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 <firstname.lastname@example.org>|
|License||MIT + file LICENSE|
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