IONiseR

DOI: 10.18129/B9.bioc.IONiseR    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see IONiseR.

Quality Assessment Tools for Oxford Nanopore MinION data

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Quality assessment tools for nanopore data
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, QualityControl, Sequencing, Software
Version	2.8.0
In Bioconductor since	BioC 3.2 (R-3.2) (4 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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData
SystemRequirements
Enhances
URL
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	IONiseR_2.8.0.tar.gz
Windows Binary	IONiseR_2.8.0.zip
Mac OS X 10.11 (El Capitan)	IONiseR_2.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/IONiseR
Source Repository (Developer Access)	git clone [email protected]:packages/IONiseR
Package Short Url	https://bioconductor.org/packages/IONiseR/
Package Downloads Report	Download Stats