recipe bioconductor-dnafusion

Identification of gene fusions using paired-end sequencing

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-dnafusion/meta.yaml

DNAfusion can identify gene fusions such as EML4-ALK based on paired-end sequencing results. This package was developed using position deduplicated BAM files generated with the AVENIO Oncology Analysis Software. These files are made using the AVENIO ctDNA surveillance kit and Illumina Nextseq 500 sequencing. This is a targeted hybridization NGS approach and includes ALK-specific but not EML4-specific probes.

package bioconductor-dnafusion

versions:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-bamsignals:

>=1.34.0,<1.35.0

depends bioconductor-biocbaseutils:

>=1.4.0,<1.5.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-genomicalignments:

>=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-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene:

>=3.18.0,<3.19.0

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-dnafusion

and update with::

   mamba update bioconductor-dnafusion

To create a new environment, run:

mamba create --name myenvname bioconductor-dnafusion

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-dnafusion:<tag>

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

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