FastqCleaner
A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
Bioconductor version: Release (3.17)
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")):
Installation
To install this package, start R (version "4.3") 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 | 1.18.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12) |
| Linking To | Rcpp |
| Suggests | BiocStyle, testthat, knitr, rmarkdown |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | FastqCleaner_1.18.0.tar.gz |
| Windows Binary | FastqCleaner_1.18.0.zip |
| macOS Binary (x86_64) | FastqCleaner_1.18.0.tgz |
| macOS Binary (arm64) | FastqCleaner_1.18.0.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 |