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compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots

Bioconductor version: Release (3.19)

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.

Author: Sydney Grant [aut, cre] , Ella Sampson [aut], Rhea Rodrigues [aut] , Gyorgy Paragh [aut]

Maintainer: Sydney Grant <Sydney.Grant at>

Citation (from within R, enter citation("compSPOT")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

compSPOT-Vignette HTML R Script
Reference Manual PDF


biocViews Classification, DNASeq, MultipleComparison, Sequencing, SingleCell, Software, Survival, Technology, WholeGenome
Version 1.2.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
License Artistic-2.0
Depends R (>= 4.3.0)
Imports stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra, utils, data.table
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Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package compSPOT_1.2.0.tar.gz
Windows Binary
macOS Binary (x86_64) compSPOT_1.2.0.tgz
macOS Binary (arm64) compSPOT_1.2.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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