compSPOT

DOI: 10.18129/B9.bioc.compSPOT  

compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots

Bioconductor version: Release (3.18)

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 roswellpark.org>

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

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("compSPOT")

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

Documentation

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

browseVignettes("compSPOT")

 

HTML R Script compSPOT-Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, DNASeq, MultipleComparison, Sequencing, SingleCell, Software, Survival, Technology, WholeGenome
Version 1.0.0
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License Artistic-2.0
Depends R (>= 4.3.0)
Imports stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra, utils, data.table
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL https://github.com/sydney-grant/compSPOT
BugReports https://github.com/sydney-grant/compSPOT/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package compSPOT_1.0.0.tar.gz
Windows Binary compSPOT_1.0.0.zip (64-bit only)
macOS Binary (x86_64) compSPOT_1.0.0.tgz
macOS Binary (arm64) compSPOT_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/compSPOT
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/compSPOT
Bioc Package Browser https://code.bioconductor.org/browse/compSPOT/
Package Short Url https://bioconductor.org/packages/compSPOT/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive

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