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SC-ION is not compatible with missing values. Previously, it was left to the user to remove missing values. Now, SC-ION will automatically filter any rows in the target, regulator, and clustering matrices with missing values. When this is performed, a message is printed to warn the user that there are missing values in the dataset which have been removed. If one wants to include the features with missing values, those values will need to be imputed.
Package compatibility has been checked for R-4.3. SC-ION should be compatible with R-4.3.