R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System

The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided.

AuthorHans-Ulrich Klein, Christoph Bartenhagen, Christian Ruckert
Date of publicationNone
MaintainerHans-Ulrich Klein <h.klein@uni-muenster.de>
LicenseLGPL-3
Version1.24.0

View on Bioconductor

Man pages

alignShortReads: Exact alignment of DNA sequences against a reference

AnnotatedVariants-class: Class "AnnotatedVariants"

annotateVariants: Adds genomic information to variants

assayDataAmp: Access the amplicon data of an AVASet.

ava2vcf: Convert an AVASet object into a VCF object

AVASet: Creating an AVASet

AVASet-class: Class to contain Amplicon Variant Analyzer Output

avaSetExample: Amplicon Variant Analyzer data import

avaSetFiltered: Amplicon Variant Analyzer data import

avaSetFiltered_annot: AVASet variant annotations

baseFrequency: Absolute And Relative Frequency Of The Four Bases.

baseQualityHist: Plot A Histogram Of The Base Qualities.

baseQualityStats: Statistics Of Base Quality

breakpoints: Putative breakpoints of chimeric reads

Breakpoints-class: Class "Breakpoints"

calculateTiTv: Calculate transition transversion ratio

captureArray: Custom capture array design

complexity.dust: Sequence Complexity Using The DUST Algorithm

complexity.entropy: Sequence Complexity Using The Shannon-Wiener Algorithm

convertCigar: Basic functions for CIGAR strings

coverageOnTarget: Computes the coverage restricted to the target region.

demultiplexReads: Performs MID/Multiplex filtering

detectBreakpoints: Clustering and consensus breakpoint detection for chimeric...

dinucleotideOddsRatio: Dinucleotide Odds Ratio

fDataAmp: Access the amplicon data of an AVASet.

featureDataAmp: Access the amplicon data of an AVASet

filterChimericReads: Extract chimeric reads and apply filtering steps to remove...

flowgramBarplot: Create A Barplot Of The Flow Intensities

gcContent: Calculate The Overall GC-Content

gcContentHist: GC-Content Histogram

gcPerPosition: GC-Content Per Position

genomeSequencerMIDs: Retrieve GS multiplex sequences

getAlignedReads: Import reads from an Amplicon Variant Analyzer project

getAminoAbbr: Get amino acid abbreviations

getVariantPercentages: Variant coverage

homopolymerHist: Create A Histogram Of The Homopolymer Stretches

htmlReport: HTML-Report Builder for the AVASet and MapperSet

MapperSet: Creating a MapperSet

MapperSet-class: Class to Contain GS Reference Mapper Output

mapperSetExample: GS Reference Mapper data import

mergeBreakpoints: Identify and merge related breakpoints caused by the same...

mutationInfo: Example data for 'plotVariants'

nucleotideCharts: Nucleotide Charts

plotAmpliconCoverage: Creates a plot visualizing the number of reads per amplicon

plotChimericReads: Plots chimeric reads

plotVariants: Plots variant positions

plotVariationFrequency: Create an AVA style variation frequency plot

positionQualityBoxplot: Boxplot Of The Quality For Each Position

qualityReportSFF: Function To Create A Quality Report In PDF Format

readLengthHist: Histogram Of The Read Lengths

readLengthStats: Statistics For The Read Lengths

readSFF: Function To Read In Roche's .sff Files

readsOnTarget: Check for each read whether it aligns within the given...

referenceSequences: Access the reference sequences of an AVASet

regions: Example data for 'plotVariants'

removeLinker: Remove linker sequences located at the start of short reads

sequenceCaptureLinkers: Retrieve NimbleGen's sequence capture linkers

sequenceQualityHist: A Histogram Of The Sequence Qualities

setVariantFilter: Filters output of variant information

sff2fastq: Write A SFFContainer Object To A FASTQ File

SFFContainer-class: Class '"SFFContainer"'

