recipe bioconductor-compspot

compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots






Clonal cell groups share common mutations within cancer, precancer, and even clinically normal appearing tissues. The frequency and location of these mutations may predict prognosis and cancer risk. It has also been well established that certain genomic regions have increased sensitivity to acquiring mutations. Mutation-sensitive genomic regions may therefore serve as markers for predicting cancer risk. This package contains multiple functions to establish significantly mutated hotspots, compare hotspot mutation burden between samples, and perform exploratory data analysis of the correlation between hotspot mutation burden and personal risk factors for cancer, such as age, gender, and history of carcinogen exposure. This package allows users to identify robust genomic markers to help establish cancer risk.

package bioconductor-compspot

(downloads) docker_bioconductor-compspot



depends r-base:


depends r-data.table:

depends r-ggplot2:

depends r-ggpubr:

depends r-gridextra:

depends r-magrittr:

depends r-plotly:



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-compspot

and update with::

   mamba update bioconductor-compspot

To create a new environment, run:

mamba create --name myenvname bioconductor-compspot

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

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