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HTML report generation missing in v0.3.2

Status: Open.

#457 In broadinstitute/CellBender;

· GiveHeartToU opened on Jun 23, 2026

output h5ad

enhancementNew feature or improvementNew feature or improvement

Status: Open.

#453 In broadinstitute/CellBender;

· sjfleming opened on Jun 1, 2026

·  

v0.5.0

Alignment pipelines that use EM counts causing cellbender to add additional counts or make counts negative

Status: Open.

#452 In broadinstitute/CellBender;

· LinearParadox opened on May 20, 2026

Stop after GPU/training phase

Status: Open.

#451 In broadinstitute/CellBender;

· benscarlson opened on May 18, 2026

slim down docker image

Status: Open.

#448 In broadinstitute/CellBender;

· sjfleming opened on May 6, 2026

Request: support Notebook 7

Status: Open.

#443 In broadinstitute/CellBender;

· aowenson-imm opened on Mar 17, 2026

Strange cell probability plot in CellBender output

Status: Open.

#442 In broadinstitute/CellBender;

· huipan1973 opened on Mar 7, 2026

Processing Parse output

Status: Open.

#441 In broadinstitute/CellBender;

· leonor-rib opened on Feb 20, 2026

AssertionError: Fewer than 4 cells passed to encoder minibatch

Status: Open.

#440 In broadinstitute/CellBender;

· athirah-29 opened on Feb 17, 2026

Unable to save all plots - IndexError

Status: Open.

#439 In broadinstitute/CellBender;

· NadineBestard opened on Feb 13, 2026

Support for GEMX 10x Droplet Data

Status: Open.

#435 In broadinstitute/CellBender;

· xiaodeng6410 opened on Dec 23, 2025

add --force-use-checkpoint to WDL

enhancementNew feature or improvementNew feature or improvement

Status: Open.

#434 In broadinstitute/CellBender;

· sjfleming opened on Dec 8, 2025