:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-gothic' .. highlight: bash bioconductor-gothic =================== .. conda:recipe:: bioconductor-gothic :replaces_section_title: :noindex: Binomial test for Hi\-C data analysis :homepage: https://bioconductor.org/packages/3.18/bioc/html/GOTHiC.html :license: GPL-3 :recipe: /`bioconductor-gothic `_/`meta.yaml `_ :links: biotools: :biotools:`gothic`, doi: :doi:`10.1101/gr.185272.114` This is a Hi\-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi\-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome. .. conda:package:: bioconductor-gothic |downloads_bioconductor-gothic| |docker_bioconductor-gothic| :versions: .. raw:: html
1.38.0-01.36.0-01.34.0-01.30.0-01.28.0-01.26.0-11.26.0-01.24.0-01.22.0-0 ``1.38.0-0``,  ``1.36.0-0``,  ``1.34.0-0``,  ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-1``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.6-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-0`` .. raw:: html
:depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0`` :depends bioconductor-genomeinfodb: ``>=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-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 bioconductor-shortread: ``>=1.60.0,<1.61.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-biocmanager: :depends r-data.table: :depends r-ggplot2: :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-gothic and update with:: mamba update bioconductor-gothic To create a new environment, run:: mamba create --name myenvname bioconductor-gothic 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-gothic: (see `bioconductor-gothic/tags`_ for valid values for ````) .. |downloads_bioconductor-gothic| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-gothic.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-gothic :alt: (downloads) .. |docker_bioconductor-gothic| image:: https://quay.io/repository/biocontainers/bioconductor-gothic/status :target: https://quay.io/repository/biocontainers/bioconductor-gothic .. _`bioconductor-gothic/tags`: https://quay.io/repository/biocontainers/bioconductor-gothic?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-gothic/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-gothic/README.html