sangerseqR: Tools for Sanger Sequencing Data in R

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

Author
Jonathon T. Hill, Bradley Demarest
Date of publication
None
Maintainer
Jonathon Hill <jhill@byu.edu>
License
GPL-2
Version
1.10.0

View on Bioconductor

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

Files in this package

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