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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("IONiseR")
In most cases, you don't need to download the package archive at all.
IONiseR
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see IONiseR.
Quality Assessment Tools for Oxford Nanopore MinION data
Bioconductor version: 3.4
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("IONiseR")
Documentation
| HTML | R Script | Quality assessment tools for nanopore data |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | DataImport, QualityControl, Sequencing, Software |
| Version | 1.4.4 |
| In Bioconductor since | BioC 3.2 (R-3.2) (1.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.3) |
| Imports | rhdf5, dplyr, magrittr, tidyr, data.table, ShortRead, Biostrings, ggplot2, methods, BiocGenerics, XVector, stats, utils |
| LinkingTo | |
| Suggests | BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | IONiseR_1.4.4.tar.gz |
| Windows Binary | IONiseR_1.4.4.zip |
| Mac OS X 10.9 (Mavericks) | IONiseR_1.4.4.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/IONiseR/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/IONiseR/ |
| Package Downloads Report | Download Stats |
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