ILoReg News
ILoReg 0.99.0 (Release date: 2020-06-25):
* The first version 0.99.0 is submitted to Bioconductor
ILoReg 0.99.5 (Release date: 2022-03-03):
* 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.
ILoReg 0.99.6 (Release date: 2022-03-08):
* An updated version 0.99.6 is submitted to GitHub. threads=1 prints now
information that is helpful in debugging.