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>
citation("IONiseR")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, QualityControl, Sequencing, Software |
| Version | 2.8.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 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 |
| Old Source Packages for BioC 3.9 | Source Archive |