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Changes in Seurat v4

We have made minor changes in v4, primarily to improve the performance of Seurat v4 on large datasets. This includes minor changes to default parameter settings, and the use of newly available packages for tasks such as the identification of k-nearest neighbors, and graph-based clustering. These changes do not adversely impact downstream results, and we provide a detailed description of key changes below. Users who wish to continue using Seurat v3, or those interested in reproducing results produced by previous versions, may continue to install previous versions here.

Changes to parameter defaults

FindNeighbors

FindMarkers

IntegrateData/TransferData

SCTransform

Removed functions

The following functions have been removed in Seurat v4: