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

Share:

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.

Author
Hans-Ulrich Klein, Christoph Bartenhagen, Christian Ruckert
Date of publication
None
Maintainer
Hans-Ulrich Klein <h.klein@uni-muenster.de>
License
LGPL-3
Version
1.24.0

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