recipe bioconductor-spectraltad

SpectralTAD: Hierarchical TAD detection using spectral clustering

Homepage:

https://bioconductor.org/packages/3.16/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:

1.14.0-0,  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 >=1.32.0,<1.33.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-hiccompare >=1.20.0,<1.21.0

• r-base >=4.2,<4.3.0a0

• r-cluster

• r-dplyr

• r-magrittr

• r-matrix

• r-primme

Required By:

Installation

With an activated Bioconda channel (see 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:<tag>

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

Download stats

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