SFFRead-class: Class '"SFFRead"'

variants: Example data for 'plotVariants'

writeSFF: Function To Write Files In Roche's .sff Format

Functions

addRead Man page
addRead,SFFContainer,SFFRead-method Man page
alignedReadsC1 Man page
alignedReadsC1<- Man page
alignedReadsC1<-,Breakpoints,list-method Man page
alignedReadsC1,Breakpoints-method Man page
alignedReadsC2 Man page
alignedReadsC2<- Man page
alignedReadsC2<-,Breakpoints,list-method Man page
alignedReadsC2,Breakpoints-method Man page
alignShortReads Man page
alignShortReads,AVASet,BSgenome,character,logical-method Man page
alignShortReads,AVASet,BSgenome,character,missing-method Man page
alignShortReads,AVASet,BSgenome,missing,logical-method Man page
alignShortReads,AVASet,BSgenome,missing,missing-method Man page
alignShortReads,AVASet,DNAStringSet,character-method Man page
alignShortReads,DNAStringSet,BSgenome,character,logical-method Man page
alignShortReads,DNAStringSet,BSgenome,character,missing-method Man page
alignShortReads,DNAStringSet,BSgenome,missing,logical-method Man page
alignShortReads,DNAStringSet,BSgenome,missing,missing-method Man page
annotatedVariants Man page
annotatedVariants<-,AnnotatedVariants,list-method Man page
annotatedVariants,AnnotatedVariants-method Man page
AnnotatedVariants-class Man page
annotateVariants Man page
annotateVariants,AVASet-method Man page
annotateVariants,AVASet,missing-method Man page
annotateVariants,data.frame,missing-method Man page
annotateVariants,MapperSet,BSgenome-method Man page
annotateVariants,MapperSet-method Man page
annotateVariants,MapperSet,missing-method Man page
assayDataAmp Man page
assayDataAmp<- Man page
assayDataAmp<-,AVASet,AssayData-method Man page
assayDataAmp,AVASet-method Man page
ava2vcf Man page
ava2vcf,AVASet-method Man page
AVASet Man page
[,AVASet,ANY,ANY,ANY-method Man page
[,AVASet,ANY,ANY-method Man page
AVASet,character,character,missing,missing,missing,missing,missi Man page
AVASet,character,missing,character,character,character,character Man page
AVASet,character,missing,character,character,character,missing,m Man page
AVASet,character,missing,missing,missing,missing,missing,missing Man page
AVASet-class Man page
avaSetExample Man page
avaSetFiltered Man page
avaSetFiltered_annot Man page
baseFrequency Man page
baseFrequency,DNAStringSet-method Man page
baseFrequency,SFFContainer-method Man page
baseFrequency,ShortRead-method Man page
baseQualityHist Man page
baseQualityHist,QualityScaledDNAStringSet-method Man page
baseQualityHist,SFFContainer-method Man page
baseQualityHist,ShortReadQ-method Man page
baseQualityStats Man page
baseQualityStats,QualityScaledDNAStringSet-method Man page
baseQualityStats,SFFContainer-method Man page
baseQualityStats,ShortReadQ-method Man page
breakpoints Man page
[,Breakpoints,ANY,ANY,ANY-method Man page
[,Breakpoints,ANY,ANY-method Man page
Breakpoints-class Man page
calculateTiTv Man page
calculateTiTv,AVASet-method Man page
calculateTiTv,MapperSet-method Man page
captureArray Man page
clipAdapterLeft Man page
clipAdapterLeft<- Man page
