Files in Bioconductor-mirror/R453Plus1Toolbox
A package for importing and analyzing data from Roche's Genome Sequencer System

DESCRIPTION
NAMESPACE
R/AllClasses.R R/AllGenerics.R R/alignShortReads.R R/annotateVariants.R R/ava2vcf.R R/calculateTiTv.R R/convertCigar.R R/coverageOnTarget.R R/demultiplexReads.R R/detectBreakpoints.R R/filterChimericReads.R R/filterVariants.R R/genomeSequencerMIDs.R R/getAlignedReads.R R/getAminoAbbr.R R/htmlReport.R R/mergeBreakpoints.R R/methods-AVASet.R R/methods-AnnotatedVariants.R R/methods-Breakpoints.R R/methods-MapperSet.R R/methods-Roche454BaseCallerMetrics.R R/methods-Roche454QualityFilterMetrics.R R/methods-SFFContainer.R R/methods-SFFRead.R R/plotAmpliconCoverage.R R/plotChimericReads.R R/plotVariants.R R/plotVariationFrequency.R R/qualityControl.R R/qualityReportSFF.R R/read454BaseCallerMetrics.R R/read454QualityFilterMetrics.R R/readSFF.R R/readsOnTarget.R R/removeLinker.R R/sequenceCaptureLinkers.R R/writeSFF.R
data/avaSetExample.RData
data/avaSetFiltered.RData
data/avaSetFiltered_annot.RData
data/breakpoints.RData
data/captureArray.RData
data/mapperSetExample.RData
data/plotVariantsExample.RData
inst/CITATION
inst/NEWS.Rd
inst/extdata/AVASet/Amplicons/ProjectDef/ampliconsProject.txt
inst/extdata/AVASet/Amplicons/Results/Align/I116/I36/I116_vs_I36.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I116/I37/I116_vs_I37.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I116/I40/I116_vs_I40.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I116/I42/I116_vs_I42.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I117/I36/I117_vs_I36.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I117/I37/I117_vs_I37.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I117/I40/I117_vs_I40.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I117/I42/I117_vs_I42.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I118/I36/I118_vs_I36.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I118/I37/I118_vs_I37.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I118/I40/I118_vs_I40.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I118/I42/I118_vs_I42.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9644/I36/I9644_vs_I36.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9644/I37/I9644_vs_I37.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9644/I40/I9644_vs_I40.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9644/I42/I9644_vs_I42.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9645/I36/I9645_vs_I36.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9645/I37/I9645_vs_I37.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9645/I40/I9645_vs_I40.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/I37/I9646_vs_I37.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9646/I37/I9646_vs_I37.readAlign.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9646/I40/I9646_vs_I40.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Align/I9646/I42/I9646_vs_I42.ampIds.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI36detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI37detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI40detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI42detectedVariants.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/I118/I118xI36detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI37detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI40detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI42detectedVariants.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/I9644/I9644xI42detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI36detectedVariants.txt
inst/extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI37detectedVariants.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/I9646/I9646xI36detectedVariants.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/currentVariantDefs.txt
inst/extdata/AVASet_doAmplicon/amp.csv
inst/extdata/AVASet_doAmplicon/reference.csv
inst/extdata/AVASet_doAmplicon/sample.csv
inst/extdata/AVASet_doAmplicon/variant.csv
inst/extdata/AVASet_doAmplicon/variantHits.csv
inst/extdata/AVAVarFreqExport/AVAVarFreqExport.xls
inst/extdata/MapperSet/N01/mapping/454HCDiffs.txt
inst/extdata/MapperSet/N01/mapping/454NewblerMetrics.txt
inst/extdata/MapperSet/N03/mapping/454HCDiffs.txt
inst/extdata/MapperSet/N03/mapping/454NewblerMetrics.txt
inst/extdata/MapperSet/N04/mapping/454HCDiffs.txt
inst/extdata/MapperSet/N04/mapping/454NewblerMetrics.txt
inst/extdata/SFF/example.sff
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_31/1.CAT.454Reads.qual
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_31/1.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_31/2.CAT.454Reads.qual
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_31/454BaseCallerMetrics.csv
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454BaseCallerMetrics.txt
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.csv
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454QualityFilterMetrics.txt
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454RuntimeMetricsAll.csv
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454RuntimeMetricsAll.txt
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/dataRunParams.xml
inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/gsRunProcessor.log
inst/extdata/SVDetection/bam/N01.bam
inst/extdata/SVDetection/chip/CaptureArray_hg19.bed
inst/extdata/qualityReport.Rnw
inst/javascript/sorttable.js
man/AVASet-class.Rd man/AVASet.Rd man/AnnotatedVariants-class.Rd man/Breakpoints-class.Rd man/MapperSet-class.Rd man/MapperSet.Rd man/SFFContainer-class.Rd man/SFFRead-class.Rd man/alignShortReads.Rd man/annotateVariants.Rd man/assayDataAmp.Rd man/ava2vcf.Rd man/avaSetExample.Rd man/avaSetFiltered.Rd man/avaSetFiltered_annot.Rd man/baseFrequency.Rd man/baseQualityHist.Rd man/baseQualityStats.Rd man/breakpoints.Rd man/calculateTiTv.Rd man/captureArray.Rd man/complexity.dust.Rd man/complexity.entropy.Rd man/convertCigar.Rd man/coverageOnTarget.Rd man/demultiplexReads.Rd man/detectBreakpoints.Rd man/dinucleotideOddsRatio.Rd man/fDataAmp.Rd man/featureDataAmp.Rd man/filterChimericReads.Rd man/flowgramBarplot.Rd man/gcContent.Rd man/gcContentHist.Rd man/gcPerPosition.Rd man/genomeSequencerMIDs.Rd man/getAlignedReads.Rd man/getAminoAbbr.Rd man/getVariantPercentages.Rd man/homopolymerHist.Rd man/htmlReport.Rd man/mapperSetExample.Rd man/mergeBreakpoints.Rd man/mutationInfo.Rd man/nucleotideCharts.Rd man/plotAmpliconCoverage.Rd man/plotChimericReads.Rd man/plotVariants.Rd man/plotVariationFrequency.Rd man/positionQualityBoxplot.Rd man/qualityReportSFF.Rd man/readLengthHist.Rd man/readLengthStats.Rd man/readSFF.Rd man/readsOnTarget.Rd man/referenceSequences.Rd man/regions.Rd man/removeLinker.Rd man/sequenceCaptureLinkers.Rd man/sequenceQualityHist.Rd man/setVariantFilter.Rd man/sff2fastq.Rd man/variants.Rd man/writeSFF.Rd
src/io_lib/os.h
src/readSFF.c
src/readSFF.h
src/writeSFF.c
src/writeSFF.h
vignettes/vignette.Rnw
Bioconductor-mirror/R453Plus1Toolbox documentation built on May 31, 2017, 10:39 p.m.