qrqc: Quick Read Quality Control

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.

AuthorVince Buffalo
Date of publicationNone
MaintainerVince Buffalo <vsbuffalo@ucdavis.edu>
LicenseGPL (>=2)
Version1.28.0
http://github.com/vsbuffalo/qrqc

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...

Functions

basePlot Man page
basePlot,list-method Man page
basePlot-methods Man page
basePlot,SequenceSummary-method Man page
calcKL Man page
calcKL,SequenceSummary-method Man page
FASTASummary-class Man page
FASTQSummary-class Man page
gcPlot Man page
gcPlot,list-method Man page
gcPlot-methods Man page
gcPlot,SequenceSummary-method Man page
geom_qlinerange Man page
getBase Man page
getBase-methods Man page
getBaseProp Man page
getBaseProp-methods Man page
getBaseProp,SequenceSummary-method Man page
getBase,SequenceSummary-method Man page
getGC Man page
getGC-methods Man page
getGC,SequenceSummary-method Man page
getKmer Man page
getKmer-methods Man page
getKmer,SequenceSummary-method Man page
getMCQual Man page
getMCQual,FASTQSummary-method Man page
getMCQual-methods Man page
getQual Man page
getQual,FASTQSummary-method Man page
getQual-methods Man page
getSeqlen Man page
getSeqlen-methods Man page
getSeqlen,SequenceSummary-method Man page
kmerEntropyPlot Man page
kmerEntropyPlot,list-method Man page
kmerEntropyPlot-methods Man page
kmerEntropyPlot,SequenceSummary-method Man page
kmerKLPlot Man page
kmerKLPlot,list-method Man page
kmerKLPlot-methods Man page
kmerKLPlot,SequenceSummary-method Man page
list2df Man page
makeReport Man page
makeReport,FASTASummary-method Man page
makeReport,FASTQSummary-method Man page
makeReport-methods Man page
plotBases Man page
plotBases-methods Man page
plotBases,SequenceSummary-method Man page
plotGC Man page
plotGC-methods Man page
plotGC,SequenceSummary-method Man page
plotQuals Man page
plotQuals,FASTQSummary-method Man page
plotQuals-methods Man page
plotSeqLengths Man page
plotSeqLengths-methods Man page
plotSeqLengths,SequenceSummary-method Man page
qualPlot Man page
qualPlot,FASTQSummary-method Man page
qualPlot,list-method Man page
qualPlot-methods Man page
readSeqFile Man page
scale_color_dna Man page
scale_color_iupac Man page
seqlenPlot Man page
seqlenPlot,list-method Man page
seqlenPlot-methods Man page
seqlenPlot,SequenceSummary-method Man page
SequenceSummary-class Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.