JinmiaoChenLab / Batch-effect-removal-benchmarking

A benchmark of batch-effect correction methods for single-cell RNA sequencing data
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How could I use .loom file in Liger method? #7

Open HelloWorldLTY opened 3 years ago

HelloWorldLTY commented 3 years ago

I meet some problems when I intend to load data in loom file to the pipeline you provide in this code, could you please give me some suggestions here?

In addition, when you use IMAP to visulaize your result, is the performance is same for every time you run a same dataset? Or in fact there will be some slight change in this part? Thanks.

Currently I am trying to run the same methods you mentioned in this paper in other platform(eg. harmony in python) but I get different clisi/asw/ilisi rate. Is it reasonable? Thanks.