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

Files in this package

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

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