qrqc: Quick Read Quality Control

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Quickly scans reads and gathers statistics on base and quality frequencies, read length, k-mers by position, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected.

Author
Vince Buffalo
Date of publication
None
Maintainer
Vince Buffalo <vsbuffalo@ucdavis.edu>
License
GPL (>=2)
Version
1.28.0
URLs

View on Bioconductor

Man pages

basePlot-methods
Plot Base Frequency or Proportion by Position
calcKL
Calculate the Kullback-Leibler Divergence Between the k-mer...
FASTASummary-class
'FASTASummary' class representing the summaries of a FASTA...
FASTQSummary-class
'FASTQSummary' class representing the summaries of a FASTQ...
gcPlot-methods
Plot GC Content by Position
geom_qlinerange
Use Line Segments and Points to Plot Quality Statistics by...
getBase-methods
Get a Data Frame of Base Frequency Data from a...
getBaseProp-methods
Get a Data Frame of Base Proportion Data from a...
getGC-methods
Get a Data Frame of GC Content from a 'SequenceSummary'...
getKmer-methods
Get a Data Frame of k-mer Frequency by Position from a...
getMCQual-methods
Get a Data Frame of Simulated Qualitied from a 'FASTQSummary'...
getQual-methods
Get a Data Frame of Quality Data from a 'FASTQSummary' object
getSeqlen-methods
Get a Data Frame of Sequence Lengths from a 'SequenceSummary'...
kmerEntropyPlot
Plot Entropy of k-mers by Position
kmerKLPlot
Plot K-L Divergence Components for a Subset of k-mers to...
list2df
Apply a function to items in list and combine into data frame
makeReport
Make an HTML report from a FASTASummary of FASTQSummary...
plotBases
Plot Bases by Position
plotGC
Plot per Base GC Content by Position
plotQuals
Plot a Base Quality Boxplot by Position
plotSeqLengths
Plot Histogram of Sequence Lengths
qualPlot-methods
Plot a Base Quality Boxplot by Position
readSeqFile
Read and Summarize a Sequence (FASTA or FASTQ) File
scale_color_dna
Set the color scheme to 'biovizBase"s for DNA
scale_color_iupac
Set the color scheme to 'biovizBase"s for IUPAC codes
seqlenPlot-methods
Plot a Histogram of Sequence Lengths
SequenceSummary-class
'SequenceSummary' class representing the summaries of a...

Files in this package

qrqc/ChangeLog
qrqc/DESCRIPTION
qrqc/NAMESPACE
qrqc/NEWS
qrqc/R
qrqc/R/AllClasses.R
qrqc/R/AllGenerics.R
qrqc/R/ggplotting-methods.R
qrqc/R/main.R
qrqc/R/plotting-methods.R
qrqc/R/report-methods.R
qrqc/R/show-methods.R
qrqc/R/utils.R
qrqc/README.md
qrqc/TODO
qrqc/build
qrqc/build/vignette.rds
qrqc/inst
qrqc/inst/NEWS
qrqc/inst/doc
qrqc/inst/doc/qrqc.R
qrqc/inst/doc/qrqc.Rnw
qrqc/inst/doc/qrqc.pdf
qrqc/inst/extdata
qrqc/inst/extdata/fasta-report-template.html
qrqc/inst/extdata/fastq-report-template.html
qrqc/inst/extdata/iupac.fastq
qrqc/inst/extdata/probes.fastq
qrqc/inst/extdata/random.fasta
qrqc/inst/extdata/test-contam.fastq
qrqc/inst/extdata/test-trimmed.fastq
qrqc/inst/extdata/test.fasta
qrqc/inst/extdata/test.fastq
qrqc/man
qrqc/man/FASTASummary-class.Rd
qrqc/man/FASTQSummary-class.Rd
qrqc/man/SequenceSummary-class.Rd
qrqc/man/basePlot-methods.Rd
qrqc/man/calcKL.Rd
qrqc/man/gcPlot-methods.Rd
qrqc/man/geom_qlinerange.Rd
qrqc/man/getBase-methods.Rd
qrqc/man/getBaseProp-methods.Rd
qrqc/man/getGC-methods.Rd
qrqc/man/getKmer-methods.Rd
qrqc/man/getMCQual-methods.Rd
qrqc/man/getQual-methods.Rd
qrqc/man/getSeqlen-methods.Rd
qrqc/man/kmerEntropyPlot.Rd
qrqc/man/kmerKLPlot.Rd
qrqc/man/list2df.Rd
qrqc/man/makeReport.Rd
qrqc/man/plotBases.Rd
qrqc/man/plotGC.Rd
qrqc/man/plotQuals.Rd
qrqc/man/plotSeqLengths.Rd
qrqc/man/qualPlot-methods.Rd
qrqc/man/readSeqFile.Rd
qrqc/man/scale_color_dna.Rd
qrqc/man/scale_color_iupac.Rd
qrqc/man/seqlenPlot-methods.Rd
qrqc/src
qrqc/src/Makevars
qrqc/src/Makevars.win
qrqc/src/R_init_io.c
qrqc/src/io.c
qrqc/src/io.h
qrqc/tests
qrqc/tests/test-functions.R
qrqc/vignettes
qrqc/vignettes/qrqc.Rnw