:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-diffbind' .. highlight: bash bioconductor-diffbind ===================== .. conda:recipe:: bioconductor-diffbind :replaces_section_title: :noindex: Differential Binding Analysis of ChIP\-Seq Peak Data :homepage: https://bioconductor.org/packages/3.18/bioc/html/DiffBind.html :license: Artistic-2.0 :recipe: /`bioconductor-diffbind `_/`meta.yaml `_ :links: biotools: :biotools:`diffbind`, usegalaxy-eu: :usegalaxy-eu:`diffbind` Compute differentially bound sites from multiple ChIP\-seq experiments using affinity \(quantitative\) data. Also enables occupancy \(overlap\) analysis and plotting functions. .. conda:package:: bioconductor-diffbind |downloads_bioconductor-diffbind| |docker_bioconductor-diffbind| :versions: .. raw:: html
3.12.0-03.10.0-03.8.0-03.4.11-13.4.11-03.4.0-03.2.7-03.2.1-03.0.15-0 ``3.12.0-0``,  ``3.10.0-0``,  ``3.8.0-0``,  ``3.4.11-1``,  ``3.4.11-0``,  ``3.4.0-0``,  ``3.2.7-0``,  ``3.2.1-0``,  ``3.0.15-0``,  ``3.0.3-0``,  ``2.16.0-2``,  ``2.16.0-1``,  ``2.16.0-0``,  ``2.14.0-0``,  ``2.12.0-1``,  ``2.10.0-1``,  ``2.10.0-0``,  ``2.8.0-0``,  ``2.6.6-0``,  ``2.6.5-0``,  ``2.6.0-0``,  ``2.4.8-16``,  ``2.2.12-1``,  ``2.2.12-0``,  ``2.0.9-3``,  ``2.0.9-2``,  ``1.16.3-0`` .. raw:: html
:depends bioconductor-apeglm: ``>=1.24.0,<1.25.0`` :depends bioconductor-apeglm: ``>=1.24.0,<1.25.0a0`` :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-genomicalignments: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0a0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicranges: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-greylistchip: ``>=1.34.0,<1.35.0`` :depends bioconductor-greylistchip: ``>=1.34.0,<1.35.0a0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-limma: ``>=3.58.1,<3.59.0a0`` :depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0`` :depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0a0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0a0`` :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 bioconductor-systempiper: ``>=2.8.0,<2.9.0`` :depends bioconductor-systempiper: ``>=2.8.0,<2.9.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends libstdcxx-ng: ``>=12`` :depends r-amap: :depends r-ashr: :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-dplyr: :depends r-ggplot2: :depends r-ggrepel: :depends r-gplots: :depends r-lattice: :depends r-locfit: :depends r-rcolorbrewer: :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-diffbind and update with:: mamba update bioconductor-diffbind To create a new environment, run:: mamba create --name myenvname bioconductor-diffbind 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-diffbind: (see `bioconductor-diffbind/tags`_ for valid values for ````) .. |downloads_bioconductor-diffbind| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-diffbind.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-diffbind :alt: (downloads) .. |docker_bioconductor-diffbind| image:: https://quay.io/repository/biocontainers/bioconductor-diffbind/status :target: https://quay.io/repository/biocontainers/bioconductor-diffbind .. _`bioconductor-diffbind/tags`: https://quay.io/repository/biocontainers/bioconductor-diffbind?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-diffbind/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-diffbind/README.html