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 (3.21)
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] (ORCID:
Maintainer: Sydney Grant <Sydney.Grant at roswellpark.org>
citation("compSPOT")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | Classification, DNASeq, MultipleComparison, Sequencing, SingleCell, Software, Survival, Technology, WholeGenome |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | compSPOT_1.5.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| 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 |