Rqc
This is the released version of Rqc; for the devel version, see Rqc.
Quality Control Tool for High-Throughput Sequencing Data
DOI: 10.18129/B9.bioc.Rqc
Bioconductor version: Release (3.23)
Rqc is an optimised tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.
Author: Welliton Souza, Benilton Carvalho <beniltoncarvalho at gmail.com>
Maintainer: Welliton Souza <well309 at gmail.com>
citation("Rqc")):
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")
BiocManager::install("Rqc")
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("Rqc")| Using Rqc | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, QualityControl, Sequencing, Software |
| Version | 1.46.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 years) |
| License | GPL (>= 2) |
| Depends | BiocParallel, ShortRead, ggplot2 |
| Imports | BiocGenerics(>= 0.25.1), Biostrings, IRanges, methods, S4Vectors, knitr (>= 1.7), BiocStyle, plyr, markdown, grid, reshape2, Rcpp (>= 0.11.6), biovizBase, shiny, Rsamtools, GenomicAlignments, GenomicFiles |
| System Requirements | |
| URL | https://github.com/labbcb/Rqc |
| Bug Reports | https://github.com/labbcb/Rqc/issues |
See More
| Suggests | rmarkdown, testthat |
| Linking To | Rcpp |
| 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 | Rqc_1.46.0.tar.gz |
| Windows Binary (x86_64) | Rqc_1.46.0.zip |
| macOS Binary (big-sur-x86_64) | Rqc_1.46.0.tgz |
| macOS Binary (sonoma-arm64) | Rqc_1.46.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Rqc |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Rqc |
| Bioc Package Browser | https://code.bioconductor.org/browse/Rqc/ |
| Package Short Url | https://bioconductor.org/packages/Rqc/ |
| Package Downloads Report | Download Stats |