recipe bioconductor-packfinder

de novo Annotation of Pack-TYPE Transposable Elements






Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)).

package bioconductor-packfinder

(downloads) docker_bioconductor-packfinder



depends bioconductor-biostrings:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-s4vectors:


depends r-ape:

depends r-base:


depends r-kmer:



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-packfinder

and update with::

   mamba update bioconductor-packfinder

To create a new environment, run:

mamba create --name myenvname bioconductor-packfinder

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<tag>

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

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