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seq.hotSPOT

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

Targeted sequencing panel design based on mutation hotspots


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("seq.hotSPOT")):

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("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")
hotSPOT-vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNASeq, Sequencing, Software, Technology, WholeGenome
Version 1.3.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License Artistic-2.0
Depends R (>= 3.5.0)
Imports R.utils, hash, stats, base, utils
System Requirements
URL https://github.com/sydney-grant/seq.hotSPOT
Bug Reports https://github.com/sydney-grant/seq.hotSPOT/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

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

Source Package seq.hotSPOT_1.3.0.tar.gz
Windows Binary seq.hotSPOT_1.3.0.zip (64-bit only)
macOS Binary (x86_64) seq.hotSPOT_1.3.0.tgz
macOS Binary (arm64) seq.hotSPOT_1.3.0.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