clipAdapterLeft,SFFContainer-method Man page
clipAdapterLeft<-,SFFContainer,numeric-method Man page
clipAdapterLeft,SFFRead-method Man page
clipAdapterLeft<-,SFFRead,numeric-method Man page
clipAdapterRight Man page
clipAdapterRight<- Man page
clipAdapterRight,SFFContainer-method Man page
clipAdapterRight<-,SFFContainer,numeric-method Man page
clipAdapterRight,SFFRead-method Man page
clipAdapterRight<-,SFFRead,numeric-method Man page
clipQualityLeft Man page
clipQualityLeft<- Man page
clipQualityLeft,SFFContainer-method Man page
clipQualityLeft<-,SFFContainer,numeric-method Man page
clipQualityLeft,SFFRead-method Man page
clipQualityLeft<-,SFFRead,numeric-method Man page
clipQualityRight Man page
clipQualityRight<- Man page
clipQualityRight,SFFContainer-method Man page
clipQualityRight<-,SFFContainer,numeric-method Man page
clipQualityRight,SFFRead-method Man page
clipQualityRight<-,SFFRead,numeric-method Man page
commonAlignC1 Man page
commonAlignC1<- Man page
commonAlignC1<-,Breakpoints,list-method Man page
commonAlignC1,Breakpoints-method Man page
commonAlignC2 Man page
commonAlignC2<- Man page
commonAlignC2<-,Breakpoints,list-method Man page
commonAlignC2,Breakpoints-method Man page
commonBpsC1 Man page
commonBpsC1<- Man page
commonBpsC1<-,Breakpoints,list-method Man page
commonBpsC1,Breakpoints-method Man page
commonBpsC2 Man page
commonBpsC2<- Man page
commonBpsC2<-,Breakpoints,list-method Man page
commonBpsC2,Breakpoints-method Man page
complexity.dust Man page
complexity.dust,DNAStringSet-method Man page
complexity.dust,SFFContainer-method Man page
complexity.dust,ShortRead-method Man page
complexity.entropy Man page
complexity.entropy,DNAStringSet-method Man page
complexity.entropy,SFFContainer-method Man page
complexity.entropy,ShortRead-method Man page
convertCigar Man page
coverageOnTarget Man page
coverageOnTarget,list,RangesList-method Man page
demultiplexReads Man page
demultiplexReads,XStringSet,XStringSet,missing,logical-method Man page
demultiplexReads,XStringSet,XStringSet,missing,missing-method Man page
demultiplexReads,XStringSet,XStringSet,numeric,logical-method Man page
demultiplexReads,XStringSet,XStringSet,numeric,missing-method Man page
detectBreakpoints Man page
detectBreakpoints,list-method Man page
dinucleotideOddsRatio Man page
dinucleotideOddsRatio,DNAStringSet-method Man page
dinucleotideOddsRatio,SFFContainer-method Man page
dinucleotideOddsRatio,ShortRead-method Man page
extendedCIGARToList Man page
fDataAmp Man page
fDataAmp,AVASet-method Man page
featureDataAmp Man page
featureDataAmp<- Man page
featureDataAmp<-,AVASet,AnnotatedDataFrame-method Man page
featureDataAmp,AVASet-method Man page
filterChimericReads Man page
filterChimericReads,list,missing,DNAString,missing,missing-metho Man page
filterChimericReads,list,missing,DNAString,numeric,numeric-metho Man page
filterChimericReads,list,missing,missing,missing,missing-method Man page
filterChimericReads,list,missing,missing,numeric,numeric-method Man page
filterChimericReads,list,RangesList,DNAString,missing,missing-me Man page
