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                                            hsuknowledge

scaleNotCenter Rcpp performance for dgCMatrix is impacted by unpruned zeroes

During data import, [this line](https://github.com/welch-lab/liger/blob/aca1681e4bea2ed988e74577547a0aff8781b3c2/R/import.R#L244) checks if the input is already a `dgCMatrix`; if not, cast it using `as("CsparseMatrix")`. As a potential solution, I tested but casting it again does...

is_installed fails to check package status

> It seems that `requireNamespace()` is loading the namespace. Is this changing the environment? The first message seems so, but it fails without loading the namespace. Quite confusing but by...

UMI deduplication is not done for calculating nuclear fraction

From our own data (analyzed via _STARsolo Velocyto_), we find that on the log-log plot, we can draw a straight line to divide the two groups, which incidentally has a...

HNSW index build reproducibility - use single thread instead

I have not touched the `batch = TRUE` setting, believing that patch is necessary for reproducibilty in the optimization step. What I found that cannot be controlled with seed was...

HNSW index build reproducibility - use single thread instead

> A workaround is to build the neighbor graph outside of `umap2` and pass the results to the `nn_method` parameter. Thank you for the advice. I now use `findKNN()` from...