Harmony is executed on the Seurat object with Study 1 (Count), Study 2(TPM) and Study 2(Count) data. The parameters and commands are derived from the Harmony documentation. In all three studies we integrate data from different sources on the basis of common gene using Supplemental_code/Data_integration.R method.
Harmony_Study1_Count ---> The data from Study 1 is used in this case. We employ a standard pipeline with Seurat's Harmony wrapper.
Harmony_Study2_TPM  ---> Here we use Study 2TPM data. In this pipeline we log transformed integrated data and skip normalization step as TPM data is already length normalized. We use standard steps in Seurat Harmony wrapper.
Harmony_Study2_Count  ---> The count data corresponding to Study 2 is used in this case. We employ a standard pipeline with Seurat's Harmony wrapper.