QSutils
This is the development version of QSutils; for the stable release version, see QSutils.
Quasispecies Diversity
Bioconductor version: Development (3.24)
Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.
Author: Mercedes Guerrero-Murillo [cre, aut]
, Josep Gregori i Font [aut]
Maintainer: Mercedes Guerrero-Murillo <mergumu at gmail.com>
citation("QSutils")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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("QSutils")
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("QSutils")| QSUtils-Alignment | HTML | R Script |
| QSutils-Diversity | HTML | R Script |
| QSutils-Simulation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, DNASeq, DataImport, GeneticVariability, Genetics, SequenceMatching, Sequencing, Software |
| Version | 1.31.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | GPL-2 |
| Depends | R (>= 3.5), Biostrings, pwalign, BiocGenerics, methods |
| Imports | ape, stats, psych |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown, ggplot2 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | longreadvqs |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | QSutils_1.31.0.tar.gz |
| Windows Binary (x86_64) | QSutils_1.31.0.zip |
| macOS Binary (big-sur-x86_64) | QSutils_1.31.0.tgz |
| macOS Binary (sonoma-arm64) | QSutils_1.31.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/QSutils |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/QSutils |
| Bioc Package Browser | https://code.bioconductor.org/browse/QSutils/ |
| Package Short Url | https://bioconductor.org/packages/QSutils/ |
| Package Downloads Report | Download Stats |