IONiseR: Quality Assessment Tools for Oxford Nanopore MinION data
Version 2.0.0

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]
Bioconductor views DataImport QualityControl Sequencing
Date of publicationNone
MaintainerMike Smith <grimbough@gmail.com>
LicenseMIT + file LICENSE
Version2.0.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("IONiseR")

Getting started

IONiseR

Popular man pages

channelHeatmap: Create layout plot of flowcell
eventData: Extract eventData slot
Fast5Summary-class: An S4 class for summarised data from a MinION sequencing run
fast5toFastq: Extract FASTQ files from fast5 files
IONiseR: IONiseR: A package for assessing quality of MinION data
readFast5Log: Read the log entry from a single fast5 file
readInfo: Extract readInfo slot
See all...

All man pages Function index File listing

Man pages

baseCalled: Extract baseCalled slot
channelActivityPlot: Visualise a specified metric over all channels over time.
channelHeatmap: Create layout plot of flowcell
eventData: Extract eventData slot
Fast5Summary-class: An S4 class for summarised data from a MinION sequencing run
fast5toFastq: Extract FASTQ files from fast5 files
fastq: Extract fastq slot
fastq2D: Extract 2D reads
fastqComplement: Extract complement reads
fastqTemplate: Extract template reads
IONiseR: IONiseR: A package for assessing quality of MinION data
layoutPlot: Create layout plot of flowcell
muxHeatmap: Create layout plot of flowcell
plotActiveChannels: Plot the number of active channels for each minute of run...
plotBaseProductionRate: Plot the mean rate at which bases are recorded
plotCurrentByTime: View changes in signal against run time.
plotEventRate: Plot the mean rate at which events occur
plotKmerFrequencyCorrelation: Display correlation between pentemer proportions in two time...
plotReadAccumulation: Plot the accumulation of reads over the duration of the...
plotReadCategoryCounts: Plot the proportion of template, complement and 2D reads...
plotReadCategoryQuals: Visualise the mean base quality of each read
plotReadTypeProduction: View changes in signal against run time.
readFast5Log: Read the log entry from a single fast5 file
readFast5Summary: Read summary data from fast5 files.
readInfo: Extract readInfo slot

Functions

Fast5Summary-class Man page
H5Fopen_tryCatch Source code
IONiseR Man page
IONiseR-package Man page
[,Fast5Summary,ANY,ANY,ANY-method Man page
baseCalled Man page
baseCalled,Fast5Summary-method Man page
channelActivityPlot Man page Source code
channelHeatmap Man page Source code
channelToXY Source code
checkOpening Source code
chooseStrand Source code
circleFun Source code
dFromFASTQ Source code
eventData Man page
eventData,Fast5Summary-method Man page
fast5status Source code
fast5toFastq Man page Source code
fast5version Source code
fastq Man page
fastq,Fast5Summary-method Man page
fastq2D Man page
fastq2D,Fast5Summary-method Man page
fastqComplement Man page
fastqComplement,Fast5Summary-method Man page
fastqTemplate Man page
fastqTemplate,Fast5Summary-method Man page
findAnalysisNumber Source code
get2D Source code
getAligned Source code
getBaseCalled Source code
getBaseCalledSummary Source code
getEvents Source code
getEventsSummary Source code
getFastqString Source code
getRawSignal Source code
getRawSummary Source code
getReadChannelMux Source code
getReadChannelMux2 Source code
getReadNumber Source code
getRunID Source code
getSamplingRate Source code
getStartTime Source code
groupExistsObj Source code
groupExistsString Source code
layoutPlot Man page Source code
length,Fast5Summary-method Man page
matchRecords Source code
muxHeatmap Man page Source code
muxToXY Source code
passFailStatus Source code
plot2DYield Source code
plotActiveChannels Man page Source code
plotBaseProductionRate Man page Source code
plotCurrentByTime Man page Source code
plotEventRate Man page Source code
plotKmerFrequencyCorrelation Man page Source code
plotReadAccumulation Man page Source code
plotReadCategoryCounts Man page Source code
plotReadCategoryQuals Man page Source code
plotReadTypeProduction Man page Source code
processFastq Source code
processFastqVec Source code
processStrandSpecifier Source code
readAttribute Source code
readFast5Log Man page Source code
readFast5Summary Man page Source code
readFast5Summary.mc Source code
readInfo Man page
readInfo,Fast5Summary-method Man page
readtypeFromFASTQ Source code
strandExistence Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/IONiseR.R
R/Methods-accessors.R
R/Methods-subsetting.R
R/classes.R
R/fast5Readers.R
R/fast5Status.R
R/fast5readers_summary.R
R/fast5utilities.R
R/fastqProcessing.R
R/plotting_kmers.R
R/plotting_layout.R
R/plotting_summaryStats.R
R/processing_bam.R
R/readSummary.R
build
build/vignette.rds
inst
inst/doc
inst/doc/IONiseR.R
inst/doc/IONiseR.Rmd
inst/doc/IONiseR.html
inst/extdata
inst/extdata/example.fast5
inst/extdata/example_not-working.fast5
inst/extdata/example_v2.fast5
man
man/Fast5Summary-class.Rd
man/IONiseR.Rd
man/baseCalled.Rd
man/channelActivityPlot.Rd
man/channelHeatmap.Rd
man/eventData.Rd
man/fast5toFastq.Rd
man/fastq.Rd
man/fastq2D.Rd
man/fastqComplement.Rd
man/fastqTemplate.Rd
man/layoutPlot.Rd
man/muxHeatmap.Rd
man/plotActiveChannels.Rd
man/plotBaseProductionRate.Rd
man/plotCurrentByTime.Rd
man/plotEventRate.Rd
man/plotKmerFrequencyCorrelation.Rd
man/plotReadAccumulation.Rd
man/plotReadCategoryCounts.Rd
man/plotReadCategoryQuals.Rd
man/plotReadTypeProduction.Rd
man/readFast5Log.Rd
man/readFast5Summary.Rd
man/readInfo.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_Fast5Summary.R
tests/testthat/test_fastq.R
tests/testthat/test_plotting.R
vignettes
vignettes/ChannelKmer.png
vignettes/IONiseR.Rmd
vignettes/bibliography.bib
vignettes/bmc-bioinformatics.csl
IONiseR documentation built on May 20, 2017, 9:51 p.m.

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