IONiseR

This is the released version of IONiseR; for the devel version, see IONiseR.

Quality Assessment Tools for Oxford Nanopore MinION data

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DOI: 10.18129/B9.bioc.IONiseR

Bioconductor version: Release (3.22)

IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.

Author: Mike Smith [aut, cre]

Maintainer: Mike Smith <grimbough at gmail.com>

Citation (from within R, enter citation("IONiseR")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("IONiseR")

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("IONiseR")

Quality assessment tools for nanopore data HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, QualityControl, Sequencing, Software

Version 2.34.0

In Bioconductor since BioC 3.2 (R-3.2) (10 years)

License MIT + file LICENSE

Depends R (>= 3.4)

Imports rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2, methods, BiocGenerics, XVector, tibble, stats, BiocParallel, bit64, stringr, utils

System Requirements

URL

Suggests BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package IONiseR_2.34.0.tar.gz

Windows Binary (x86_64) IONiseR_2.34.0.zip

macOS Binary (x86_64) IONiseR_2.34.0.tgz

macOS Binary (arm64) IONiseR_2.34.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/IONiseR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/IONiseR

Bioc Package Browser https://code.bioconductor.org/browse/IONiseR/

Package Short Url https://bioconductor.org/packages/IONiseR/

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