:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-derfinder' .. highlight: bash bioconductor-derfinder ====================== .. conda:recipe:: bioconductor-derfinder :replaces_section_title: :noindex: Annotation\-agnostic differential expression analysis of RNA\-seq data at base\-pair resolution via the DER Finder approach :homepage: https://bioconductor.org/packages/3.18/bioc/html/derfinder.html :license: Artistic-2.0 :recipe: /`bioconductor-derfinder `_/`meta.yaml `_ :links: biotools: :biotools:`derfinder` This package provides functions for annotation\-agnostic differential expression analysis of RNA\-seq data. Two implementations of the DER Finder approach are included in this package\: \(1\) single base\-level F\-statistics and \(2\) DER identification at the expressed regions\-level. The DER Finder approach can also be used to identify differentially bounded ChIP\-seq peaks. .. conda:package:: bioconductor-derfinder |downloads_bioconductor-derfinder| |docker_bioconductor-derfinder| :versions: .. raw:: html
1.36.0-01.34.0-01.32.0-01.28.0-01.26.0-01.24.2-01.24.0-01.22.0-01.20.0-0 ``1.36.0-0``,  ``1.34.0-0``,  ``1.32.0-0``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.2-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.3-0``,  ``1.16.1-0``,  ``1.14.0-0``,  ``1.12.0-0`` .. raw:: html
:depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-bumphunter: ``>=1.44.0,<1.45.0`` :depends bioconductor-derfinderhelper: ``>=1.36.0,<1.37.0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicfiles: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-qvalue: ``>=2.34.0,<2.35.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-hmisc: :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-derfinder and update with:: mamba update bioconductor-derfinder To create a new environment, run:: mamba create --name myenvname bioconductor-derfinder 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-derfinder: (see `bioconductor-derfinder/tags`_ for valid values for ````) .. |downloads_bioconductor-derfinder| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-derfinder.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-derfinder :alt: (downloads) .. |docker_bioconductor-derfinder| image:: https://quay.io/repository/biocontainers/bioconductor-derfinder/status :target: https://quay.io/repository/biocontainers/bioconductor-derfinder .. _`bioconductor-derfinder/tags`: https://quay.io/repository/biocontainers/bioconductor-derfinder?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-derfinder/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-derfinder/README.html