:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-spectraltad' .. highlight: bash bioconductor-spectraltad ======================== .. conda:recipe:: bioconductor-spectraltad :replaces_section_title: :noindex: SpectralTAD\: Hierarchical TAD detection using spectral clustering :homepage: https://bioconductor.org/packages/3.14/bioc/html/SpectralTAD.html :license: MIT + file LICENSE :recipe: /`bioconductor-spectraltad `_/`meta.yaml `_ SpectralTAD is an R package designed to identify Topologically Associated Domains \(TADs\) from Hi\-C contact matrices. It uses a modified version of spectral clustering that uses a sliding window to quickly detect TADs. The function works on a range of different formats of contact matrices and returns a bed file of TAD coordinates. The method does not require users to adjust any parameters to work and gives them control over the number of hierarchical levels to be returned. .. conda:package:: bioconductor-spectraltad |downloads_bioconductor-spectraltad| |docker_bioconductor-spectraltad| :versions: ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-1`` :depends bioconductor-biocparallel: ``>=1.28.0,<1.29.0`` :depends bioconductor-genomicranges: ``>=1.46.0,<1.47.0`` :depends bioconductor-hiccompare: ``>=1.16.0,<1.17.0`` :depends r-base: ``>=4.1,<4.2.0a0`` :depends r-cluster: :depends r-dplyr: :depends r-magrittr: :depends r-matrix: :depends r-primme: :requirements: .. rubric:: Installation With an activated Bioconda channel (see :ref:`set-up-channels`), install with:: conda install bioconductor-spectraltad and update with:: conda update bioconductor-spectraltad or use the docker container:: docker pull quay.io/biocontainers/bioconductor-spectraltad: (see `bioconductor-spectraltad/tags`_ for valid values for ````) .. |downloads_bioconductor-spectraltad| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-spectraltad.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-spectraltad :alt: (downloads) .. |docker_bioconductor-spectraltad| image:: https://quay.io/repository/biocontainers/bioconductor-spectraltad/status :target: https://quay.io/repository/biocontainers/bioconductor-spectraltad .. _`bioconductor-spectraltad/tags`: https://quay.io/repository/biocontainers/bioconductor-spectraltad?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-spectraltad/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-spectraltad/README.html