# The GASSCO method for correcting for slide-dependent gene-specific dye bias

## Documentation for package ‘dyebias’ version 1.10.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

dyebias-package | The GASSCO method for correcting for slide-dependent gene-specific dye bias
dyebias | The GASSCO method for correcting for slide-dependent gene-specific dye bias
dyebias.application.subset | Return a subset of reporters that can be dye bias-corrected reasonably well
dyebias.apply.correction | Perform dye bias correction using the GASSCO method
dyebias.boxplot | Creates boxplots of the reporters with the strongest dye bias
dyebias.estimate.iGSDBs | Estimate intrinsic gene specific dye biases (part of the GASSCO method)
dyebias.maplot | Produce scatterplots of the hybridization, with strongest dye biases highlighted.
dyebias.monotonicity | Calculate the degree of monotonicity of the dye bias across the slides. DEPRACATED
dyebias.monotonicityplot | Show the degree of monotonicity of the dye bias across the slides. DEPRACATED
dyebias.rgplot | Produce scatterplots of the hybridization, with strongest dye biases highlighted.
dyebias.trendplot | Creates a trend-plot of all reporters, binned by dye bias, with all slides ordered by slide bias.