recipe bioconductor-syntenet

Inference And Analysis Of Synteny Networks

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/syntenet.html

License:

GPL-3

Recipe:

/bioconductor-syntenet/meta.yaml

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-ggnetwork

• r-ggplot2

• r-igraph

• r-intergraph

• r-labdsv

• r-networkd3

• r-pheatmap

• r-rcolorbrewer

• r-rcpp >=1.0.8

• r-testthat

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>)

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