filterChimericReads,list,RangesList,DNAString,numeric,numeric-me Man page
filterChimericReads,list,RangesList,missing,missing,missing-meth Man page
filterChimericReads,list,RangesList,missing,numeric,numeric-meth Man page
flowChars Man page
flowChars<- Man page
flowChars<-,SFFContainer,character-method Man page
flowChars,SFFContainer-method Man page
flowChars<-,SFFRead,character-method Man page
flowChars,SFFRead-method Man page
flowgram Man page
flowgram<- Man page
flowgramBarplot Man page
flowgramBarplot,SFFRead-method Man page
flowgramFormat Man page
flowgramFormat<- Man page
flowgramFormat,SFFContainer-method Man page
flowgramFormat<-,SFFContainer,numeric-method Man page
flowgramFormat,SFFRead-method Man page
flowgramFormat<-,SFFRead,numeric-method Man page
flowgrams Man page
flowgrams<- Man page
flowgram,SFFRead-method Man page
flowgram<-,SFFRead,numeric-method Man page
flowgrams<-,SFFContainer,list-method Man page
flowgrams,SFFContainer-method Man page
flowIndexes Man page
flowIndexes<- Man page
flowIndexes<-,SFFContainer,list-method Man page
flowIndexes,SFFContainer-method Man page
flowIndexes,SFFRead-method Man page
flowIndexes<-,SFFRead,numeric-method Man page
gcContent Man page
gcContent,DNAStringSet-method Man page
gcContentHist Man page
gcContentHist,DNAStringSet-method Man page
gcContentHist,SFFContainer-method Man page
gcContentHist,ShortRead-method Man page
gcContent,SFFContainer-method Man page
gcContent,ShortRead-method Man page
gcPerPosition Man page
gcPerPosition,DNAStringSet-method Man page
gcPerPosition,SFFContainer-method Man page
gcPerPosition,ShortRead-method Man page
genomeSequencerMIDs Man page
genomeSequencerMIDs,character-method Man page
genomeSequencerMIDs,missing-method Man page
getAlignedReads Man page
getAlignedReads,AVASet-method Man page
getAminoAbbr Man page
getRead Man page
getRead,SFFContainer,character-method Man page
getReadStatus Man page
getReadStatus,MapperSet-method Man page
getVariantPercentages Man page
getVariantPercentages,AVASet-method Man page
getVariantPercentages,MapperSet-method Man page
homopolymerHist Man page
homopolymerHist,SFFRead-method Man page
htmlReport Man page
htmlReport,AVASet-method Man page
htmlReport,MapperSet-method Man page
keySequence Man page
keySequence<- Man page
keySequence<-,SFFContainer,character-method Man page
keySequence,SFFContainer-method Man page
keySequence<-,SFFRead,character-method Man page
keySequence,SFFRead-method Man page
length,Breakpoints-method Man page
listToExtendedCIGAR Man page
MapperSet Man page
MapperSet,character-method Man page
MapperSet-class Man page
mapperSetExample Man page
mergeBreakpoints Man page
mergeBreakpoints,Breakpoints,missing,list-method Man page
mergeBreakpoints,Breakpoints,missing,missing-method Man page
mergeBreakpoints,Breakpoints,numeric,missing-method Man page
mutationInfo Man page
name Man page
name<- Man page
names<-,AnnotatedVariants,character-method Man page
names,AnnotatedVariants-method Man page
names<-,Breakpoints,ANY-method Man page
names,Breakpoints-method Man page
name<-,SFFContainer,character-method Man page
