recipe bioconductor-modstrings

Working with modified nucleotide sequences

Homepage

https://bioconductor.org/packages/3.11/bioc/html/Modstrings.html

License

Artistic-2.0

Recipe

/bioconductor-modstrings/meta.yaml

Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionallity for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.

package bioconductor-modstrings

Versions

1.4.0-0,  1.2.0-0,  1.0.3-0

Depends

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-biostrings >=2.56.0,<2.57.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-xvector >=0.28.0,<0.29.0

• r-assertive

• r-base >=4.0,<4.1.0a0

• r-crayon

• r-stringi

• r-stringr

Required By

• bioconductor-epitxdb

• bioconductor-trna

• bioconductor-trnadbimport

• bioconductor-rnamodr

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-modstrings

and update with:

conda update bioconductor-modstrings

or use the docker container:

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

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

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-modstrings/README.html)