recipe bioconductor-svaretro

Retrotransposed transcript detection from structural variants

Homepage:

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

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-svaretro/meta.yaml

svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported by events and annotated with information of the inserted transcripts.

package bioconductor-svaretro

Versions:

1.4.0-0,  1.0.0-0

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-structuralvariantannotation >=1.13.0,<1.14.0

• bioconductor-variantannotation >=1.44.0,<1.45.0

• r-assertthat

• r-base >=4.2,<4.3.0a0

• r-dplyr

• r-rlang

• r-stringr

Required By:

Installation

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

conda install bioconductor-svaretro

and update with:

conda update bioconductor-svaretro

or use the docker container:

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

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

Download stats

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