Issues

• Log transform in preprocessing

  theislab/scvelo#1346 · Filter by author gjhuizing opened on Aug 5, 2026

• Compatibility issues with newer versions of dependencies

  theislab/scvelo#1344 · Filter by author GirayEryilmaz opened on Jul 28, 2026
  1

• BUG: leastsq_generalized raises ValueError under NumPy 2.x due to size-one array assignment

  bug
  theislab/scvelo#1341 · Filter by author sd68515 opened on Jul 16, 2026

• velocity_embedding_stream fails with NumPy 2.x when X_umap is float32: "'x' values must be equally spaced"

  bug
  theislab/scvelo#1339 · Filter by author sd68515 opened on May 13, 2026

• scvelo.tl.velocity ValueError

  bug
  theislab/scvelo#1338 · Filter by author hschult opened on Feb 26, 2026
  7

• scvelo on different conditions from same Seurat obj

  theislab/scvelo#1335 · Filter by author OlgaLanzetta opened on Jan 25, 2026

• transition_matrix ignores basis_constraint for velocity_graph_neg

  bug
  theislab/scvelo#1330 · Filter by author andrewni4313 opened on Nov 17, 2025

• Remove neighbors function

  theislab/scvelo#1329 · Filter by author WeilerP opened on Nov 13, 2025

• proportions different between the clipped and unclipped data when using different groupby parameters

  bug
  theislab/scvelo#1313 · Filter by author MYDongHongJie opened on Oct 20, 2025

• Discrepancy between root estimate and the early velocity (pseudo)time point

  bug
  theislab/scvelo#1312 · Filter by author ogandril opened on Sep 23, 2025

• how to show my interested genes in the function scv.pl.heatmap

  theislab/scvelo#1309 · Filter by author zysmu opened on Jul 18, 2025

• Removing Duplicate Cells

  bug
  theislab/scvelo#1307 · Filter by author charisqi opened on Jul 16, 2025

• about scv.pl.scatter

  theislab/scvelo#1306 · Filter by author tonitsk-8264 opened on Jul 8, 2025
  1

• df = scv.get_df(adata, 'paga/transitions_confidence', precision=2).T

  bug
  theislab/scvelo#1304 · Filter by author bigmoore opened on May 25, 2025

• DeprecationWarnings: log1p and omp_set_nested deprecated — suggest updated practices

  theislab/scvelo#1303 · Filter by author BenjaminDEMAILLE opened on May 15, 2025
  1

• scv.tl.velocity(), SVD did not converge

  bug
  theislab/scvelo#1301 · Filter by author MengjurJ opened on Apr 17, 2025
  1

• Clarifying rank_velocity_genes output and interpretation

  enhancement
  theislab/scvelo#1300 · Filter by author katieaney opened on Apr 2, 2025

• Interpretation of differences between pseudotime and velocity stream

  theislab/scvelo#1299 · Filter by author LioLenr opened on Mar 17, 2025

• velocity_clusters fails if match_with is not in obs

  bug
  theislab/scvelo#1294 · Filter by author IsaacUtah1379 opened on Feb 5, 2025

• Identification of gene with similar velocity

  theislab/scvelo#1293 · Filter by author Dalhte opened on Jan 29, 2025

• Plotting issues with MuData (layers not available)

  bug
  theislab/scvelo#1290 · Filter by author dawe opened on Jan 3, 2025

• error in tl.paga: Invalid vertex ID

  theislab/scvelo#1266 · Filter by author sokratiag opened on Jul 26, 2024
  3

• NaN in velocity_umap

  theislab/scvelo#1265 · Filter by author wahdeeyau opened on Jul 22, 2024

• scv.pl.proportions() -- "axis 1 is out of bounds for array of dimension 1"

  theislab/scvelo#1237 · Filter by author Alvis-Jiang opened on Apr 18, 2024
  1

• an error in failing to save stream figures aftering installing some packages like "mpi4py petsc petsc4py"

  bug
  theislab/scvelo#1236 · Filter by author Shiywa opened on Apr 14, 2024