IONiseR: Quality Assessment Tools for Oxford Nanopore MinION data

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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]
Date of publication
None
Maintainer
Mike Smith <grimbough@gmail.com>
License
MIT + file LICENSE
Version
1.4.3

View on Bioconductor

Man pages

baseCalled
Extract baseCalled slot
channelActivityPlot
Visualise a specified metric over all channels over time.
channelHeatmap
Create layout plot of flowcell
Fast5Summary-class
An S4 class for summarised data from a MinION sequencing run
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.
rawData
Extract rawData slot
readFast5Summary
Read summary data from fast5 files.
readInfo
Extract readInfo slot

Files in this package

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