name,SFFContainer-method Man page
name<-,SFFRead,character-method Man page
name,SFFRead-method Man page
nucleotideCharts Man page
nucleotideCharts,DNAStringSet-method Man page
nucleotideCharts,SFFContainer-method Man page
nucleotideCharts,ShortRead-method Man page
plotAmpliconCoverage Man page
plotAmpliconCoverage,AVASet,character,logical-method Man page
plotAmpliconCoverage,AVASet,character,missing-method Man page
plotAmpliconCoverage,AVASet,missing,logical-method Man page
plotAmpliconCoverage,AVASet,missing,missing-method Man page
plotChimericReads Man page
plotChimericReads,Breakpoints-method Man page
plotVariants Man page
plotVariants,AnnotatedVariants,character-method Man page
plotVariants,data.frame,character-method Man page
plotVariationFrequency Man page
plotVariationFrequency,character,numeric-method Man page
positionQualityBoxplot Man page
positionQualityBoxplot,QualityScaledDNAStringSet-method Man page
positionQualityBoxplot,SFFContainer-method Man page
positionQualityBoxplot,ShortReadQ-method Man page
quality<- Man page
qualityReportSFF Man page
quality<-,SFFRead,BString-method Man page
quality,SFFRead-method Man page
read Man page
read<- Man page
readLengthHist Man page
readLengthHist,DNAStringSet-method Man page
readLengthHist,SFFContainer-method Man page
readLengthHist,ShortRead-method Man page
readLengthStats Man page
readLengthStats,DNAStringSet-method Man page
readLengthStats,SFFContainer-method Man page
readLengthStats,ShortRead-method Man page
reads Man page
reads<- Man page
readSFF Man page
read,SFFRead-method Man page
read<-,SFFRead,QualityScaledDNAStringSet-method Man page
readsOnTarget Man page
readsOnTarget,list,RangesList-method Man page
reads,SFFContainer-method Man page
reads<-,SFFContainer,QualityScaledDNAStringSet-method Man page
referenceSequences Man page
referenceSequences<- Man page
referenceSequences<-,AVASet,AlignedRead-method Man page
referenceSequences,AVASet-method Man page
regions Man page
removeLinker Man page
removeLinker,XStringSet,DNAString,logical,numeric,numeric-method Man page
removeLinker,XStringSet,DNAString,missing,missing,missing-method Man page
seqsC1 Man page
seqsC1<- Man page
seqsC1<-,Breakpoints,list-method Man page
seqsC1,Breakpoints-method Man page
seqsC2 Man page
seqsC2<- Man page
seqsC2<-,Breakpoints,list-method Man page
seqsC2,Breakpoints-method Man page
sequenceCaptureLinkers Man page
sequenceCaptureLinkers,character-method Man page
sequenceCaptureLinkers,missing-method Man page
sequenceQualityHist Man page
sequenceQualityHist,QualityScaledDNAStringSet-method Man page
sequenceQualityHist,SFFContainer-method Man page
sequenceQualityHist,ShortReadQ-method Man page
setVariantFilter Man page
setVariantFilter,AVASet-method Man page
setVariantFilter,MapperSet-method Man page
sff2fastq Man page
sff2fastq,SFFContainer-method Man page
SFFContainer Man page
[,SFFContainer,ANY,ANY,ANY-method Man page
[,SFFContainer,ANY,ANY-method Man page
SFFContainer-class Man page
SFFRead Man page
SFFRead-class Man page
variants Man page
writeSFF Man page

