recipe bioconductor-svaretro

Retrotransposed transcript detection from structural variants

Homepage:

https://bioconductor.org/packages/3.18/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:

1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-structuralvariantannotation:

>=1.18.0,<1.19.0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-rlang:

depends r-stringr:

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-svaretro

and update with::

   mamba update bioconductor-svaretro

To create a new environment, run:

mamba create --name myenvname bioconductor-svaretro

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-svaretro:<tag>

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

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