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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>

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

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")
compSPOT-Vignette HTML R Script
Reference Manual PDF
NEWS Text

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
System Requirements
URL https://github.com/sydney-grant/compSPOT
Bug Reports https://github.com/sydney-grant/compSPOT/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
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Build Report 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) compSPOT_1.1.0.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