IONiseR

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see IONiseR.

All versions

3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2

Quality Assessment Tools for Oxford Nanopore MinION data

Bioconductor version: Release (3.23)

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")):

Mike Smith. IONiseR: Quality Assessment Tools for Oxford Nanopore MinION data. doi:10.18129/B9.bioc.IONiseR, R package version 2.35.0, https://bioconductor.org/packages/IONiseR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	2.35.0
In Bioconductor since	BioC 3.2 (R-3.2) (11 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
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	IONiseR_2.35.0.tar.gz
Windows Binary (x86_64)	IONiseR_2.35.0.zip
macOS Binary (big-sur-x86_64)	IONiseR_2.35.0.tgz
macOS Binary (sonoma-arm64)	IONiseR_2.35.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/IONiseR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IONiseR
Package Short Url	https://bioconductor.org/packages/IONiseR/
Package Downloads Report	Download Stats