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