Questions tagged [umap]

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votes
3answers
57 views

umap and Louvain clustering on normalized data

I know that scaled data must be used for PCA for example as it is based on variance maximization. However I'm wondering if it's the same case for UMAP ? If the data are single-cell RNA seq, after ...
0
votes
2answers
73 views

Adding certain barcodes to metadata in Seurat

I want to upload an excel file sheet that has certain barcodes that I would like to show on my umap. How do I go about adding the file and linking it to the metadata? Below is my following code. <...
1
vote
1answer
46 views

umap highlighting two different models

I'm trying to create a umap for single cell data from human samples and ptx samples. I can get the umap to where it shows the umap with the different clusters but I want to show where the ptx samples ...
0
votes
2answers
399 views

Running python script from terminal: umap issue

Some time ago I asked the question: RunUMAP in Seurat not working: module 'umap' has no attribute 'UMAP' It was solved by following the answer in it, however, it is still not ...
3
votes
1answer
3k views

RunUMAP in Seurat not working: module 'umap' has no attribute 'UMAP'

I am trying to run UMAP in the following way: ...