seq.hotSPOT
This is the development version of seq.hotSPOT; for the stable release version, see seq.hotSPOT.
All Bioconductor versions of seq.hotSPOT
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17
Targeted sequencing panel design based on mutation hotspots
Bioconductor version: 3.24 · Package version: 1.13.0
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"):
Sydney Grant, Lei Wei, Gyorgy Paragh. seq.hotSPOT: Targeted sequencing panel design based on mutation hotspots. doi:10.18129/B9.bioc.seq.hotSPOT, R package version 1.13.0, https://bioconductor.org/packages/seq.hotSPOT.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("seq.hotSPOT")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.13.0 |
| License | Artistic-2.0 |
| URL | https://github.com/sydney-grant/seq.hotSPOT |
| Bug Reports | https://github.com/sydney-grant/seq.hotSPOT/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3 years) |
| Downloads rank | 2180 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNASeq, Sequencing, Software, Technology, WholeGenome |
| Package Short Url | https://bioconductor.org/packages/seq.hotSPOT/ |
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 | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | seq.hotSPOT_1.13.0.tar.gz |
| Windows binary (x86_64) | seq.hotSPOT_1.13.0.zip |
| macOS binary (arm64) | seq.hotSPOT_1.13.0.tgz |
| macOS binary (x86_64) | seq.hotSPOT_1.13.0.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 |
| Package Downloads Report | Download Stats |