:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-diffhic' .. highlight: bash bioconductor-diffhic ==================== .. conda:recipe:: bioconductor-diffhic :replaces_section_title: :noindex: Differential Analysis of Hi\-C Data :homepage: https://bioconductor.org/packages/3.20/bioc/html/diffHic.html :license: GPL-3 :recipe: /`bioconductor-diffhic `_/`meta.yaml `_ :links: biotools: :biotools:`diffhic` Detects differential interactions across biological conditions in a Hi\-C experiment. Methods are provided for read alignment and data pre\-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available. .. conda:package:: bioconductor-diffhic |downloads_bioconductor-diffhic| |docker_bioconductor-diffhic| :versions: .. raw:: html
1.38.0-01.34.0-11.34.0-01.32.0-01.30.0-11.30.0-01.26.0-21.26.0-11.26.0-0 ``1.38.0-0``,  ``1.34.0-1``,  ``1.34.0-0``,  ``1.32.0-0``,  ``1.30.0-1``,  ``1.30.0-0``,  ``1.26.0-2``,  ``1.26.0-1``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-1``,  ``1.14.0-0`` .. raw:: html
:depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0`` :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0a0`` :depends bioconductor-biostrings: ``>=2.74.0,<2.75.0`` :depends bioconductor-biostrings: ``>=2.74.0,<2.75.0a0`` :depends bioconductor-bsgenome: ``>=1.74.0,<1.75.0`` :depends bioconductor-bsgenome: ``>=1.74.0,<1.75.0a0`` :depends bioconductor-csaw: ``>=1.40.0,<1.41.0`` :depends bioconductor-csaw: ``>=1.40.0,<1.41.0a0`` :depends bioconductor-edger: ``>=4.4.0,<4.5.0`` :depends bioconductor-edger: ``>=4.4.0,<4.5.0a0`` :depends bioconductor-genomeinfodb: ``>=1.42.0,<1.43.0`` :depends bioconductor-genomeinfodb: ``>=1.42.0,<1.43.0a0`` :depends bioconductor-genomicranges: ``>=1.58.0,<1.59.0`` :depends bioconductor-genomicranges: ``>=1.58.0,<1.59.0a0`` :depends bioconductor-interactionset: ``>=1.34.0,<1.35.0`` :depends bioconductor-interactionset: ``>=1.34.0,<1.35.0a0`` :depends bioconductor-iranges: ``>=2.40.0,<2.41.0`` :depends bioconductor-iranges: ``>=2.40.0,<2.41.0a0`` :depends bioconductor-limma: ``>=3.62.0,<3.63.0`` :depends bioconductor-limma: ``>=3.62.0,<3.63.0a0`` :depends bioconductor-rhdf5: ``>=2.50.0,<2.51.0`` :depends bioconductor-rhdf5: ``>=2.50.0,<2.51.0a0`` :depends bioconductor-rhtslib: ``>=3.2.0,<3.3.0`` :depends bioconductor-rhtslib: ``>=3.2.0,<3.3.0a0`` :depends bioconductor-rsamtools: ``>=2.22.0,<2.23.0`` :depends bioconductor-rsamtools: ``>=2.22.0,<2.23.0a0`` :depends bioconductor-rtracklayer: ``>=1.66.0,<1.67.0`` :depends bioconductor-rtracklayer: ``>=1.66.0,<1.67.0a0`` :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0`` :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0a0`` :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0`` :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0a0`` :depends bioconductor-zlibbioc: ``>=1.52.0,<1.53.0`` :depends bioconductor-zlibbioc: ``>=1.52.0,<1.53.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc: ``>=13`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends liblzma: ``>=5.6.3,<6.0a0`` :depends libstdcxx: ``>=13`` :depends libzlib: ``>=1.3.1,<2.0a0`` :depends r-base: ``>=4.4,<4.5.0a0`` :depends r-locfit: :depends r-rcpp: :requirements: :additional platforms: .. raw:: html linux-aarch64 .. 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-diffhic and update with:: mamba update bioconductor-diffhic To create a new environment, run:: mamba create --name myenvname bioconductor-diffhic 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-diffhic: (see `bioconductor-diffhic/tags`_ for valid values for ````) .. |downloads_bioconductor-diffhic| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-diffhic.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-diffhic :alt: (downloads) .. |docker_bioconductor-diffhic| image:: https://quay.io/repository/biocontainers/bioconductor-diffhic/status :target: https://quay.io/repository/biocontainers/bioconductor-diffhic .. _`bioconductor-diffhic/tags`: https://quay.io/repository/biocontainers/bioconductor-diffhic?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-diffhic/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-diffhic/README.html