Statistical analysis of Solexa sequencing data

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Documentation for package ‘Rolexa’ version 1.1.7

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Rolexa-package Probabilistic Base Calling of Solexa Sequencing Data
BatchAnalysis Batch Analysis
BuildInfileList Build File Lists
BuildOutfileList Build File Lists
ChannelHistogram Selected diagnostic plots
CombinedPlot Selected diagnostic plots
DeCorrelateChannels Correct for global correlations
DeCorrelateCycles Correct for global correlations
FilterResults Save Results
ForkBatch Multi-threaded Probabilistic Base Calling
InitializeFromIntensities Fit and Plot Intensities
InitializeFromSequence Fit and Plot Intensities
InitializeModel Fit and Plot Intensities
LoadFastQ Load Intensities, Sequences or Scores from Files
LoadIntensities Load Intensities, Sequences or Scores from Files
LoadResults Load Intensities, Sequences or Scores from Files
LoadSeq Load Intensities, Sequences or Scores from Files
LoadSolexaResults Load Intensities, Sequences or Scores from Files
OneBatchEval Multi-threaded Probabilistic Base Calling
OneBatchFit Multi-threaded Probabilistic Base Calling
OptimizeAngle Correct for global correlations
OptimizeRate Correct for global correlations
PlotEvalCycles Fit and Plot Intensities
PlotFitCycles Fit and Plot Intensities
QualityBoxPlots Batch Analysis
Rolexa Probabilistic Base Calling of Solexa Sequencing Data
SaveResults Save Results
SeqEvalScore Fit and Plot Intensities
SeqFitScore Fit and Plot Intensities
TileImage Local background intensity correction
TileNormalize Local background intensity correction