Package: IONiseR 2.31.0

Mike Smith

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_2.31.0.tar.gz
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IONiseR.pdf |IONiseR.html✨
IONiseR/json (API)
NEWS

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

Peer review:

On BioConductor:IONiseR-2.29.0(bioc 3.20)IONiseR-2.28.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

qualitycontroldataimportsequencing

4.30 score 5 scripts 327 downloads 2 mentions 22 exports 89 dependencies

Last updated 23 days agofrom:5d8cf1e0d9. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macNOTEOct 31 2024

Exports:baseCalledchannelActivityPlotchannelHeatmapeventDatafast5toFastqfastqfastq2DfastqComplementfastqTemplatelayoutPlotplotActiveChannelsplotBaseProductionRateplotCurrentByTimeplotEventRateplotKmerFrequencyCorrelationplotReadAccumulationplotReadCategoryCountsplotReadCategoryQualsplotReadTypeProductionreadFast5LogreadFast5SummaryreadInfo

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsclicodetoolscolorspacecpp11crayoncurlDelayedArraydeldirdplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehttrhwriterinterpIRangesisobandjpegjsonlitelabelinglambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigpngpurrrpwalignR6RColorBrewerRcppRcppEigenrhdf5rhdf5filtersRhdf5libRhtslibrlangRsamtoolsS4ArraysS4VectorsscalesShortReadsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

IONiseR

Mike L. Smith

Rendered fromIONiseR.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2020-09-21
Started: 2015-06-17

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