FastqCleaner
This is the released version of FastqCleaner; for the devel version, see FastqCleaner.
A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
Bioconductor version: Release (3.23)
An interactive web application for quality control, filtering and trimming of FASTQ files. This user-friendly tool combines a pipeline for data processing based on Biostrings and ShortRead infrastructure, with a cutting-edge visual environment. Single-Read and Paired-End files can be locally processed. Diagnostic interactive plots (CG content, per-base sequence quality, etc.) are provided for both the input and output files.
Author: Leandro Roser [aut, cre], Fernán Agüero [aut], Daniel Sánchez [aut]
Maintainer: Leandro Roser <learoser at gmail.com>
citation("FastqCleaner")):
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("FastqCleaner")
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("FastqCleaner")| An Introduction to FastqCleaner | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | QualityControl, SangerSeq, SequenceMatching, Sequencing, Software |
| Version | 1.30.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12) |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, testthat, knitr, rmarkdown |
| 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 | FastqCleaner_1.30.0.tar.gz |
| Windows Binary (x86_64) | FastqCleaner_1.30.0.zip |
| macOS Binary (big-sur-x86_64) | FastqCleaner_1.30.0.tgz |
| macOS Binary (sonoma-arm64) | FastqCleaner_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/FastqCleaner |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/FastqCleaner |
| Bioc Package Browser | https://code.bioconductor.org/browse/FastqCleaner/ |
| Package Short Url | https://bioconductor.org/packages/FastqCleaner/ |
| Package Downloads Report | Download Stats |