simslab / cluster_diffex2018 Goto Github PK
View Code? Open in Web Editor NEWscRNA-seq clustering, visualization, and differential expression pipeline from Sims Lab papers
License: MIT License
scRNA-seq clustering, visualization, and differential expression pipeline from Sims Lab papers
License: MIT License
This version of the pipeline does not seem to include error handling for NaN's in the distance matrices. The old version included something like this, for example:
sp_matrix[np.isnan(sp_matrix)] = 0
This might not be the most best approach, but something is needed because this is an exceedingly common error and it crashes UMAP and results in nonsensical knn graphs.
As an illustrative example, the pipeline crashes on the 10x T cell matrix, which is a high-quality and commonly used benchmarking dataset. Here, NaN's likely occur because the data contain a single cellular lineage (and is therefore fairly homogeneous with small number of drop-out genes) and relatively low coverage (because T cells are small).
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