Files

R453Plus1Toolbox/DESCRIPTION
R453Plus1Toolbox/NAMESPACE
R453Plus1Toolbox/R
R453Plus1Toolbox/R/AllClasses.R R453Plus1Toolbox/R/AllGenerics.R R453Plus1Toolbox/R/alignShortReads.R R453Plus1Toolbox/R/annotateVariants.R R453Plus1Toolbox/R/ava2vcf.R R453Plus1Toolbox/R/calculateTiTv.R R453Plus1Toolbox/R/convertCigar.R R453Plus1Toolbox/R/coverageOnTarget.R R453Plus1Toolbox/R/demultiplexReads.R R453Plus1Toolbox/R/detectBreakpoints.R R453Plus1Toolbox/R/filterChimericReads.R R453Plus1Toolbox/R/filterVariants.R R453Plus1Toolbox/R/genomeSequencerMIDs.R R453Plus1Toolbox/R/getAlignedReads.R R453Plus1Toolbox/R/getAminoAbbr.R R453Plus1Toolbox/R/htmlReport.R R453Plus1Toolbox/R/mergeBreakpoints.R R453Plus1Toolbox/R/methods-AVASet.R R453Plus1Toolbox/R/methods-AnnotatedVariants.R R453Plus1Toolbox/R/methods-Breakpoints.R R453Plus1Toolbox/R/methods-MapperSet.R R453Plus1Toolbox/R/methods-Roche454BaseCallerMetrics.R R453Plus1Toolbox/R/methods-Roche454QualityFilterMetrics.R R453Plus1Toolbox/R/methods-SFFContainer.R R453Plus1Toolbox/R/methods-SFFRead.R R453Plus1Toolbox/R/plotAmpliconCoverage.R R453Plus1Toolbox/R/plotChimericReads.R R453Plus1Toolbox/R/plotVariants.R R453Plus1Toolbox/R/plotVariationFrequency.R R453Plus1Toolbox/R/qualityControl.R R453Plus1Toolbox/R/qualityReportSFF.R R453Plus1Toolbox/R/read454BaseCallerMetrics.R R453Plus1Toolbox/R/read454QualityFilterMetrics.R R453Plus1Toolbox/R/readSFF.R R453Plus1Toolbox/R/readsOnTarget.R R453Plus1Toolbox/R/removeLinker.R R453Plus1Toolbox/R/sequenceCaptureLinkers.R R453Plus1Toolbox/R/writeSFF.R
R453Plus1Toolbox/build
R453Plus1Toolbox/build/vignette.rds
R453Plus1Toolbox/data
R453Plus1Toolbox/data/avaSetExample.RData
R453Plus1Toolbox/data/avaSetFiltered.RData
R453Plus1Toolbox/data/avaSetFiltered_annot.RData
R453Plus1Toolbox/data/breakpoints.RData
R453Plus1Toolbox/data/captureArray.RData
R453Plus1Toolbox/data/mapperSetExample.RData
R453Plus1Toolbox/data/plotVariantsExample.RData
R453Plus1Toolbox/inst
R453Plus1Toolbox/inst/CITATION
R453Plus1Toolbox/inst/NEWS.Rd
R453Plus1Toolbox/inst/doc
R453Plus1Toolbox/inst/doc/vignette.R
R453Plus1Toolbox/inst/doc/vignette.Rnw
R453Plus1Toolbox/inst/doc/vignette.pdf
R453Plus1Toolbox/inst/extdata
R453Plus1Toolbox/inst/extdata/AVASet
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/ProjectDef
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/ProjectDef/ampliconsProject.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I116
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I116/I36
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I116/I36/I116_vs_I36.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I116/I37
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I116/I37/I116_vs_I37.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I116/I40
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I116/I40/I116_vs_I40.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I116/I42
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I116/I42/I116_vs_I42.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I117
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I117/I36
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I117/I36/I117_vs_I36.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I117/I37
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I117/I37/I117_vs_I37.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I117/I40
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I117/I40/I117_vs_I40.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I117/I42
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I117/I42/I117_vs_I42.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I118
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I118/I36
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I118/I36/I118_vs_I36.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I118/I37
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I118/I37/I118_vs_I37.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I118/I40
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I118/I40/I118_vs_I40.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I118/I42
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I118/I42/I118_vs_I42.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9644
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9644/I36
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9644/I36/I9644_vs_I36.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9644/I37
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9644/I37/I9644_vs_I37.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9644/I40
