Table A3.

The comparison methods used in this study.

Tools	Output	Language	Availability
iMAP [7]	Normalized gene expression matrix	Python	https://github.com/Svvord/iMAP (last access date: 12 February 2022)
MNN [6]	Normalized gene expression matrix	Python/R	https://github.com/MarioniLab/MNN2017 (last access date: 12 February 2022)
Scanorama [9]	Normalized dimension reduction vectors	Python/R	https://github.com/brianhie/scanorama (last access date: 12 February 2022)
Harmony [10]	Normalized feature reduction vectors	Python/R	https://github.com/immunogenomics/harmony (last access date: 12 February 2022)
SCALEX [8]	Normalized feature reduction vectors and Normalized gene expression matrix	Python	https://github.com/jsxlei/SCALEX (last access date: 12 February 2022)
BBKNN [12]	Connectivity graph and normalized dimension reduction vectors	Python	https://github.com/Teichlab/bbknn (last access date: 12 February 2022)