Issues

• RunAzimuth assay parameter conflict

  satijalab/azimuth#300 · Filter by author pdcharles opened on Oct 13, 2026

• RunAzimuth() 0.5.1 fails in PercentageFeatureSet/LayerData with "counts" interpreted as a feature

  satijalab/azimuth#299 · Filter by author Rabouali75 opened on Aug 12, 2026
  1

• Error in Layers(): ! assay must be one of "RNA", not "SCT".

  satijalab/azimuth#297 · Filter by author wudustan opened on Jun 5, 2026
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• Error in possible.ids[apply(X = prediction.scores, MARGIN = 1, FUN = which.max)] : invalid subscript type 'list'

  satijalab/azimuth#296 · Filter by author SEWilhelmsen opened on Jun 2, 2026

• Query on assay objects returned after running RunAzimuth function.

  satijalab/azimuth#289 · Filter by author Chiranjit1504 opened on Mar 3, 2026

• Unexpected renaming of cell names in pca embeddings

  satijalab/azimuth#287 · Filter by author dimitrios-pm opened on Dec 15, 2025

• Error in proj.pca.list[[1]] : subscript out of bounds

  satijalab/azimuth#286 · Filter by author amayizara opened on Dec 14, 2025

• Clarification about message "Only 1 SCT model detected, no need to select" and how to do consider batches during RunAzimuth

  satijalab/azimuth#285 · Filter by author denvercal1234GitHub opened on Dec 13, 2025

• How to use our own reference

  satijalab/azimuth#283 · Filter by author Daisy-Chilin opened on Dec 1, 2025

• Failure of Azimuth installation

  satijalab/azimuth#282 · Filter by author TheangeawK opened on Nov 28, 2025
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• RunAzimuth > TransferData throws "invalid subscript type 'list'"

  satijalab/azimuth#279 · Filter by author smo-1212 opened on Oct 22, 2025
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• zenodo for mouse pansci only includes original rds, not ref.rds and idx.annoy like other references - suspect error in snakemake file

  satijalab/azimuth#277 · Filter by author turkeyri opened on Oct 3, 2025
  3

• Unable to download TSV and full results data

  satijalab/azimuth#276 · Filter by author poconnel3 opened on Oct 3, 2025

• Mouse Pansci reference data - markers for Sub_cell_types

  satijalab/azimuth#275 · Filter by author sgaedcke opened on Oct 2, 2025

• IntegrateLayers(method = scVIIntegration) fails with “ModuleNotFoundError: No module named ‘scanpy’” even when conda_env points to a working scvi-tools environment

  satijalab/azimuth#273 · Filter by author Doreen320 opened on Aug 9, 2025

• IntegrateLayers(method = scVIIntegration) fails with “ModuleNotFoundError: No module named ‘scanpy’” even when conda_env points to a working scvi-tools environment

  satijalab/azimuth#272 · Filter by author Doreen320 opened on Aug 9, 2025

• AzimuthReference() fails when called inside functions

  satijalab/azimuth#270 · Filter by author AnthonyChristidis opened on Aug 4, 2025

• Reference assay is SCT, but query assay is RNA. Mixing SCT and non-SCT in FindTransferAnchors is not supported.

  satijalab/azimuth#269 · Filter by author sunta3iouxos opened on Jun 29, 2025
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• merging different rds references

  satijalab/azimuth#268 · Filter by author sunta3iouxos opened on Jun 29, 2025

• RunAzimuth and FeaturePlot require different Seurat Versions

  satijalab/azimuth#267 · Filter by author Rfriedmancolumbia opened on Jun 13, 2025
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• Cannot run the RunAzimuth Function

  satijalab/azimuth#263 · Filter by author MC2511 opened on May 27, 2025
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• Kept getting error running azimuth due to assay difference

  satijalab/azimuth#262 · Filter by author MC2511 opened on May 23, 2025
  2

• Can not load the vizgen data to run your vignette

  satijalab/azimuth#260 · Filter by author AuritaP opened on May 1, 2025

• Bug Report: RunAzimuth() fails due to duplicate feature names after underscore replacement

  satijalab/azimuth#259 · Filter by author BenjaminDEMAILLE opened on Apr 30, 2025

• RunAzimuth() Error: Error in reference[["SCT"]]: ! 'SCT' not found in this Seurat object

  satijalab/azimuth#258 · Filter by author chrishklee opened on Apr 24, 2025
  7