seq.hotSPOT

DOI: 10.18129/B9.bioc.seq.hotSPOT  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see seq.hotSPOT.

Targeted sequencing panel design based on mutation hotspots

Bioconductor version: 3.17

seq.hotSPOT provides a resource for designing effective sequencing panels to help improve mutation capture efficacy for ultradeep sequencing projects. Using SNV datasets, this package designs custom panels for any tissue of interest and identify the genomic regions likely to contain the most mutations. Establishing efficient targeted sequencing panels can allow researchers to study mutation burden in tissues at high depth without the economic burden of whole-exome or whole-genome sequencing. This tool was developed to make high-depth sequencing panels to study low-frequency clonal mutations in clinically normal and cancerous tissues.

Author: Sydney Grant [aut, cre], Lei Wei [aut], Gyorgy Paragh [aut]

Maintainer: Sydney Grant <sydney.grant at roswellpark.org>

Installation

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

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

BiocManager::install("seq.hotSPOT")

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("seq.hotSPOT")

 

HTML	R Script	hotSPOT-vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNASeq, Sequencing, Software, Technology, WholeGenome
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	Artistic-2.0
Depends	R (>= 3.5.0)
Imports	R.utils, hash, stats, base, utils
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/sydney-grant/seq.hotSPOT
BugReports	https://github.com/sydney-grant/seq.hotSPOT/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	seq.hotSPOT_1.0.0.tar.gz
Windows Binary	seq.hotSPOT_1.0.0.zip
macOS Binary (x86_64)	seq.hotSPOT_1.0.0.tgz
macOS Binary (arm64)	seq.hotSPOT_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/seq.hotSPOT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/seq.hotSPOT
Bioc Package Browser	https://code.bioconductor.org/browse/seq.hotSPOT/
Package Short Url	https://bioconductor.org/packages/seq.hotSPOT/
Package Downloads Report	Download Stats