sangerseqR: Tools for Sanger Sequencing Data in R
Version 1.12.0

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

Browse man pages Browse package API and functions Browse package files

AuthorJonathon T. Hill, Bradley Demarest
Bioconductor views SNP Sequencing Visualization
Date of publicationNone
MaintainerJonathon Hill <jhill@byu.edu>
LicenseGPL-2
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("sangerseqR")

Man pages

abif-class: ABIF Class Objects
chromatogram: Generate Chromatogram
makeBaseCalls: Make Basecalls
PolyPeakParser: Run Poly Peak Parser
read.abif: Read ABIF Files
readsangerseq: Read Scf or ABIF Files
read.scf: Read Scf Files
sangerseqAccessors: Sangerseq Accessor Functions
sangerseq-class: Sangerseq Class Objects
sangerseqR-package: Tools for Sanger Sequencing Data in R
scf-class: Scf Class Objects
setAllelePhase: Set Reference and Alternate Alleles

Functions

PolyPeakParser Man page Source code
RTC Source code
SInt16 Source code
SInt32 Source code
SInt8 Source code
UInt16 Source code
UInt32 Source code
UInt8 Source code
abif Man page
abif-class Man page
basecalldf Source code
chromatogram Man page
chromatogram,sangerseq-method Man page
convertPoints Source code
f32 Source code
f64 Source code
getpeaks Source code
makeBaseCalls Man page
makeBaseCalls,sangerseq-method Man page
peakAmpMatrix Man page
peakAmpMatrix,sangerseq-method Man page
peakAmpMatrix<- Man page
peakAmpMatrix<-,sangerseq-method Man page
peakPosMatrix Man page
peakPosMatrix,sangerseq-method Man page
peakPosMatrix<- Man page
peakPosMatrix<-,sangerseq-method Man page
peakvalues Source code
primarySeq Man page
primarySeq,sangerseq-method Man page
primarySeq<- Man page
primarySeq<-,sangerseq-method Man page
primarySeqID Man page
primarySeqID,sangerseq-method Man page
primarySeqID<- Man page
primarySeqID<-,sangerseq-method Man page
read.abif Man page Source code
read.scf Man page Source code
readBinaryData Source code
readsangerseq Man page Source code
sangerseq Man page
sangerseq,abif-method Man page
sangerseq,scf-method Man page
sangerseq-class Man page
sangerseqR Man page
sangerseqR-package Man page
scf Man page
scf-class Man page
secondarySeq Man page
secondarySeq,sangerseq-method Man page
secondarySeq<- Man page
secondarySeq<-,sangerseq-method Man page
secondarySeqID Man page
secondarySeqID,sangerseq-method Man page
secondarySeqID<- Man page
secondarySeqID<-,sangerseq-method Man page
setAllelePhase Man page
setAllelePhase,sangerseq-method Man page
traceMatrix Man page
traceMatrix,sangerseq-method Man page
traceMatrix<- Man page
traceMatrix<-,sangerseq-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/PPPfunction.R
R/ReadFileFunctions.R
R/UnExportedFunctions.R
R/sangerseqmethods.R
build
build/vignette.rds
inst
inst/CITATION
inst/PolyPeakParser
inst/PolyPeakParser/example.ab1
inst/PolyPeakParser/framed.sty
inst/PolyPeakParser/fullpage.sty
inst/PolyPeakParser/geometry.sty
inst/PolyPeakParser/instructions.html
inst/PolyPeakParser/needspace.sty
inst/PolyPeakParser/pdflscape.sty
inst/PolyPeakParser/peakparser_report.Rnw
inst/PolyPeakParser/polypeakfunctions.R
inst/PolyPeakParser/server.R
inst/PolyPeakParser/ui.R
inst/PolyPeakParser/www
inst/PolyPeakParser/www/chromatogram.png
inst/PolyPeakParser/www/logo.png
inst/PolyPeakParser/www/logo2.png
inst/PolyPeakParser/www/logo3.png
inst/PolyPeakParser/www/styleupdates.css
inst/doc
inst/doc/sangerseq_walkthrough.R
inst/doc/sangerseq_walkthrough.Rnw
inst/doc/sangerseq_walkthrough.pdf
inst/extdata
inst/extdata/heterozygous.ab1
inst/extdata/heterozygous.scf
inst/extdata/homozygous.scf
inst/extdata/noprintabif.ab1
inst/testData
inst/testData/heterozygousabif.rds
inst/testData/heterozygousscf.rds
inst/testData/noprintabif.rds
inst/unitTests
inst/unitTests/test_readfilefunctions.R
man
man/PolyPeakParser.Rd
man/abif-class.Rd
man/chromatogram.Rd
man/makeBaseCalls.Rd
man/read.abif.Rd
man/read.scf.Rd
man/readsangerseq.Rd
man/sangerseq-class.Rd
man/sangerseqAccessors.Rd
man/sangerseqR-package.Rd
man/scf-class.Rd
man/setAllelePhase.Rd
tests
tests/runTests.R
vignettes
vignettes/sangerseq_walkthrough.Rnw
sangerseqR documentation built on May 20, 2017, 10:28 p.m.