Rqc: Quality Control Tool for High-Throughput Sequencing Data
Version 1.10.0

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.

AuthorWelliton Souza, Benilton Carvalho <beniltoncarvalho@gmail.com>
Bioconductor views DataImport QualityControl Sequencing
Date of publicationNone
MaintainerWelliton Souza <well309@gmail.com>
LicenseGPL (>= 2)
Version1.10.0
URL https://github.com/labbcb/Rqc
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Rqc")

Getting started

Package overview
README.md

Popular man pages

fromRRDNA: Revert codified DNA sequences to original DNA sequences.
rqc: Main Rqc function
rqcCycleAverageQualityPcaPlot: Biplot of PCA of per cycle read average quality
rqcCycleAverageQualityPlot: Per cycle average quality by files
rqcCycleBaseCallsPlot: Per cycle base calls plot
Rqc-package: Quality Control Tool for High-Throughput Sequencing Data
rqcReport: Quality Control HTML Report
See all...

All man pages Function index File listing

Man pages

checkpoint: Save time storing longer analysis step on disk
detectFileFormat: Detect file format
fromRRDNA: Revert codified DNA sequences to original DNA sequences.
matdist: Distance matrix of the similarity between the DNA sequences.
rqc: Main Rqc function
rqcCycleAverageQualityPcaPlot: Biplot of PCA of per cycle read average quality
rqcCycleAverageQualityPlot: Per cycle average quality by files
rqcCycleBaseCallsPlot: Per cycle base calls plot
rqcCycleGCPlot: Per cycle percentual GC plot
rqcCycleQualityBoxPlot: Per cycle quality box plot
rqcCycleQualityPlot: Per cycle quality plot
rqcFileHeatmap: Heatmap of distance matrix of top over-represented reads
rqcGroupCycleAverageQualityPlot: Per group average quality across cycles
Rqc-package: Quality Control Tool for High-Throughput Sequencing Data
rqcQA: Quality Assessment Rqc function
rqcReadFrequencyPlot: Read frequency plot
rqcReadQualityBoxPlot: Per read mean quality box plot
rqcReadQualityPlot: Per read quality plot
rqcReadWidthPlot: Per read width plot
rqcReport: Quality Control HTML Report
RqcResultSet-class: Class RqcResultSet
rqcShinyReport: Interactive Quality Control Report
stats4trim: Minimun read mean quality and maximum percentage loss of...
subsetByGroup: Subset RqcResultSet object by group name.
subsetByPair: Subset RqcResultSet object by pair files.
toRRDNA: Title: Convert DNA sequences to Reduced Representation format

