# \#scarches

**URL:** https://discourse.scverse.org/tag/scarches/32.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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## [How to handle batch effects within the query dataset when using scArches + SCVI?](https://discourse.scverse.org/t/how-to-handle-batch-effects-within-the-query-dataset-when-using-scarches-scvi/3728)

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**Author:** [@ashenflower](https://discourse.scverse.org/u/ashenflower)\
**Replies:** 1\
**Last updated:** [July 31, 2025, 12:14pm UTC](https://discourse.scverse.org/t/how-to-handle-batch-effects-within-the-query-dataset-when-using-scarches-scvi/3728 "2025-07-31T12:14:23Z")

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Hello everyone, I’m new to scArches and currently exploring how it works in combination with SCVI, particularly for integrating new datasets into a reference atlas. I’m following this tutorial, where a SCVI model is fi…

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## [scArches with multiple covariates](https://discourse.scverse.org/t/scarches-with-multiple-covariates/1372)

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**Author:** [@jesswhitts](https://discourse.scverse.org/u/jesswhitts)\
**Replies:** 9\
**Last updated:** [September 22, 2024, 9:08pm UTC](https://discourse.scverse.org/t/scarches-with-multiple-covariates/1372 "2024-09-22T21:08:33Z")

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Hi, I want to use scArches to query disease samples to a normal reference. My data comes from a range of studies, using different single cell technologies, each including different patient samples. My reference model l…

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## [Handling Non-Matching Categorical Labels in scArches](https://discourse.scverse.org/t/handling-non-matching-categorical-labels-in-scarches/2517)

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**Author:** [@yojetsharma](https://discourse.scverse.org/u/yojetsharma)\
**Replies:** 0\
**Last updated:** [September 13, 2024, 8:46pm UTC](https://discourse.scverse.org/t/handling-non-matching-categorical-labels-in-scarches/2517 "2024-09-13T20:46:50Z")

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I’m using scArches to compare gene expression profiles between disease and normal samples. My query dataset contains cells from stem cells of healthy individuals and patients, labeled as WT, LSP2, and LSP3. The reference…

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## [How is the scArches scvi/scanvi pipeline different from the one on SCVI tutorials?](https://discourse.scverse.org/t/how-is-the-scarches-scvi-scanvi-pipeline-different-from-the-one-on-scvi-tutorials/2516)

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**Author:** [@yojetsharma](https://discourse.scverse.org/u/yojetsharma)\
**Replies:** 0\
**Last updated:** [September 13, 2024, 7:42pm UTC](https://discourse.scverse.org/t/how-is-the-scarches-scvi-scanvi-pipeline-different-from-the-one-on-scvi-tutorials/2516 "2024-09-13T19:42:19Z")

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Since scArches makes use of SCVI and scanvi in their tutorials for mapping, I was wondering why not just direct us to SCVI tutorial? How are the two different?

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## [Scpoli use guidance](https://discourse.scverse.org/t/scpoli-use-guidance/1964)

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**Author:** [@Nusob888](https://discourse.scverse.org/u/Nusob888)\
**Replies:** 0\
**Last updated:** [December 21, 2023, 12:06pm UTC](https://discourse.scverse.org/t/scpoli-use-guidance/1964 "2023-12-21T12:06:52Z")

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Hi, If any of the developers of scPoli are here, I would be grateful for some guidance on the best approach for an analysis. I read the paper and have had a look at the documentation, but the documentation is a little …

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## [Sequential scArches](https://discourse.scverse.org/t/sequential-scarches/1771)

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**Author:** [@Tinos94](https://discourse.scverse.org/u/Tinos94)\
**Replies:** 0\
**Last updated:** [September 24, 2023, 12:23pm UTC](https://discourse.scverse.org/t/sequential-scarches/1771 "2023-09-24T12:23:41Z")

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Hi, Thank you for this amazing tool-kit! Is it possible to perform sequential scArches, i.e. starting with a trained scVI reference model, and adding a single query dataset at a time? If so, how can I save the concaten…

