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IONiseR

This is the development version of IONiseR; for the stable release version, see IONiseR.

Quality Assessment Tools for Oxford Nanopore MinION data

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DataImport, QualityControl, Sequencing, Software
Version 2.25.0
In Bioconductor since BioC 3.2 (R-3.2) (8 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
Linking To
Suggests BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData
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 IONiseR_2.25.0.tar.gz
Windows Binary IONiseR_2.25.0.zip
macOS Binary (x86_64) IONiseR_2.25.0.tgz
macOS Binary (arm64) IONiseR_2.25.0.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/
Package Downloads Report Download Stats