recipe bioconductor-fscanr

Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output

Homepage:

https://bioconductor.org/packages/3.16/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:

1.8.0-01.4.0-01.2.0-01.0.0-21.0.0-1

Depends:
Required By:

Installation

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

conda install bioconductor-fscanr

and update with:

conda update bioconductor-fscanr

or 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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