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Benchmark datasets

Status: Open.

#36 In schwartzlab-methods/CellNEST;

· hayimroe-dotcom opened on Jun 3, 2026

Small suggestion: avoid sparse-to-dense conversion to prevent CUDA OOM

Status: Open.

#34 In schwartzlab-methods/CellNEST;

· DDDoGGie opened on Feb 10, 2026

output_graph_picture output is not readable

Status: Open.

#32 In schwartzlab-methods/CellNEST;

· pikapika505 opened on Feb 6, 2026

P-value script issue

Status: Open.

#30 In schwartzlab-methods/CellNEST;

· visanuwan opened on Dec 6, 2025

Singularity image pulling issue

Status: Open.

#29 In schwartzlab-methods/CellNEST;

· yurasong opened on Nov 26, 2025

Question about the large number of training epochs (60k or 80k) in the example​

Status: Open.

#28 In schwartzlab-methods/CellNEST;

· wyywyy999 opened on Sep 28, 2025

How to construct synthetic data

Status: Open.

#27 In schwartzlab-methods/CellNEST;

· Weicheng-Gu opened on Sep 22, 2025

Issue with CCC edges only within spots when using deconvoluted data (Cytospace output: same coordinates for multiple cells)

Status: Open.

#26 In schwartzlab-methods/CellNEST;

· Ron-bio opened on Aug 31, 2025

Some questions about the CellNEST

Status: Open.

#25 In schwartzlab-methods/CellNEST;

· litun-fkby opened on Aug 29, 2025

Improve visualization functions

Status: Open.

#23 In schwartzlab-methods/CellNEST;

· OMIC-coding opened on Aug 14, 2025

How to run CellNEST_interactive on a remote server without xdg-open, and access via browser URL/port ?

Status: Open.

#22 In schwartzlab-methods/CellNEST;

· Sawakotx opened on Aug 13, 2025

nest to cellnest in setup.sh

Status: Open.

#20 In schwartzlab-methods/CellNEST;

· northNomad opened on Aug 7, 2025