Functions

Rqc Man page
Rqc-package Man page
RqcResultSet-class Man page
checkpoint Man page Source code
cycleBasecall Source code
cycleQuality Source code
detectFileFormat Man page Source code
fileInfo Source code
fromRRDNA Man page Source code
matdist Man page Source code
mergeCycleBasecall Source code
mergeCycleQuality Source code
mergeReadFrequency Source code
mergeReadQuality Source code
mergeReadWidth Source code
perCycleBasecall Man page
perCycleBasecall,RqcResultSet-method Man page
perCycleBasecall,list-method Man page
perCycleQuality Man page
perCycleQuality,RqcResultSet-method Man page
perCycleQuality,list-method Man page
perFileInformation Man page
perFileInformation,RqcResultSet-method Man page
perFileInformation,list-method Man page
perFileTopReads Man page
perFileTopReads,RqcResultSet-method Man page
perFileTopReads,list-method Man page
perReadFrequency Man page
perReadFrequency,RqcResultSet-method Man page
perReadFrequency,list-method Man page
perReadQuality Man page
perReadQuality,RqcResultSet-method Man page
perReadQuality,list-method Man page
perReadWidth Man page
perReadWidth,RqcResultSet-method Man page
perReadWidth,list-method Man page
readFrequency Source code
readMeanQuality Source code
readQuality Source code
readWidth Source code
rqc Man page Source code
rqcCycleAverageQualityCalc Man page Source code
rqcCycleAverageQualityPcaCalc Man page Source code
rqcCycleAverageQualityPcaPlot Man page Source code
rqcCycleAverageQualityPlot Man page Source code
rqcCycleBaseCallsCalc Man page Source code
rqcCycleBaseCallsLinePlot Man page Source code
rqcCycleBaseCallsPlot Man page Source code
rqcCycleGCCalc Man page Source code
rqcCycleGCPlot Man page Source code
rqcCycleQualityBoxCalc Man page Source code
rqcCycleQualityBoxPlot Man page Source code
rqcCycleQualityCalc Man page Source code
rqcCycleQualityPlot Man page Source code
rqcFileHeatmap Man page Source code
rqcGroupCycleAverageQualityCalc Man page Source code
rqcGroupCycleAverageQualityPlot Man page Source code
rqcQA Man page
rqcQA,BamFile-method Man page
rqcQA,FastqFile-method Man page
rqcQA,character-method Man page
rqcQA,list-method Man page
rqcReadFrequencyCalc Man page Source code
rqcReadFrequencyPlot Man page Source code
rqcReadQualityBoxCalc Man page Source code
rqcReadQualityBoxPlot Man page Source code
rqcReadQualityCalc Man page Source code
rqcReadQualityPlot Man page Source code
rqcReadWidthCalc Man page Source code
rqcReadWidthPlot Man page Source code
rqcReport Man page Source code
rqcShinyReport Man page Source code
server.Rqc Source code
stats4trim Man page Source code
subsetByGroup Man page Source code
subsetByPair Man page Source code
toRRDNA Man page Source code
ui.Rqc Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/RcppExports.R
R/Rqc-package.R
R/RqcResultSet.R
R/checkpoint.R
R/detectFileFormat.R
R/rqc.R
R/rqcCycleAverageQualityCalc.R
R/rqcCycleAverageQualityPcaCalc.R
R/rqcCycleAverageQualityPcaPlot.R
R/rqcCycleAverageQualityPlot.R
R/rqcCycleBaseCallsCalc.R
R/rqcCycleBaseCallsLinePlot.R
R/rqcCycleBaseCallsPlot.R
R/rqcCycleGCCalc.R
R/rqcCycleGCPlot.R
R/rqcCycleQualityBoxCalc.R
R/rqcCycleQualityBoxPlot.R
R/rqcCycleQualityCalc.R
R/rqcCycleQualityPlot.R
R/rqcFileHeatmap.R
R/rqcGroupCycleAverageQualityCalc.R
R/rqcGroupCycleAverageQualityPlot.R
R/rqcQA-methods.R
R/rqcReadFrquencyCalc.R
R/rqcReadFrquencyPlot.R
R/rqcReadQualityBoxCalc.R
R/rqcReadQualityBoxPlot.R
R/rqcReadQualityCalc.R
R/rqcReadQualityPlot.R
R/rqcReadWidthCalc.R
R/rqcReadWidthPlot.R
R/rqcReport.R
R/rqcShinyReport.R
R/stats4trim.R
R/subsetByGroup.R
R/subsetByPair.R
R/utils.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/Rqc.R
inst/doc/Rqc.Rmd
inst/doc/Rqc.html
inst/extdata
inst/extdata/Rqc.rda
inst/templates
inst/templates/rqc_report.Rmd
man
man/Rqc-package.Rd
man/RqcResultSet-class.Rd
man/checkpoint.Rd
man/detectFileFormat.Rd
man/fromRRDNA.Rd
man/matdist.Rd
man/rqc.Rd
man/rqcCycleAverageQualityPcaPlot.Rd
man/rqcCycleAverageQualityPlot.Rd
man/rqcCycleBaseCallsPlot.Rd
man/rqcCycleGCPlot.Rd
man/rqcCycleQualityBoxPlot.Rd
man/rqcCycleQualityPlot.Rd
man/rqcFileHeatmap.Rd
man/rqcGroupCycleAverageQualityPlot.Rd
man/rqcQA.Rd
man/rqcReadFrequencyPlot.Rd
man/rqcReadQualityBoxPlot.Rd
man/rqcReadQualityPlot.Rd
man/rqcReadWidthPlot.Rd
man/rqcReport.Rd
man/rqcShinyReport.Rd
man/stats4trim.Rd
man/subsetByGroup.Rd
man/subsetByPair.Rd
man/toRRDNA.Rd
src
src/RRDNA.cpp
src/RcppExports.cpp
tests
tests/testthat
tests/testthat.R
tests/testthat/test-rqcQA.R
tests/testthat/test_merge.R
tests/testthat/test_rrdna.R
vignettes
vignettes/Rqc.Rmd
Rqc documentation built on May 20, 2017, 9:55 p.m.

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