\-Seq fInDER :homepage: https://bioconductor.org/packages/3.18/bioc/html/OUTRIDER.html :license: MIT + file LICENSE :recipe: /`bioconductor-outrider `_/`meta.yaml `_ Identification of aberrant gene expression in RNA\-seq data. Read count expectations are modeled by an autoencoder to control for confounders in the data. Given these expectations\, the RNA\-seq read counts are assumed to follow a negative binomial distribution with a gene\-specific dispersion. Outliers are then identified as read counts that significantly deviate from this distribution. Furthermore\, OUTRIDER provides useful plotting functions to analyze and visualize the results. .. conda:package:: bioconductor-outrider |downloads_bioconductor-outrider| |docker_bioconductor-outrider| :versions: .. raw:: html
1.20.0-01.18.1-01.16.0-11.16.0-01.12.0-21.12.0-11.12.0-01.10.0-01.8.0-1 ``1.20.0-0``,  ``1.18.1-0``,  ``1.16.0-1``,  ``1.16.0-0``,  ``1.12.0-2``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-1``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-1``,  ``1.0.2-0``,  ``1.0.1-0`` .. raw:: html
:depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0a0`` :depends bioconductor-deseq2: ``>=1.42.0,<1.43.0`` :depends bioconductor-deseq2: ``>=1.42.0,<1.43.0a0`` :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-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0`` :depends bioconductor-pcamethods: ``>=1.94.0,<1.95.0`` :depends bioconductor-pcamethods: ``>=1.94.0,<1.95.0a0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-s4vectors: ``>=0.40.2,<0.41.0a0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0a0`` :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-bbmisc: :depends r-data.table: :depends r-generics: :depends r-ggplot2: :depends r-heatmaply: :depends r-matrixstats: :depends r-pheatmap: :depends r-plotly: :depends r-plyr: :depends r-prroc: :depends r-rcolorbrewer: :depends r-rcpp: :depends r-rcpparmadillo: :depends r-reshape2: :depends r-scales: :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-outrider and update with:: mamba update bioconductor-outrider To create a new environment, run:: mamba create --name myenvname bioconductor-outrider 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-outrider: (see `bioconductor-outrider/tags`_ for valid values for ````) .. |downloads_bioconductor-outrider| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-outrider.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-outrider :alt: (downloads) .. |docker_bioconductor-outrider| image:: https://quay.io/repository/biocontainers/bioconductor-outrider/status :target: https://quay.io/repository/biocontainers/bioconductor-outrider .. _`bioconductor-outrider/tags`: https://quay.io/repository/biocontainers/bioconductor-outrider?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-outrider/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-outrider/README.html