- 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:
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
- 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¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-spectraltad/README.html)