Statistical analysis of Solexa sequencing data


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Documentation for package ‘Rolexa’ version 1.2.0

User Guides and Package Vignettes

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BatchAnalysis Batch Analysis
BatchAnalysis,RolexaRun-method Batch Analysis
ChannelHistogram Diagnostic plots
ChannelHistogram,SolexaIntensity-method Diagnostic plots
CombinedPlot Diagnostic plots
CombinedPlot,RolexaRun-method Diagnostic plots
CombineFastQ SaveResults
CombineFastQ,RolexaRun,SolexaPath-method SaveResults
CombineReads SaveResults
CombineReads,RolexaRun,SolexaPath-method SaveResults
DeCorrelateChannels Correct for global correlations and biases
DeCorrelateChannels,array-method Correct for global correlations and biases
DeCorrelateChannels,SolexaIntensity-method Correct for global correlations and biases
DeCorrelateCycles Correct for global correlations and biases
DeCorrelateCycles,array-method Correct for global correlations and biases
DeCorrelateCycles,SolexaIntensity-method Correct for global correlations and biases
FilterResults FilterResults
FilterResults,RolexaRun-method FilterResults
ForkBatch Multi-threaded Probabilistic Base Calling
OneBatch Multi-threaded Probabilistic Base Calling
OneBatch,RolexaRun-method Multi-threaded Probabilistic Base Calling
OptimizeAngle Correct for global correlations and biases
OptimizeAngle,SolexaIntensity-method Correct for global correlations and biases
OptimizeRate Correct for global correlations and biases
OptimizeRate,SolexaIntensity-method Correct for global correlations and biases
PlotCycles Batch Analysis
PlotCycles,RolexaRun-method Batch Analysis
QualityBoxPlots Batch Analysis
SaveResults SaveResults
SaveResults,RolexaRun-method SaveResults
SeqScore Fit and Plot intensities
SeqScore,RolexaRun-method Fit and Plot intensities
TileImage Reconstruct tile image
TileImage,SolexaIntensity-method Reconstruct tile image
TileNormalize Correct for global correlations and biases
TileNormalize,RolexaRun-method Correct for global correlations and biases