pqsfinder
This is the development version of pqsfinder; for the stable release version, see pqsfinder.
Identification of potential quadruplex forming sequences
Bioconductor version: Development (3.24)
Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.
Author: Jiri Hon, Dominika Labudova, Matej Lexa and Tomas Martinek
Maintainer: Jiri Hon <jiri.hon at gmail.com>
citation("pqsfinder")):
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("pqsfinder")
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("pqsfinder")| pqsfinder: User Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneRegulation, MotifDiscovery, SequenceMatching, Software |
| Version | 2.29.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | BSD_2_clause + file LICENSE |
| Depends | R (>= 3.5.0), Biostrings |
| Imports | Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods |
| System Requirements | GNU make, C++11 |
| URL | https://pqsfinder.fi.muni.cz |
See More
| Suggests | BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi |
| Linking To | Rcpp, BH (>= 1.78.0) |
| 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 | pqsfinder_2.29.0.tar.gz |
| Windows Binary (x86_64) | pqsfinder_2.29.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | pqsfinder_2.29.0.tgz |
| macOS Binary (sonoma-arm64) | pqsfinder_2.29.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/pqsfinder |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/pqsfinder |
| Bioc Package Browser | https://code.bioconductor.org/browse/pqsfinder/ |
| Package Short Url | https://bioconductor.org/packages/pqsfinder/ |
| Package Downloads Report | Download Stats |