recipe bioconductor-structstrings

Implementation of the dot bracket annotations with Biostrings

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-structstrings/meta.yaml

The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.

package bioconductor-structstrings

Versions:

1.14.0-1,  1.14.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.1-0,  1.6.0-0,  1.4.0-0, 

1.14.0-1,  1.14.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.1-0,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.3-0

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-xvector >=0.38.0,<0.39.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• r-base >=4.2,<4.3.0a0

• r-crayon

• r-stringi

• r-stringr

Required By:

• bioconductor-trnascanimport

• bioconductor-trna

• bioconductor-trnadbimport

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-structstrings

and update with:

conda update bioconductor-structstrings

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-structstrings:<tag>

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

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