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9644/I40/I9644_vs_I40.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9644/I42
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9644/I42/I9644_vs_I42.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9645
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9645/I36
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9645/I36/I9645_vs_I36.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9645/I37
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9645/I37/I9645_vs_I37.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9645/I40
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9645/I40/I9645_vs_I40.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9645/I42
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9645/I42/I9645_vs_I42.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9646
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9646/I36
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9646/I36/I9646_vs_I36.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9646/I37
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9646/I37/I9646_vs_I37.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9646/I37/I9646_vs_I37.readAlign.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9646/I40
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9646/I40/I9646_vs_I40.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9646/I42
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Align/I9646/I42/I9646_vs_I42.ampIds.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I116
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI36detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI37detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI40detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI42detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I117
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I117/I117xI36detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I117/I117xI37detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I117/I117xI40detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I117/I117xI42detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I118
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI36detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI37detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI40detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI42detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9644
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI36detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI37detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI40detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI42detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9645
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI36detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI37detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI40detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI42detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9646
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI36detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI37detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI40detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI42detectedVariants.txt
R453Plus1Toolbox/inst/extdata/AVASet/Amplicons/Results/Variants/currentVariantDefs.txt
R453Plus1Toolbox/inst/extdata/AVASet_doAmplicon
R453Plus1Toolbox/inst/extdata/AVASet_doAmplicon/amp.csv
R453Plus1Toolbox/inst/extdata/AVASet_doAmplicon/reference.csv
R453Plus1Toolbox/inst/extdata/AVASet_doAmplicon/sample.csv
R453Plus1Toolbox/inst/extdata/AVASet_doAmplicon/variant.csv
R453Plus1Toolbox/inst/extdata/AVASet_doAmplicon/variantHits.csv
R453Plus1Toolbox/inst/extdata/AVAVarFreqExport
R453Plus1Toolbox/inst/extdata/AVAVarFreqExport/AVAVarFreqExport.xls
R453Plus1Toolbox/inst/extdata/MapperSet
R453Plus1Toolbox/inst/extdata/MapperSet/N01
R453Plus1Toolbox/inst/extdata/MapperSet/N01/mapping
R453Plus1Toolbox/inst/extdata/MapperSet/N01/mapping/454HCDiffs.txt
R453Plus1Toolbox/inst/extdata/MapperSet/N01/mapping/454NewblerMetrics.txt
R453Plus1Toolbox/inst/extdata/MapperSet/N03
R453Plus1Toolbox/inst/extdata/MapperSet/N03/mapping
R453Plus1Toolbox/inst/extdata/MapperSet/N03/mapping/454HCDiffs.txt
R453Plus1Toolbox/inst/extdata/MapperSet/N03/mapping/454NewblerMetrics.txt
R453Plus1Toolbox/inst/extdata/MapperSet/N04
R453Plus1Toolbox/inst/extdata/MapperSet/N04/mapping
R453Plus1Toolbox/inst/extdata/MapperSet/N04/mapping/454HCDiffs.txt
R453Plus1Toolbox/inst/extdata/MapperSet/N04/mapping/454NewblerMetrics.txt
