recipe bioconductor-ripat

Retroviral Integration Pattern Analysis Tool (RIPAT)






RIPAT is developed as an R package for retroviral integration sites annotation and distribution analysis. RIPAT needs local alignment results from BLAST and BLAT. Specific input format is depicted in RIPAT manual. RIPAT provides RV integration pattern analysis result as forms of R objects, excel file with multiple sheets and plots.

package bioconductor-ripat

(downloads) docker_bioconductor-ripat



depends bioconductor-biomart:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-karyoploter:


depends bioconductor-regioner:


depends bioconductor-rtracklayer:


depends r-base:


depends r-ggplot2:


depends r-openxlsx:


depends r-plyr:


depends r-stringr:




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-ripat

and update with::

   mamba update bioconductor-ripat

To create a new environment, run:

mamba create --name myenvname bioconductor-ripat

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-ripat/tags`_ for valid values for ``<tag>``)

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