recipe bioconductor-orfhunter

Predict open reading frames in nucleotide sequences

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-orfhunter/meta.yaml

The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. It efficiently implements the machine learning model based on vectorization of nucleotide sequences and the random forest classification algorithm. The ORFhunteR package consists of a set of functions written in the R language in conjunction with C++. The efficiency of the package was confirmed by the examples of the analysis of RNA molecules from the NCBI RefSeq and Ensembl databases. The package can be used in basic and applied biomedical research related to the study of the transcriptome of normal as well as altered (for example, cancer) human cells.

package bioconductor-orfhunter

Versions:

1.6.0-0,  1.2.0-2,  1.2.0-1,  1.2.0-0,  1.0.0-0

Depends:

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0

• 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-data.table

• r-peptides

• r-randomforest

• r-rcpp >=1.0.3

• r-stringr

• r-xfun

Required By:

Installation

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

conda install bioconductor-orfhunter

and update with:

conda update bioconductor-orfhunter

or use the docker container:

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

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

Download stats

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-orfhunter/README.html)