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How to impute all genes from SC data for Spatial data

Status: Open.

#88 In dpeerlab/ENVI;

· wjwei-handsome opened on Aug 4, 2025

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

Status: Open.

#73 In dpeerlab/ENVI;

· zyll123 opened on Nov 7, 2024

Computing niches in cosmx data using fov as batch_key

Status: Open.

#72 In dpeerlab/ENVI;

· sarajimenez opened on Oct 31, 2024

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

Status: Open.

#70 In dpeerlab/ENVI;

· KarolineHoller opened on Sep 16, 2024

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

enhancementNew feature or requestNew feature or request

Status: Open.

#68 In dpeerlab/ENVI;

· tddough98 opened on Jul 17, 2024

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

Status: Open.

#67 In dpeerlab/ENVI;

· dangeles opened on Jul 16, 2024

Is this algorithm suitable for analyzing 10X Visium data?

Status: Open.

#66 In dpeerlab/ENVI;

· EddieLv opened on Jun 12, 2024

Issue with latent space embedding with new version of ENVI

Status: Open.

#65 In dpeerlab/ENVI;

· rmathieu25 opened on Jun 12, 2024

Question on computing niche cell type composition

Status: Open.

#56 In dpeerlab/ENVI;

· ankitbioinfo opened on May 6, 2024

An error when installing envi

Status: Open.

#9 In dpeerlab/ENVI;

· HelloWorldLTY opened on Apr 5, 2024

Question on computing niches on spatial data

Status: Open.

#8 In dpeerlab/ENVI;

· abs51295 opened on Apr 3, 2024

Question on input to ENVI

Status: Open.

#7 In dpeerlab/ENVI;

· soerenab opened on Mar 20, 2024