seq.hotSPOT
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see seq.hotSPOT.
Targeted sequencing panel design based on mutation hotspots
Bioconductor version: 3.18
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("seq.hotSPOT")):
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")| hotSPOT-vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNASeq, Sequencing, Software, Technology, WholeGenome |
| Version | 1.2.0 |
| 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 | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | seq.hotSPOT_1.2.0.tar.gz |
| Windows Binary | seq.hotSPOT_1.2.0.zip (64-bit only) |
| macOS Binary (x86_64) | seq.hotSPOT_1.2.0.tgz |
| macOS Binary (arm64) | seq.hotSPOT_1.2.0.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 |