Updated compensation script to improve compensation and transformation. Also, manually updated Yale compensation due to poor compensation controls for FITC-A and PerCP-Cy5-5-A.
Updated transformation scripts to extract optimal values of FCSTrans width and allow more custom settings, such as using spillover matrix from FCS keywords.
Updated B-cell preprocessing to use median of FCSTrans widths.
Rearranged Bcell script for clarity.
Added a script to produce plots for a large number of candidate transformation parameter pairs.
Improved B-cell transformations for some markers and centers.
Updated the remaining panels' preprocessing scripts to use median width for transformations.
Added boundary filter to Bcell pipeline.
Updated Bcell munging script to apply upstream gates before estimating transformation parameters.
Updated munging scripts to set up GatingSets with latest center-specific transformation method.
Updated B-cell and T-cell pipelines.
Merge remote-tracking branch 'origin/master'