recipe bioconductor-spectraltad

SpectralTAD: Hierarchical TAD detection using spectral clustering

Homepage:

https://bioconductor.org/packages/3.18/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.

package bioconductor-spectraltad

versions:

1.18.0-0,  1.16.0-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0, 

1.18.0-0,  1.16.0-0,  1.14.0-0,  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:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-hiccompare:

>=1.24.0,<1.25.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cluster:

depends r-dplyr:

depends r-magrittr:

depends r-matrix:

depends r-primme:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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-spectraltad

and update with::

   mamba update bioconductor-spectraltad

To create a new environment, run:

mamba create --name myenvname bioconductor-spectraltad

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-spectraltad:<tag>

(see `bioconductor-spectraltad/tags`_ for valid values for ``<tag>``)

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Link to this page

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