recipe bioconductor-scanmirapp

scanMiR shiny application






A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.

package bioconductor-scanmirapp

(downloads) docker_bioconductor-scanmirapp



depends bioconductor-annotationdbi:


depends bioconductor-annotationfilter:


depends bioconductor-annotationhub:


depends bioconductor-biocparallel:


depends bioconductor-biostrings:


depends bioconductor-ensembldb:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicfeatures:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


depends bioconductor-scanmir:


depends bioconductor-scanmirdata:


depends r-base:


depends r-data.table:

depends r-digest:

depends r-dt:

depends r-fst:

depends r-ggplot2:

depends r-htmlwidgets:

depends r-matrix:

depends r-plotly:

depends r-rintrojs:

depends r-shiny:

depends r-shinycssloaders:

depends r-shinydashboard:

depends r-shinyjqui:

depends r-waiter:



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-scanmirapp

and update with::

   mamba update bioconductor-scanmirapp

To create a new environment, run:

mamba create --name myenvname bioconductor-scanmirapp

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

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