recipe bioconductor-fscanr

Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/FScanR.html

License:

Artistic-2.0

Recipe:

/bioconductor-fscanr/meta.yaml

'FScanR' identifies Programmed Ribosomal Frameshifting (PRF) events from BLASTX homolog sequence alignment between targeted genomic/cDNA/mRNA sequences against the peptide library of the same species or a close relative. The output by BLASTX or diamond BLASTX will be used as input of 'FScanR' and should be in a tabular format with 14 columns. For BLASTX, the output parameter should be: -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qframe sframe'. For diamond BLASTX, the output parameter should be: -outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qframe qframe.

package bioconductor-fscanr

(downloads) docker_bioconductor-fscanr

versions:

1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-2,  1.0.0-1

depends r-base:

>=4.3,<4.4.0a0

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-fscanr

and update with::

   mamba update bioconductor-fscanr

To create a new environment, run:

mamba create --name myenvname bioconductor-fscanr

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-fscanr:<tag>

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

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Link to this page

Render an install-with-bioconda 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-fscanr/README.html)