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## [Transferring labels from combined embedding back to query with scArches](https://discourse.scverse.org/t/transferring-labels-from-combined-embedding-back-to-query-with-scarches/1314)

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**Author:** [@bennjmo](https://discourse.scverse.org/u/bennjmo)\
**Replies:** 2\
**Last updated:** [April 14, 2023, 12:28pm UTC](https://discourse.scverse.org/t/transferring-labels-from-combined-embedding-back-to-query-with-scarches/1314 "2023-04-14T12:28:04Z")

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I am following this tutorial to query the HCLA so that I can get cell labels. Unless I’m missing it, I can’t figure out how it is recommended to transfer the cell labels in the combined embedding back to my query ann…

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## [Matching features in query data and reference model](https://discourse.scverse.org/t/matching-features-in-query-data-and-reference-model/934)

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**Author:** [@emdann](https://discourse.scverse.org/u/emdann)\
**Replies:** 3\
**Last updated:** [November 23, 2022, 2:04pm UTC](https://discourse.scverse.org/t/matching-features-in-query-data-and-reference-model/934 "2022-11-23T14:04:44Z")

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Hi, I have a question on matching features between a trained xVI model and a query dataset (apologies if this is a duplicate). By default load\_query\_data wants matching features (fair enough). If you set inplace\_subset…

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## [Label transfer from CITE-seq](https://discourse.scverse.org/t/label-transfer-from-cite-seq/725)

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**Author:** [@FelixTheStudent](https://discourse.scverse.org/u/FelixTheStudent)\
**Replies:** 5\
**Last updated:** [September 16, 2022, 7:12pm UTC](https://discourse.scverse.org/t/label-transfer-from-cite-seq/725 "2022-09-16T19:12:40Z")

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Hi all, I’m looking for a way to transfer labels from a CITE-seq reference to a CITE-seq query. Initially I thought this should not be much different than the usual workflow with scvi or scArches. I thought I’d simply r…

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## [Freezing layers: register\_hook vs. requires\_grad](https://discourse.scverse.org/t/freezing-layers-register-hook-vs-requires-grad/553)

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**Author:** [@yugeji](https://discourse.scverse.org/u/yugeji)\
**Replies:** 1\
**Last updated:** [July 3, 2022, 11:22am UTC](https://discourse.scverse.org/t/freezing-layers-register-hook-vs-requires-grad/553 "2022-07-03T11:22:51Z")

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Hello, Looking at the way scArches module freezing is implemented at scvi-tools/\_archesmixin.py at 096099e34568b1bf94aad5273b9f92c202c9c755 · scverse/scvi-tools · GitHub for key, mod in module.named\_modules(): …

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## [Query data formatting to map onto a reference](https://discourse.scverse.org/t/query-data-formatting-to-map-onto-a-reference/510)

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**Author:** [@LuckyMD](https://discourse.scverse.org/u/LuckyMD)\
**Replies:** 3\
**Last updated:** [June 22, 2022, 10:25pm UTC](https://discourse.scverse.org/t/query-data-formatting-to-map-onto-a-reference/510 "2022-06-22T22:25:28Z")

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Hey scvi-tools team! I was wondering what the requirements are on the query AnnData object for prepare\_query\_anndata(). The documentation just says the query object should be: organized in the same way as data used to…

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## [Creating an atlas for online updating / architectural surgury using scANVI and partially labelled data](https://discourse.scverse.org/t/creating-an-atlas-for-online-updating-architectural-surgury-using-scanvi-and-partially-labelled-data/403)

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**Author:** [@JGM](https://discourse.scverse.org/u/JGM)\
**Replies:** 1\
**Last updated:** [April 14, 2022, 2:41am UTC](https://discourse.scverse.org/t/creating-an-atlas-for-online-updating-architectural-surgury-using-scanvi-and-partially-labelled-data/403 "2022-04-14T02:41:28Z")

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I am currently trying to combine data from two studies with multiple donors per study were we are integrating on donors. One of the studies has labels, the other doesn’t. This is a clear cut case for scANVI and it works …