Issues

• Publishing on every merged PR is hard to control

  dpeerlab/ENVI#95 · Filter by author Marius1311 opened on Aug 5, 2026
  1

• Splitting COVET into its own distribution: what it would take

  dpeerlab/ENVI#94 · Filter by author Marius1311 opened on Aug 5, 2026

• compute_covet(): log1p-transformed data incorrectly detected as raw counts, causing double log-transformation

  dpeerlab/ENVI#90 · Filter by author NoeCoursi opened on Apr 1, 2026

• How to impute all genes from SC data for Spatial data

  dpeerlab/ENVI#88 · Filter by author wjwei-handsome opened on Aug 4, 2025
  1

• How can I use other algorithms (e.g., UMAP, PHATE) to do the dimensional reduction?

  dpeerlab/ENVI#73 · Filter by author zyll123 opened on Nov 7, 2024

• Computing niches in cosmx data using fov as batch_key

  dpeerlab/ENVI#72 · Filter by author sarajimenez opened on Oct 31, 2024

• Output st_data.obsm['COVET'] of scenvi.compute_covet has the shape nx64x64, irrespective of k and g

  dpeerlab/ENVI#70 · Filter by author KarolineHoller opened on Sep 16, 2024

• Allow ENVI to cache COVET matrices on disk to avoid recomputing COVET and to enable larger datasets

  enhancement
  dpeerlab/ENVI#68 · Filter by author tddough98 opened on Jul 17, 2024

• How do you deal with the square root of negative covariance terms?

  dpeerlab/ENVI#67 · Filter by author dangeles opened on Jul 16, 2024

• Is this algorithm suitable for analyzing 10X Visium data?

  dpeerlab/ENVI#66 · Filter by author EddieLv opened on Jun 12, 2024

• Issue with latent space embedding with new version of ENVI

  dpeerlab/ENVI#65 · Filter by author rmathieu25 opened on Jun 12, 2024
  2

• Question on computing niche cell type composition

  dpeerlab/ENVI#56 · Filter by author ankitbioinfo opened on May 6, 2024
  1

• An error when installing envi

  dpeerlab/ENVI#9 · Filter by author HelloWorldLTY opened on Apr 5, 2024
  6

• Question on computing niches on spatial data

  dpeerlab/ENVI#8 · Filter by author abs51295 opened on Apr 3, 2024
  2

• Question on input to ENVI

  dpeerlab/ENVI#7 · Filter by author soerenab opened on Mar 20, 2024
  3