R453Plus1Toolbox/inst/extdata/SFF
R453Plus1Toolbox/inst/extdata/SFF/example.sff
R453Plus1Toolbox/inst/extdata/SVDetection
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.CAT.454Reads.fna
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.CAT.454Reads.qual
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.TCA.454Reads.fna
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.TCA.454Reads.qual
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.CAT.454Reads.fna
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.CAT.454Reads.qual
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.TCA.454Reads.fna
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.TCA.454Reads.qual
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454BaseCallerMetrics.csv
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454BaseCallerMetrics.txt
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454DataProcessingDir.xml
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454QualityFilterMetrics.csv
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454QualityFilterMetrics.txt
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454RuntimeMetricsAll.csv
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454RuntimeMetricsAll.txt
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/dataRunParams.xml
R453Plus1Toolbox/inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/gsRunProcessor.log
R453Plus1Toolbox/inst/extdata/SVDetection/bam
R453Plus1Toolbox/inst/extdata/SVDetection/bam/N01.bam
R453Plus1Toolbox/inst/extdata/SVDetection/chip
R453Plus1Toolbox/inst/extdata/SVDetection/chip/CaptureArray_hg19.bed
R453Plus1Toolbox/inst/extdata/qualityReport.Rnw
R453Plus1Toolbox/inst/javascript
R453Plus1Toolbox/inst/javascript/sorttable.js
R453Plus1Toolbox/man
R453Plus1Toolbox/man/AVASet-class.Rd R453Plus1Toolbox/man/AVASet.Rd R453Plus1Toolbox/man/AnnotatedVariants-class.Rd R453Plus1Toolbox/man/Breakpoints-class.Rd R453Plus1Toolbox/man/MapperSet-class.Rd R453Plus1Toolbox/man/MapperSet.Rd R453Plus1Toolbox/man/SFFContainer-class.Rd R453Plus1Toolbox/man/SFFRead-class.Rd R453Plus1Toolbox/man/alignShortReads.Rd R453Plus1Toolbox/man/annotateVariants.Rd R453Plus1Toolbox/man/assayDataAmp.Rd R453Plus1Toolbox/man/ava2vcf.Rd R453Plus1Toolbox/man/avaSetExample.Rd R453Plus1Toolbox/man/avaSetFiltered.Rd R453Plus1Toolbox/man/avaSetFiltered_annot.Rd R453Plus1Toolbox/man/baseFrequency.Rd R453Plus1Toolbox/man/baseQualityHist.Rd R453Plus1Toolbox/man/baseQualityStats.Rd R453Plus1Toolbox/man/breakpoints.Rd R453Plus1Toolbox/man/calculateTiTv.Rd R453Plus1Toolbox/man/captureArray.Rd R453Plus1Toolbox/man/complexity.dust.Rd R453Plus1Toolbox/man/complexity.entropy.Rd R453Plus1Toolbox/man/convertCigar.Rd R453Plus1Toolbox/man/coverageOnTarget.Rd R453Plus1Toolbox/man/demultiplexReads.Rd R453Plus1Toolbox/man/detectBreakpoints.Rd R453Plus1Toolbox/man/dinucleotideOddsRatio.Rd R453Plus1Toolbox/man/fDataAmp.Rd R453Plus1Toolbox/man/featureDataAmp.Rd R453Plus1Toolbox/man/filterChimericReads.Rd R453Plus1Toolbox/man/flowgramBarplot.Rd R453Plus1Toolbox/man/gcContent.Rd R453Plus1Toolbox/man/gcContentHist.Rd R453Plus1Toolbox/man/gcPerPosition.Rd R453Plus1Toolbox/man/genomeSequencerMIDs.Rd R453Plus1Toolbox/man/getAlignedReads.Rd R453Plus1Toolbox/man/getAminoAbbr.Rd R453Plus1Toolbox/man/getVariantPercentages.Rd R453Plus1Toolbox/man/homopolymerHist.Rd R453Plus1Toolbox/man/htmlReport.Rd R453Plus1Toolbox/man/mapperSetExample.Rd R453Plus1Toolbox/man/mergeBreakpoints.Rd R453Plus1Toolbox/man/mutationInfo.Rd R453Plus1Toolbox/man/nucleotideCharts.Rd R453Plus1Toolbox/man/plotAmpliconCoverage.Rd R453Plus1Toolbox/man/plotChimericReads.Rd R453Plus1Toolbox/man/plotVariants.Rd R453Plus1Toolbox/man/plotVariationFrequency.Rd R453Plus1Toolbox/man/positionQualityBoxplot.Rd R453Plus1Toolbox/man/qualityReportSFF.Rd R453Plus1Toolbox/man/readLengthHist.Rd R453Plus1Toolbox/man/readLengthStats.Rd R453Plus1Toolbox/man/readSFF.Rd R453Plus1Toolbox/man/readsOnTarget.Rd R453Plus1Toolbox/man/referenceSequences.Rd R453Plus1Toolbox/man/regions.Rd R453Plus1Toolbox/man/removeLinker.Rd R453Plus1Toolbox/man/sequenceCaptureLinkers.Rd R453Plus1Toolbox/man/sequenceQualityHist.Rd R453Plus1Toolbox/man/setVariantFilter.Rd R453Plus1Toolbox/man/sff2fastq.Rd R453Plus1Toolbox/man/variants.Rd R453Plus1Toolbox/man/writeSFF.Rd
R453Plus1Toolbox/src
R453Plus1Toolbox/src/io_lib
R453Plus1Toolbox/src/io_lib/os.h
R453Plus1Toolbox/src/readSFF.c
R453Plus1Toolbox/src/readSFF.h
R453Plus1Toolbox/src/writeSFF.c
R453Plus1Toolbox/src/writeSFF.h
R453Plus1Toolbox/vignettes
R453Plus1Toolbox/vignettes/vignette.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.