IONiseR: Quality Assessment Tools for Oxford Nanopore MinION data

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.

AuthorMike Smith [aut, cre]
Date of publicationNone
MaintainerMike Smith <grimbough@gmail.com>
LicenseMIT + file LICENSE
Version1.4.3

View on Bioconductor

Functions

baseCalled Man page
baseCalled,Fast5Summary-method Man page
channelActivityPlot Man page
channelHeatmap Man page
[,Fast5Summary,ANY,ANY,ANY-method Man page
Fast5Summary-class Man page
fastq Man page
fastq2D Man page
fastq2D,Fast5Summary-method Man page
fastqComplement Man page
fastqComplement,Fast5Summary-method Man page
fastq,Fast5Summary-method Man page
fastqTemplate Man page
fastqTemplate,Fast5Summary-method Man page
IONiseR Man page
IONiseR-package Man page
layoutPlot Man page
length,Fast5Summary-method Man page
muxHeatmap Man page
plotActiveChannels Man page
plotBaseProductionRate Man page
plotCurrentByTime Man page
plotEventRate Man page
plotKmerFrequencyCorrelation Man page
plotReadAccumulation Man page
plotReadCategoryCounts Man page
plotReadCategoryQuals Man page
plotReadTypeProduction Man page
rawData Man page
rawData,Fast5Summary-method Man page
readFast5Summary Man page
readInfo Man page
readInfo,Fast5Summary-method Man page

Files

IONiseR/DESCRIPTION
IONiseR/LICENSE
IONiseR/NAMESPACE
IONiseR/NEWS
IONiseR/R
IONiseR/R/IONiseR.R IONiseR/R/Methods-accessors.R IONiseR/R/Methods-subsetting.R IONiseR/R/classes.R IONiseR/R/fast5Readers.R IONiseR/R/fastqProcessing.R IONiseR/R/plotting_kmers.R IONiseR/R/plotting_layout.R IONiseR/R/plotting_summaryStats.R IONiseR/R/processing_bam.R IONiseR/R/readSummary.R
IONiseR/build
IONiseR/build/vignette.rds
IONiseR/inst
IONiseR/inst/doc
IONiseR/inst/doc/IONiseR.R
IONiseR/inst/doc/IONiseR.Rmd
IONiseR/inst/doc/IONiseR.html
IONiseR/inst/extdata
IONiseR/inst/extdata/example.fast5
IONiseR/inst/extdata/example_v2.fast5
IONiseR/man
IONiseR/man/Fast5Summary-class.Rd IONiseR/man/IONiseR.Rd IONiseR/man/baseCalled.Rd IONiseR/man/channelActivityPlot.Rd IONiseR/man/channelHeatmap.Rd IONiseR/man/fastq.Rd IONiseR/man/fastq2D.Rd IONiseR/man/fastqComplement.Rd IONiseR/man/fastqTemplate.Rd IONiseR/man/layoutPlot.Rd IONiseR/man/muxHeatmap.Rd IONiseR/man/plotActiveChannels.Rd IONiseR/man/plotBaseProductionRate.Rd IONiseR/man/plotCurrentByTime.Rd IONiseR/man/plotEventRate.Rd IONiseR/man/plotKmerFrequencyCorrelation.Rd IONiseR/man/plotReadAccumulation.Rd IONiseR/man/plotReadCategoryCounts.Rd IONiseR/man/plotReadCategoryQuals.Rd IONiseR/man/plotReadTypeProduction.Rd IONiseR/man/rawData.Rd IONiseR/man/readFast5Summary.Rd IONiseR/man/readInfo.Rd
IONiseR/tests
IONiseR/tests/testthat
IONiseR/tests/testthat.R
IONiseR/tests/testthat/test_Fast5Summary.R
IONiseR/vignettes
IONiseR/vignettes/ChannelKmer.png
IONiseR/vignettes/IONiseR.Rmd
IONiseR/vignettes/bibliography.bib
IONiseR/vignettes/bmc-bioinformatics.csl

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.