# muon

**URL:** https://discourse.scverse.org/c/help/muon/34.md

[Latest](https://discourse.scverse.org/latest.md) · [Categories](https://discourse.scverse.org/categories.md) · [Tags](https://discourse.scverse.org/tags.md)

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## [About the muon category](https://discourse.scverse.org/t/about-the-muon-category/328)

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**Author:** [@adamgayoso](https://discourse.scverse.org/u/adamgayoso)\
**Replies:** 0

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## [Cell hashing analysis using muon](https://discourse.scverse.org/t/cell-hashing-analysis-using-muon/3445)

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**Author:** [@urjabhatt](https://discourse.scverse.org/u/urjabhatt)\
**Replies:** 1\
**Last updated:** [July 12, 2025, 2:36pm UTC](https://discourse.scverse.org/t/cell-hashing-analysis-using-muon/3445 "2025-07-12T14:36:13Z")

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I am wondering how I can obtain counts of cell hashing barcodes when I load data using muon. Currently, Seurat has HTODemux to assign singlets to each hash BC. I wondering which software to use in the scanpy universe? I …

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## [Preprocessing CITE-seq with muon](https://discourse.scverse.org/t/preprocessing-cite-seq-with-muon/3658)

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**Author:** [@shihsama](https://discourse.scverse.org/u/shihsama)\
**Replies:** 0\
**Last updated:** [May 19, 2025, 7:36am UTC](https://discourse.scverse.org/t/preprocessing-cite-seq-with-muon/3658 "2025-05-19T07:36:35Z")

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Hi, I’m a fresh guy in processing CITE-seq data and so glad to see such a wonderful framework for multimodal data. I only had filtered data, so I chose CLR normalization for my ADT matrix. However, I was confused about…

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## [Mu.pp.intersect\_obs()](https://discourse.scverse.org/t/mu-pp-intersect-obs/3301)

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**Author:** [@Drito](https://discourse.scverse.org/u/Drito)\
**Replies:** 7\
**Last updated:** [May 9, 2025, 4:04pm UTC](https://discourse.scverse.org/t/mu-pp-intersect-obs/3301 "2025-05-09T16:04:00Z")

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Hello, I’m trying to integrate scATAC-seq and scRNA-seq from a 10x Genomics Multiome experiment, but I’m having problems when I run mu.pp.intersect\_obs(mdata). This is the error message: ValueError: Value passed for k…

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## [Daf (Data in Axes in Formats)](https://discourse.scverse.org/t/daf-data-in-axes-in-formats/2531)

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**Author:** [@orenbenkiki](https://discourse.scverse.org/u/orenbenkiki)\
**Replies:** 0\
**Last updated:** [September 24, 2024, 6:01am UTC](https://discourse.scverse.org/t/daf-data-in-axes-in-formats/2531 "2024-09-24T06:01:23Z")

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I understand there are ongoing discussions about the future of AnnData. I have just released alpha versions of GitHub - tanaylab/DataAxesFormats.jl: Data in Axes in Formats and dafpy · PyPI - R wrappers are WIP. This t…

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## [WNN neighborhood graph construction failing](https://discourse.scverse.org/t/wnn-neighborhood-graph-construction-failing/1930)

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**Author:** [@abbass2](https://discourse.scverse.org/u/abbass2)\
**Replies:** 1\
**Last updated:** [July 23, 2024, 11:46pm UTC](https://discourse.scverse.org/t/wnn-neighborhood-graph-construction-failing/1930 "2024-07-23T23:46:41Z")

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Hi everyone, Currently facing an issue where I am trying to run WNN in muon to integrate RNA and ATAC. The problem is that the neighborhood graph calculation is failing because there are cells in the ATAC graph that app…

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## [Sharing OBS between modalities](https://discourse.scverse.org/t/sharing-obs-between-modalities/1566)

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**Author:** [@djlisko01](https://discourse.scverse.org/u/djlisko01)\
**Replies:** 3\
**Last updated:** [May 9, 2024, 12:47am UTC](https://discourse.scverse.org/t/sharing-obs-between-modalities/1566 "2024-05-09T00:47:52Z")

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Hello, all, I’m new to the scverse and I love it so far! Just one quick question with muon object. I’m trying to load .obs with data for RNA and abt after I’ve already created the muon data object. My question is will I…

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## [Loading ATAC dataset](https://discourse.scverse.org/t/loading-atac-dataset/998)

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**Author:** [@PanosO](https://discourse.scverse.org/u/PanosO)\
**Replies:** 3\
**Last updated:** [October 23, 2023, 4:46pm UTC](https://discourse.scverse.org/t/loading-atac-dataset/998 "2023-10-23T16:46:22Z")

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Hello - I’m a novice with multimodal analysis, but relatively comfortable with scanpy. I have a scATAC dataset (GEO Accession viewer) that I’m trying to pair with another scRNA dataset, but I’m having trouble loading the…

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## [How to properly save and load a TotalVI trained model that's based on mudata?](https://discourse.scverse.org/t/how-to-properly-save-and-load-a-totalvi-trained-model-thats-based-on-mudata/1749)

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**Author:** [@hmnzo5gy](https://discourse.scverse.org/u/hmnzo5gy)\
**Replies:** 1\
**Last updated:** [September 7, 2023, 8:52pm UTC](https://discourse.scverse.org/t/how-to-properly-save-and-load-a-totalvi-trained-model-thats-based-on-mudata/1749 "2023-09-07T20:52:41Z")

