compSPOT

DOI: 10.18129/B9.bioc.compSPOT  

This is the development version of compSPOT; for the stable release version, see compSPOT.

compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots

Bioconductor version: Development (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 roswellpark.org>

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	1.1.0
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_1.1.0.tar.gz
Windows Binary	compSPOT_1.1.0.zip
macOS Binary (x86_64)	compSPOT_1.1.0.tgz
macOS Binary (arm64)
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