recipe pipmir

We developed the PIPmiR algorithm to identify novel plant miRNA genes from a combination of deep sequencing data and genomic features.



PIPmiR is provided for academic use only, if you wish to use it in another setting please contact Uwe Ohler.




biotools: pipmir, doi: 10.1101/gr.123547.111

package pipmir

(downloads) docker_pipmir



depends openjdk:

depends samtools:

depends viennarna:




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 pipmir

and update with::

   mamba update pipmir

To create a new environment, run:

mamba create --name myenvname pipmir

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 `pipmir/tags`_ for valid values for ``<tag>``)

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