Quality Assessment Tools for Oxford Nanopore MinION data

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Documentation for package ‘IONiseR’ version 2.33.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

IONiseR-package	IONiseR: A package for assessing quality of MinION data
baseCalled	Extract baseCalled slot
baseCalled-method	An S4 class for summarised data from a MinION sequencing run
channelActivityPlot	Visualise a specified metric over all channels over time.
channelHeatmap	Create layout plot of flowcell
eventData	Extract eventData slot
eventData-method	An S4 class for summarised data from a MinION sequencing run
Fast5Summary-class	An S4 class for summarised data from a MinION sequencing run
fast5toFastq	Extract FASTQ files from fast5 files
fastq	Extract fastq slot
fastq-method	An S4 class for summarised data from a MinION sequencing run
fastq2D	Extract 2D reads
fastq2D-method	An S4 class for summarised data from a MinION sequencing run
fastqComplement	Extract complement reads
fastqComplement-method	An S4 class for summarised data from a MinION sequencing run
fastqTemplate	Extract template reads
fastqTemplate-method	An S4 class for summarised data from a MinION sequencing run
IONiseR	IONiseR: A package for assessing quality of MinION data
layoutPlot	Create layout plot of flowcell
length-method	An S4 class for summarised data from a MinION sequencing run
muxHeatmap	Create layout plot of flowcell
plotActiveChannels	Plot the number of active channels for each minute of run time
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 windows
plotReadAccumulation	Plot the accumulation of reads over the duration of the experiment.
plotReadCategoryCounts	Plot the proportion of template, complement and 2D reads found a dataset.
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
readInfo-method	An S4 class for summarised data from a MinION sequencing run
[-method	An S4 class for summarised data from a MinION sequencing run