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Fine-tuning predicts only one cell type label regardless of input data

Status: Open.

#345 In bowang-lab/scGPT;

· Echozhao225 opened on Dec 15, 2025

Discrepancy between Supplementary Table 4 and Multi-omics tutorial results

Status: Open.

#343 In bowang-lab/scGPT;

· nc1m opened on Nov 12, 2025

Subject: Inquiry about ground truth labels for scGPT evaluation datasets (MS & Pancreas)

Status: Open.

#341 In bowang-lab/scGPT;

· mewjjjjn opened on Nov 11, 2025

Clarification on attention mask "order of prediction" and location of iterative selection code

Status: Open.

#338 In bowang-lab/scGPT;

· nc1m opened on Oct 29, 2025

Are any of the models listed in the README trained on CITE-seq?

Status: Open.

#337 In bowang-lab/scGPT;

· immunai-alyssam opened on Oct 24, 2025

Can the pretrained scGPT model be applied to bulk RNA-seq data (~10k samples)?

Status: Open.

#336 In bowang-lab/scGPT;

· aaaaaaaaaayong opened on Oct 14, 2025

Metrics discrepancy between Tutorial_Multiomics.ipynb and Supplementary Table 4

Status: Open.

#335 In bowang-lab/scGPT;

· nc1m opened on Oct 10, 2025

Retrieving Gene Embedding Question

Status: Open.

#334 In bowang-lab/scGPT;

· Hanxi-002 opened on Sep 30, 2025

Default pip install gives incompatible package versions

Status: Open.

#333 In bowang-lab/scGPT;

· james-vincent opened on Sep 29, 2025

environment.yml or equivalent from working install

Status: Open.

#332 In bowang-lab/scGPT;

· james-vincent opened on Sep 28, 2025

Problem installing scGPT

Status: Open.

#330 In bowang-lab/scGPT;

· imerelli opened on Sep 18, 2025

Support newer torch > 2.2.2

enhancementNew feature or requestNew feature or request

Status: Open.

#328 In bowang-lab/scGPT;

· subercui opened on Aug 30, 2025