# \#clustering

**URL:** https://discourse.scverse.org/tag/clustering/23.md

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## [What to do with small clusters outside larger clusters in UMAP? Remove or keep?](https://discourse.scverse.org/t/what-to-do-with-small-clusters-outside-larger-clusters-in-umap-remove-or-keep/3935)

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**Author:** [@mmartimis](https://discourse.scverse.org/u/mmartimis)\
**Replies:** 2\
**Last updated:** [February 10, 2026, 10:00am UTC](https://discourse.scverse.org/t/what-to-do-with-small-clusters-outside-larger-clusters-in-umap-remove-or-keep/3935 "2026-02-10T10:00:54Z")

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Hi, I have a UMAP that is generally nicely clustered (with Harmony), but there are areas where I get long “tendrils” sticking out of the clusters or just spots of smaller clusters. What do you suggest doing with these? …

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## [Excluding Ig and ribosomal genes from HVG selection in scVI, best practice?](https://discourse.scverse.org/t/excluding-ig-and-ribosomal-genes-from-hvg-selection-in-scvi-best-practice/3833)

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**Author:** [@marencc](https://discourse.scverse.org/u/marencc)\
**Replies:** 1\
**Last updated:** [October 22, 2025, 9:15am UTC](https://discourse.scverse.org/t/excluding-ig-and-ribosomal-genes-from-hvg-selection-in-scvi-best-practice/3833 "2025-10-22T09:15:23Z")

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Hi everyone, I’m working with single-cell RNA-seq data from CD45⁺ immune cells (mostly lymphoid lineages) and integrating multiple batches using scVI, which so far has given the best batch correction results. We’re now…

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## [ST: clustering on each tissue section or clustering on all combined in anndata object?](https://discourse.scverse.org/t/st-clustering-on-each-tissue-section-or-clustering-on-all-combined-in-anndata-object/2460)

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**Author:** [@IbrahimFangary](https://discourse.scverse.org/u/IbrahimFangary)\
**Replies:** 0\
**Last updated:** [August 19, 2024, 6:44pm UTC](https://discourse.scverse.org/t/st-clustering-on-each-tissue-section-or-clustering-on-all-combined-in-anndata-object/2460 "2024-08-19T18:44:27Z")

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I’m new to MERFISH spatial transcriptomics and wondering whether I should preprocess and cluster cells for each tissue section separately or combine all the tissue sections into a single AnnData object for preprocessing …

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## [Clustering with scVI latent space](https://discourse.scverse.org/t/clustering-with-scvi-latent-space/1467)

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**Author:** [@maflot](https://discourse.scverse.org/u/maflot)\
**Replies:** 1\
**Last updated:** [May 26, 2023, 7:52pm UTC](https://discourse.scverse.org/t/clustering-with-scvi-latent-space/1467 "2023-05-26T19:52:19Z")

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Hey, I was just checking out the sc best practices: https://www.sc-best-practices.org/cellular\_structure/clustering.html Is it feasible to use the scVI latent space as base for computing the neighbor graph? Or are th…

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## [Subclustering of one single cluster in my UMAP Plot](https://discourse.scverse.org/t/subclustering-of-one-single-cluster-in-my-umap-plot/1255)

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**Author:** [@hamza](https://discourse.scverse.org/u/hamza)\
**Replies:** 0\
**Last updated:** [March 23, 2023, 10:36am UTC](https://discourse.scverse.org/t/subclustering-of-one-single-cluster-in-my-umap-plot/1255 "2023-03-23T10:36:00Z")

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Hi everybody, I am just a beginner and i did UMAP plot to cluster different cell types. now i am interested in one cluster and want to dig that one ( wanna do subclustering of that big cluster). can anyone help me with t…

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## [Choosing a Clustering Resolution](https://discourse.scverse.org/t/choosing-a-clustering-resolution/1132)

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**Author:** [@danamcc](https://discourse.scverse.org/u/danamcc)\
**Replies:** 1\
**Last updated:** [February 17, 2023, 7:44am UTC](https://discourse.scverse.org/t/choosing-a-clustering-resolution/1132 "2023-02-17T07:44:27Z")

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Hi, I have a large dataset where there is no ground truth to what clusters should be, so I can’t used annotation based validation. I’m having difficulty choosing an appropriate resolution when doing leiden clustering. I…

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## [How to decide the number of Optimal clusters while clustering the subtypes of cells](https://discourse.scverse.org/t/how-to-decide-the-number-of-optimal-clusters-while-clustering-the-subtypes-of-cells/568)

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**Author:** [@AkilaRanjith](https://discourse.scverse.org/u/AkilaRanjith)\
**Replies:** 1\
**Last updated:** [July 8, 2022, 1:43am UTC](https://discourse.scverse.org/t/how-to-decide-the-number-of-optimal-clusters-while-clustering-the-subtypes-of-cells/568 "2022-07-08T01:43:23Z")

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Hello All, I am working on approximately five hundred thousand cells belonging to brain tissue. I want to do clustering the neuronal and non-neuronal subtypes. For example: In microglia cell type would like to see home…

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## [Clustering subsets of cells](https://discourse.scverse.org/t/clustering-subsets-of-cells/204)

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**Author:** [@Diogo\_de\_Moraes](https://discourse.scverse.org/u/Diogo_de_Moraes)\
**Replies:** 3\
**Last updated:** [November 15, 2021, 1:27pm UTC](https://discourse.scverse.org/t/clustering-subsets-of-cells/204 "2021-11-15T13:27:36Z")

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Hello. I have some datasets I would like to integrate, select a few cell types that interest me and recluster them. However, I think I might have a problem with the second time I select variable genes and train the mode…