NEWS

ILoReg 0.99.6 (2022-03-08)

An updated version 0.99.6 is submitted to GitHub. threads=1 prints now information that is helpful in debugging.

An updated version 0.99.5 is submitted to GitHub. Includes an experimental feature that can be used to accelerate the ICP. "icp.batch.size" parameter in RunParallelICP can be set to, e.g. 2000 to use 2000 cells when learning the model. When running ICP in parallel, the order of the ICP runs in the result list was previously random, which affected the the principal components and the visualizations using t-SNE/UMAP. The ICP runs are now sorted based on the standard deviation of the probability matrices, which will very likely always produce the same order and the same visualizations. Finally, there was one bug that affected the DE analysis. The logFC values were by mistake retransformed to log-scale. Now the average values of the two groups are subtracted. The pseudocount.use parameter was removed. The method now assumes that the input data are log-transformed.