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