- recipe bioconductor-syntenet
Inference And Analysis Of Synteny Networks
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/syntenet.html
- License:
GPL-3
- Recipe:
syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood.
- package bioconductor-syntenet¶
-
- Versions:
1.0.0-0
- Depends:
bioconductor-biostrings
>=2.66.0,<2.67.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-rtracklayer
>=1.58.0,<1.59.0
libblas
>=3.9.0,<4.0a0
libgcc-ng
>=12
liblapack
>=3.9.0,<4.0a0
libstdcxx-ng
>=12
r-base
>=4.2,<4.3.0a0
r-rcpp
>=1.0.8
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install bioconductor-syntenet
and update with:
conda update bioconductor-syntenet
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-syntenet:<tag>
(see bioconductor-syntenet/tags for valid values for
<tag>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
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