IONiseR
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.
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("IONiseR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
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_2.35.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/IONiseR/ |
| Package Short Url | https://bioconductor.org/packages/IONiseR/ |
| Package Downloads Report | Download Stats |