Package: IONiseR 2.13.1

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.

Authors:Mike Smith [aut, cre]

IONiseR_2.13.1.tar.gz
IONiseR_2.13.1.zip(r-4.7-any)IONiseR_2.13.1.zip(r-4.6-any)IONiseR_2.13.1.zip(r-4.5-any)
IONiseR_2.13.1.tgz(r-4.6-any)IONiseR_2.13.1.tgz(r-4.5-any)
IONiseR_2.13.1.tar.gz(r-4.7-any)IONiseR_2.13.1.tar.gz(r-4.6-any)
IONiseR_2.13.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
IONiseR/json (API)

# Install 'IONiseR' in R:
install.packages('IONiseR', repos = c('https://grimbough.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/grimbough/ioniser/issues

On CRAN:

Conda:

qualitycontroldataimportsequencing

2.40 score 5 scripts 22 exports 71 dependencies

Last updated from:47d8ab1e1d. Checks:8 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develERROR286
source / vignettesERROR206
linux-releaseERROR263
macos-releaseERROR216
macos-oldrelERROR183
windows-develERROR229
windows-releaseERROR251
windows-oldrelERROR180
wasm-releaseOK136

Exports:baseCalledchannelActivityPlotchannelHeatmapeventDatafast5toFastqfastqfastq2DfastqComplementfastqTemplatelayoutPlotplotActiveChannelsplotBaseProductionRateplotCurrentByTimeplotEventRateplotKmerFrequencyCorrelationplotReadAccumulationplotReadCategoryCountsplotReadCategoryQualsplotReadTypeProductionreadFast5LogreadFast5SummaryreadInfo

Dependencies:BHBiobaseBiocGenericsbiocmakeBiocParallelBiostringsbitbit64bitopscigarilloclicodetoolscpp11crayondeldirdir.expirydplyrfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehwriterinterpIRangesisobandjpeglabelinglambda.rlatticelatticeExtralifecyclemagrittrMASSpillarpkgconfigpngpurrrpwalignR6RColorBrewerRcppRcppEigenrhdf5rhdf5filtersRhdf5libRhtslibrlangRsamtoolsS4VectorsS7scalesSeqinfoShortReadsnowstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithrXVector

Readme and manuals

Help Manual

Help pageTopics
Extract baseCalled slotbaseCalled
Visualise a specified metric over all channels over time.channelActivityPlot
Create layout plot of flowcellchannelHeatmap
Extract eventData sloteventData
An S4 class for summarised data from a MinION sequencing runbaseCalled,Fast5Summary-method eventData,Fast5Summary-method Fast5Summary-class fastq,Fast5Summary-method fastq2D,Fast5Summary-method fastqComplement,Fast5Summary-method fastqTemplate,Fast5Summary-method length,Fast5Summary-method readInfo,Fast5Summary-method [,Fast5Summary,ANY,ANY,ANY-method
Extract FASTQ files from fast5 filesfast5toFastq
Extract fastq slotfastq
Extract 2D readsfastq2D
Extract complement readsfastqComplement
Extract template readsfastqTemplate
IONiseR: A package for assessing quality of MinION dataIONiseR-package IONiseR
Create layout plot of flowcelllayoutPlot
Create layout plot of flowcellmuxHeatmap
Plot the number of active channels for each minute of run timeplotActiveChannels
Plot the mean rate at which bases are recordedplotBaseProductionRate
View changes in signal against run time.plotCurrentByTime
Plot the mean rate at which events occurplotEventRate
Display correlation between pentemer proportions in two time windowsplotKmerFrequencyCorrelation
Plot the accumulation of reads over the duration of the experiment.plotReadAccumulation
Plot the proportion of template, complement and 2D reads found a dataset.plotReadCategoryCounts
Visualise the mean base quality of each readplotReadCategoryQuals
View changes in signal against run time.plotReadTypeProduction
Read the log entry from a single fast5 filereadFast5Log
Read summary data from fast5 files.readFast5Summary
Extract readInfo slotreadInfo