Package: Rqc 1.41.0

Welliton Souza

Rqc: Quality Control Tool for High-Throughput Sequencing Data

Rqc is an optimised tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.

Authors:Welliton Souza, Benilton Carvalho <[email protected]>

Rqc_1.41.0.tar.gz
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Rqc.pdf |Rqc.html✨
Rqc/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/labbcb/rqc/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:Rqc-1.41.0(bioc 3.21)Rqc-1.40.0(bioc 3.20)

sequencingqualitycontroldataimport

5.94 score 58 scripts 576 downloads 3 mentions 43 exports 150 dependencies

Last updated 23 days agofrom:beb1258014. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-win-x86_64NOTENov 19 2024
R-4.5-linux-x86_64NOTENov 19 2024
R-4.4-win-x86_64NOTENov 19 2024
R-4.4-mac-x86_64NOTENov 19 2024
R-4.4-mac-aarch64NOTENov 19 2024
R-4.3-win-x86_64NOTENov 19 2024
R-4.3-mac-x86_64NOTENov 19 2024
R-4.3-mac-aarch64NOTENov 19 2024

Exports:checkpointdetectFileFormatfromRRDNAmatdistperCycleBasecallperCycleQualityperFileInformationperFileTopReadsperReadFrequencyperReadQualityperReadWidthrqcrqcCycleAverageQualityCalcrqcCycleAverageQualityPcaCalcrqcCycleAverageQualityPcaPlotrqcCycleAverageQualityPlotrqcCycleBaseCallsCalcrqcCycleBaseCallsLinePlotrqcCycleBaseCallsPlotrqcCycleGCCalcrqcCycleGCPlotrqcCycleQualityBoxCalcrqcCycleQualityBoxPlotrqcCycleQualityCalcrqcCycleQualityPlotrqcFileHeatmaprqcGroupCycleAverageQualityCalcrqcGroupCycleAverageQualityPlotrqcQArqcReadFrequencyCalcrqcReadFrequencyPlotrqcReadQualityBoxCalcrqcReadQualityBoxPlotrqcReadQualityCalcrqcReadQualityPlotrqcReadWidthCalcrqcReadWidthPlotrqcReportrqcShinyReportstats4trimsubsetByGroupsubsetByPairtoRRDNA

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiocStyleBiostringsbiovizBasebitbit64bitopsblobbookdownBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecommonmarkcpp11crayoncurldata.tableDBIDelayedArraydeldirdichromatdigestensembldbevaluatefansifarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttpuvhttrhwriterinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrmarkdownMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrplyrpngpromisesProtGenericspwalignR6rappdirsRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalesshinyShortReadsnowsourcetoolsSparseArraystringistringrSummarizedExperimentsystibbletinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxtableXVectoryamlzlibbioc

Rqc - Quality Control Tool for High-Throughput Sequencing Data

Welliton Souza, Benilton Carvalho

Rendered fromRqc.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2019-03-01
Started: 2014-10-09

Readme and manuals

Help Manual

Help pageTopics
Quality Control Tool for High-Throughput Sequencing DataRqc-package Rqc
Save time storing longer analysis step on diskcheckpoint
Detect file formatdetectFileFormat
Revert codified DNA sequences to original DNA sequences.fromRRDNA
Distance matrix of the similarity between the DNA sequences.matdist
Main Rqc functionrqc
Per cycle average quality by filesrqcCycleAverageQualityCalc rqcCycleAverageQualityPlot
Biplot of PCA of per cycle read average qualityrqcCycleAverageQualityPcaCalc rqcCycleAverageQualityPcaPlot
Per cycle base calls plotrqcCycleBaseCallsCalc rqcCycleBaseCallsLinePlot rqcCycleBaseCallsPlot
Per cycle percentual GC plotrqcCycleGCCalc rqcCycleGCPlot
Per cycle quality box plotrqcCycleQualityBoxCalc rqcCycleQualityBoxPlot
Per cycle quality plotrqcCycleQualityCalc rqcCycleQualityPlot
Heatmap of distance matrix of top over-represented readsrqcFileHeatmap
Per group average quality across cyclesrqcGroupCycleAverageQualityCalc rqcGroupCycleAverageQualityPlot
Quality Assessment Rqc functionrqcQA rqcQA,BamFile-method rqcQA,character-method rqcQA,FastqFile-method rqcQA,list-method
Read frequency plotrqcReadFrequencyCalc rqcReadFrequencyPlot
Per read mean quality box plotrqcReadQualityBoxCalc rqcReadQualityBoxPlot
Per read quality plotrqcReadQualityCalc rqcReadQualityPlot
Per read width plotrqcReadWidthCalc rqcReadWidthPlot
Quality Control HTML ReportrqcReport
Class RqcResultSetperCycleBasecall perCycleBasecall,list-method perCycleBasecall,RqcResultSet-method perCycleQuality perCycleQuality,list-method perCycleQuality,RqcResultSet-method perFileInformation perFileInformation,list-method perFileInformation,RqcResultSet-method perFileTopReads perFileTopReads,list-method perFileTopReads,RqcResultSet-method perReadFrequency perReadFrequency,list-method perReadFrequency,RqcResultSet-method perReadQuality perReadQuality,list-method perReadQuality,RqcResultSet-method perReadWidth perReadWidth,list-method perReadWidth,RqcResultSet-method RqcResultSet-class
Interactive Quality Control ReportrqcShinyReport
Minimun read mean quality and maximum percentage loss of reads estimations for trimming step.stats4trim
Subset RqcResultSet object by group name.subsetByGroup
Subset RqcResultSet object by pair files.subsetByPair
Title: Convert DNA sequences to Reduced Representation formattoRRDNA