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.

Author
Welliton Souza, Benilton Carvalho <beniltoncarvalho@gmail.com>
Date of publication
None
Maintainer
Welliton Souza <well309@gmail.com>
License
GPL (>= 2)
Version
1.8.0
URLs

View on Bioconductor

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

Files in this package

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