README.md

The original BBKNN preprint performed some analyses that got ultimately removed from the BBKNN manuscript. All of the corresponding objects can be downloaded from ftp://ngs.sanger.ac.uk/production/teichmann/BBKNN/

• pancreas.ipynb constructed a pancreas object, and ran through the various BBKNN parameter options.
• pancreas-2-mnnCorrect.ipynb, pancreas-3-CCA.ipynb, pancreas-4-Scanorama.ipynb, pancreas-5-Harmony-kBET.ipynb process the pancreas data with the top batch correction packages 2018 had to offer. Some of these run instructions are antiquated by now.
• pbmc.ipynb runs BBKNN on 10X protocol variant PBMCs.
• mouse-exploratory-visualisation.ipynb is a browser notebook for the murine atlas/transcription factor network objects that can be downloaded from ftp://ngs.sanger.ac.uk/production/teichmann/BBKNN/MouseAtlas.zip