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...

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

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