├── .Rbuildignore ├── .gitignore ├── ChangeLog ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── AllClasses.R ├── AllGenerics.R ├── ggplotting-methods.R ├── knitr-methods.R ├── main.R ├── plotting-methods.R ├── report-methods.R ├── show-methods.R └── utils.R ├── README.md ├── TODO ├── inst ├── NEWS └── extdata │ ├── fasta-report-template.html │ ├── fastq-report-template.html │ ├── iupac.fastq │ ├── knitr-report-template.Rhtml │ ├── knitr-report-template.Rnw │ ├── probes.fastq │ ├── random.fasta │ ├── test-contam.fastq │ ├── test-trimmed.fastq │ ├── test.fasta │ └── test.fastq ├── man ├── FASTASummary-class.Rd ├── FASTQSummary-class.Rd ├── SequenceSummary-class.Rd ├── basePlot-methods.Rd ├── calcKL.Rd ├── gcPlot-methods.Rd ├── geom_qlinerange.Rd ├── getBase-methods.Rd ├── getBaseProp-methods.Rd ├── getGC-methods.Rd ├── getKmer-methods.Rd ├── getMCQual-methods.Rd ├── getQual-methods.Rd ├── getSeqlen-methods.Rd ├── kmerEntropyPlot.Rd ├── kmerKLPlot.Rd ├── list2df.Rd ├── makeReport.Rd ├── plotBases.Rd ├── plotGC.Rd ├── plotQuals.Rd ├── plotSeqLengths.Rd ├── qualPlot-methods.Rd ├── readSeqFile.Rd ├── scale_color_dna.Rd ├── scale_color_iupac.Rd └── seqlenPlot-methods.Rd ├── src ├── Makevars ├── Makevars.win ├── R_init_io.c ├── io.c └── io.h ├── tests └── test-functions.R └── vignettes ├── qrqc.Rnw └── qrqc.pdf /.Rbuildignore: -------------------------------------------------------------------------------- 1 | \.git.* 2 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vsbuffalo/qrqc/HEAD/.gitignore -------------------------------------------------------------------------------- /ChangeLog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vsbuffalo/qrqc/HEAD/ChangeLog -------------------------------------------------------------------------------- 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