recipe bioconductor-orfhunter

Predict open reading frames in nucleotide sequences

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/ORFhunteR.html

License:

MIT License

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:

1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.2.0-2,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-biostrings:

>=2.70.1,<2.71.0a0

depends bioconductor-bsgenome.hsapiens.ucsc.hg38:

>=1.4.0,<1.5.0

depends bioconductor-bsgenome.hsapiens.ucsc.hg38:

>=1.4.5,<1.5.0a0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-peptides:

depends r-randomforest:

depends r-rcpp:

>=1.0.3

depends r-stringr:

depends r-xfun:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-orfhunter

and update with::

   mamba update bioconductor-orfhunter

To create a new environment, run:

mamba create --name myenvname bioconductor-orfhunter

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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