Introduction | Basic Workflow | Quality control report | File Information | Per Read Mean Quality Distribution of Files | Average Quality | Cycle-specific Average Quality | Read Frequency | Heatmap of top represented reads | Read Length Distribution | Cycle-specific GC Content | Cycle-specific Quality Distribution | PCA Biplot (cycle-specific read average quality) | Cycle-specific Quality Distribution - Boxplot | Cycle-specific Base Call Proportion | Advanced Workflow | Defining input files | Processing files | Generating report | Parallel processing | Graphics | Writing personalized quality control reports | Final Considerations | Session Information
Package: Rqc 1.47.0
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:
Rqc_1.47.0.tar.gz
Rqc_1.47.0.zip(r-4.7)Rqc_1.47.0.zip(r-4.6)Rqc_1.47.0.zip(r-4.5)
Rqc_1.47.0.tgz(r-4.6-x86_64)Rqc_1.47.0.tgz(r-4.6-arm64)Rqc_1.47.0.tgz(r-4.5-x86_64)Rqc_1.47.0.tgz(r-4.5-arm64)
Rqc_1.47.0.tar.gz(r-4.7-arm64)Rqc_1.47.0.tar.gz(r-4.7-x86_64)Rqc_1.47.0.tar.gz(r-4.6-arm64)Rqc_1.47.0.tar.gz(r-4.6-x86_64)
Rqc_1.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rqc/json (API)
| # Install 'Rqc' in R: |
| install.packages('Rqc', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/labbcb/rqc/issues
On BioConductor:Rqc-1.47.0(bioc 3.24)Rqc-1.46.0(bioc 3.23)
sequencingqualitycontroldataimportcpp
Last updated from:7a000f155f. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 245 | ||
| linux-devel-arm64 | NOTE | 417 | ||
| linux-devel-x86_64 | NOTE | 506 | ||
| source / vignettes | OK | 374 | ||
| linux-release-arm64 | NOTE | 417 | ||
| linux-release-x86_64 | NOTE | 542 | ||
| macos-release-arm64 | NOTE | 250 | ||
| macos-release-x86_64 | NOTE | 602 | ||
| macos-oldrel-arm64 | NOTE | 240 | ||
| macos-oldrel-x86_64 | NOTE | 523 | ||
| windows-devel | NOTE | 454 | ||
| windows-release | NOTE | 397 | ||
| windows-oldrel | NOTE | 456 | ||
| wasm-release | OK | 185 |
Exports:checkpointdetectFileFormatfromRRDNAmatdistperCycleBasecallperCycleQualityperFileInformationperFileTopReadsperReadFrequencyperReadQualityperReadWidthrqcrqcCycleAverageQualityCalcrqcCycleAverageQualityPcaCalcrqcCycleAverageQualityPcaPlotrqcCycleAverageQualityPlotrqcCycleBaseCallsCalcrqcCycleBaseCallsLinePlotrqcCycleBaseCallsPlotrqcCycleGCCalcrqcCycleGCPlotrqcCycleQualityBoxCalcrqcCycleQualityBoxPlotrqcCycleQualityCalcrqcCycleQualityPlotrqcFileHeatmaprqcGroupCycleAverageQualityCalcrqcGroupCycleAverageQualityPlotrqcQArqcReadFrequencyCalcrqcReadFrequencyPlotrqcReadQualityBoxCalcrqcReadQualityBoxPlotrqcReadQualityCalcrqcReadQualityPlotrqcReadWidthCalcrqcReadWidthPlotrqcReportrqcShinyReportstats4trimsubsetByGroupsubsetByPairtoRRDNA
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocManagerBiocParallelBiocStyleBiostringsbiovizBasebitbit64bitopsblobbookdownBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecommonmarkcpp11crayoncurldata.tableDBIDelayedArraydeldirdichromatdigestensembldbevaluatefarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttpuvhttrhwriterinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclelitedownmagrittrmarkdownMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslotelpkgconfigplyrpngpromisesProtGenericspwalignR6rappdirsRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoshinyShortReadsnowsourcetoolsSparseArraystringistringrSummarizedExperimentsystinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLxtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Quality Control Tool for High-Throughput Sequencing Data | Rqc-package Rqc |
| Save time storing longer analysis step on disk | checkpoint |
| Detect file format | detectFileFormat |
| Revert codified DNA sequences to original DNA sequences. | fromRRDNA |
| Distance matrix of the similarity between the DNA sequences. | matdist |
| Main Rqc function | rqc |
| Per cycle average quality by files | rqcCycleAverageQualityCalc rqcCycleAverageQualityPlot |
| Biplot of PCA of per cycle read average quality | rqcCycleAverageQualityPcaCalc rqcCycleAverageQualityPcaPlot |
| Per cycle base calls plot | rqcCycleBaseCallsCalc rqcCycleBaseCallsLinePlot rqcCycleBaseCallsPlot |
| Per cycle percentual GC plot | rqcCycleGCCalc rqcCycleGCPlot |
| Per cycle quality box plot | rqcCycleQualityBoxCalc rqcCycleQualityBoxPlot |
| Per cycle quality plot | rqcCycleQualityCalc rqcCycleQualityPlot |
| Heatmap of distance matrix of top over-represented reads | rqcFileHeatmap |
| Per group average quality across cycles | rqcGroupCycleAverageQualityCalc rqcGroupCycleAverageQualityPlot |
| Quality Assessment Rqc function | rqcQA rqcQA,BamFile-method rqcQA,character-method rqcQA,FastqFile-method rqcQA,list-method |
| Read frequency plot | rqcReadFrequencyCalc rqcReadFrequencyPlot |
| Per read mean quality box plot | rqcReadQualityBoxCalc rqcReadQualityBoxPlot |
| Per read quality plot | rqcReadQualityCalc rqcReadQualityPlot |
| Per read width plot | rqcReadWidthCalc rqcReadWidthPlot |
| Quality Control HTML Report | rqcReport |
| Class RqcResultSet | perCycleBasecall 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 Report | rqcShinyReport |
| 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 format | toRRDNA |
