sangerseqR: Tools for Sanger Sequencing Data in R

This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms.

AuthorJonathon T. Hill, Bradley Demarest
Date of publicationNone
MaintainerJonathon Hill <jhill@byu.edu>
LicenseGPL-2
Version1.10.0

View on Bioconductor

Functions

abif Man page
abif-class Man page
chromatogram Man page
chromatogram,sangerseq-method Man page
makeBaseCalls Man page
makeBaseCalls,sangerseq-method Man page
peakAmpMatrix Man page
peakAmpMatrix<- Man page
peakAmpMatrix<-,sangerseq-method Man page
peakAmpMatrix,sangerseq-method Man page
peakPosMatrix Man page
peakPosMatrix<- Man page
peakPosMatrix<-,sangerseq-method Man page
peakPosMatrix,sangerseq-method Man page
PolyPeakParser Man page
primarySeq Man page
primarySeq<- Man page
primarySeqID Man page
primarySeqID<- Man page
primarySeqID<-,sangerseq-method Man page
primarySeqID,sangerseq-method Man page
primarySeq<-,sangerseq-method Man page
primarySeq,sangerseq-method Man page
read.abif Man page
readsangerseq Man page
read.scf Man page
sangerseq Man page
sangerseq,abif-method Man page
sangerseq-class Man page
sangerseqR Man page
sangerseqR-package Man page
sangerseq,scf-method Man page
scf Man page
scf-class Man page
secondarySeq Man page
secondarySeq<- Man page
secondarySeqID Man page
secondarySeqID<- Man page
secondarySeqID<-,sangerseq-method Man page
secondarySeqID,sangerseq-method Man page
secondarySeq<-,sangerseq-method Man page
secondarySeq,sangerseq-method Man page
setAllelePhase Man page
setAllelePhase,sangerseq-method Man page
traceMatrix Man page
traceMatrix<- Man page
traceMatrix<-,sangerseq-method Man page
traceMatrix,sangerseq-method Man page

Files

sangerseqR/DESCRIPTION
sangerseqR/NAMESPACE
sangerseqR/R
sangerseqR/R/AllClasses.R sangerseqR/R/AllGenerics.R sangerseqR/R/PPPfunction.R sangerseqR/R/ReadFileFunctions.R sangerseqR/R/UnExportedFunctions.R sangerseqR/R/sangerseqmethods.R
sangerseqR/build
sangerseqR/build/vignette.rds
sangerseqR/inst
sangerseqR/inst/CITATION
sangerseqR/inst/PolyPeakParser
sangerseqR/inst/PolyPeakParser/example.ab1
sangerseqR/inst/PolyPeakParser/framed.sty
sangerseqR/inst/PolyPeakParser/fullpage.sty
sangerseqR/inst/PolyPeakParser/geometry.sty
sangerseqR/inst/PolyPeakParser/instructions.html
sangerseqR/inst/PolyPeakParser/needspace.sty
sangerseqR/inst/PolyPeakParser/pdflscape.sty
sangerseqR/inst/PolyPeakParser/peakparser_report.Rnw
sangerseqR/inst/PolyPeakParser/polypeakfunctions.R
sangerseqR/inst/PolyPeakParser/server.R
sangerseqR/inst/PolyPeakParser/ui.R
sangerseqR/inst/PolyPeakParser/www
sangerseqR/inst/PolyPeakParser/www/chromatogram.png
sangerseqR/inst/PolyPeakParser/www/logo.png
sangerseqR/inst/PolyPeakParser/www/logo2.png
sangerseqR/inst/PolyPeakParser/www/logo3.png
sangerseqR/inst/PolyPeakParser/www/styleupdates.css
sangerseqR/inst/doc
sangerseqR/inst/doc/sangerseq_walkthrough.R
sangerseqR/inst/doc/sangerseq_walkthrough.Rnw
sangerseqR/inst/doc/sangerseq_walkthrough.pdf
sangerseqR/inst/extdata
sangerseqR/inst/extdata/heterozygous.ab1
sangerseqR/inst/extdata/heterozygous.scf
sangerseqR/inst/extdata/homozygous.scf
sangerseqR/inst/extdata/noprintabif.ab1
sangerseqR/inst/testData
sangerseqR/inst/testData/heterozygousabif.rds
sangerseqR/inst/testData/heterozygousscf.rds
sangerseqR/inst/testData/noprintabif.rds
sangerseqR/inst/unitTests
sangerseqR/inst/unitTests/test_readfilefunctions.R
sangerseqR/man
sangerseqR/man/PolyPeakParser.Rd sangerseqR/man/abif-class.Rd sangerseqR/man/chromatogram.Rd sangerseqR/man/makeBaseCalls.Rd sangerseqR/man/read.abif.Rd sangerseqR/man/read.scf.Rd sangerseqR/man/readsangerseq.Rd sangerseqR/man/sangerseq-class.Rd sangerseqR/man/sangerseqAccessors.Rd sangerseqR/man/sangerseqR-package.Rd sangerseqR/man/scf-class.Rd sangerseqR/man/setAllelePhase.Rd
sangerseqR/tests
sangerseqR/tests/runTests.R
sangerseqR/vignettes
sangerseqR/vignettes/sangerseq_walkthrough.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.