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I set up the totalVI model using mudata scvi.model.TOTALVI.setup\_mudata( mdata, rna\_layer="counts", protein\_layer=None, batch\_key="batch", modalities={ "rna\_layer": "rna\_subset", "pro…

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## [How to best integrate Genomic Variant Information](https://discourse.scverse.org/t/how-to-best-integrate-genomic-variant-information/1673)

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**Author:** [@votti](https://discourse.scverse.org/u/votti)\
**Replies:** 1\
**Last updated:** [August 16, 2023, 8:49pm UTC](https://discourse.scverse.org/t/how-to-best-integrate-genomic-variant-information/1673 "2023-08-16T20:49:25Z")

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Hi there, I am currently evaluating Muon to provide the backend for multi-omics, patient level (=not single cell) datasets. What I have not found yet is if there is already a recommended way/example how to include geno…

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## [Muon function mofa.plot\_factors](https://discourse.scverse.org/t/muon-function-mofa-plot-factors/1328)

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**Author:** [@Ffht](https://discourse.scverse.org/u/Ffht)\
**Replies:** 2\
**Last updated:** [April 18, 2023, 3:05pm UTC](https://discourse.scverse.org/t/muon-function-mofa-plot-factors/1328 "2023-04-18T15:05:33Z")

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Hello, I am following Muon’s tutorial “Processing and integrating 5k PBMCs CITE-seq data” and I get an error on the mofa.plot\_factors function. This happens both with my data and with the ones provided by the tutorial i…

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## [Error with .var\_names\_make\_unique()](https://discourse.scverse.org/t/error-with-var-names-make-unique/1195)

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**Author:** [@fcat](https://discourse.scverse.org/u/fcat)\
**Replies:** 1\
**Last updated:** [March 9, 2023, 12:10am UTC](https://discourse.scverse.org/t/error-with-var-names-make-unique/1195 "2023-03-09T00:10:15Z")

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Hello, I am running my multiome data (atac + gex) with muon and am getting an error that pertains to the names saving back to the index. To be clear I am running muon on data that was created from bamtofastq as we no l…

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## [Muon: multiple set of data comparative analysis](https://discourse.scverse.org/t/muon-multiple-set-of-data-comparative-analysis/1034)

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**Author:** [@mdbabumiamssm](https://discourse.scverse.org/u/mdbabumiamssm)\
**Replies:** 2\
**Last updated:** [February 21, 2023, 7:45pm UTC](https://discourse.scverse.org/t/muon-multiple-set-of-data-comparative-analysis/1034 "2023-02-21T19:45:55Z")

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Hi , i’m using Muon for CITE-Seq data analysis. Can you help me to resolve certain issues :slight\_smile: I need to perform comparative analysis of multiple groups in same notebook. How to INTEGRATE or analyze multipl…

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## [3 sets of CITE-Seq data, how to concatenate or make single file for further analysis?](https://discourse.scverse.org/t/3-sets-of-cite-seq-data-how-to-concatenate-or-make-single-file-for-further-analysis/1116)

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**Author:** [@mdbabumiamssm](https://discourse.scverse.org/u/mdbabumiamssm)\
**Replies:** 0\
**Last updated:** [February 7, 2023, 10:17pm UTC](https://discourse.scverse.org/t/3-sets-of-cite-seq-data-how-to-concatenate-or-make-single-file-for-further-analysis/1116 "2023-02-07T22:17:02Z")

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Hi everyone , I have 3 sets of similar CITE-Seq data, i performed pre-processing individually using Muon+scanpy. Now, I want to make them as single file and perform comparative analysis. Any help ? Thanks in advance. …

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## [Error running mu.tl.mofa](https://discourse.scverse.org/t/error-running-mu-tl-mofa/1060)

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**Author:** [@nelkazwi](https://discourse.scverse.org/u/nelkazwi)\
**Replies:** 2\
**Last updated:** [January 16, 2023, 9:31am UTC](https://discourse.scverse.org/t/error-running-mu-tl-mofa/1060 "2023-01-16T09:31:36Z")

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Hi there, I am using muon to run MOFA on my multi-omics data. The data is first passed to MuData and mu.pp.intersect\_obs. When I run mu.tl.mofa , MOFA just gets interrupted: Attempting to save the model at the curren…

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## [Workaround for loading atac fragments without index file](https://discourse.scverse.org/t/workaround-for-loading-atac-fragments-without-index-file/703)

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**Author:** [@bio-la](https://discourse.scverse.org/u/bio-la)\
**Replies:** 0\
**Last updated:** [August 24, 2022, 8:24am UTC](https://discourse.scverse.org/t/workaround-for-loading-atac-fragments-without-index-file/703 "2022-08-24T08:24:22Z")

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Hello! i’m replicating the Teaseq analysis tutorial but i can’t load the fragments file cause I don’t have the index file, it’s not on GEO do you have a recommended workaround to read the fragment file without the index…

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## [Muon CITE-Seq analysis](https://discourse.scverse.org/t/muon-cite-seq-analysis/659)

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**Author:** [@LivR](https://discourse.scverse.org/u/LivR)\
**Replies:** 1\
**Last updated:** [August 5, 2022, 11:44am UTC](https://discourse.scverse.org/t/muon-cite-seq-analysis/659 "2022-08-05T11:44:25Z")

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Hi! Trying to follow the Muon tutorial, I get stuck on: pt.pp.dsb(mdata, raw=mdata\_raw, empty\_droplets=droplets) NameError: name ‘droplets’ is not defined Can anyone help?