Third ACE release (update): BMC Bioinformatics

This release includes some minor bug fixes, inclusion of a US Census data table, and update of new data set references. This represents the current status of ACE on resubmission of the ACE manuscript to BMC Bioinformatics on 9 March 2026.

Third ACE release: BMC Bioinformatics

This release includes several major and minor updates from version 2.0.0

• More data: Added at least nine new data sets in disease and cell type atlasing, including a blood cell type data set, as well as multiple patch-seq studies
• Data downloads: Data behind plots can now be downloaded in addition to the plots themselves in many cases
• Calculating statistics: Push-button calculation of statistics for multiple visualizations (e.g., correlation, Cramer's V, Kruskal Wallace)
• Improved filtering: Grep filter for categorical variables, and histogram showing distribution of numeric variables
• Reformatting of the app for improved user experience
• Additional link-outs, include short videos demonstrating how to use the tool
• Many bug fixes

Second ACE release: Webinar version

This release includes several major and minor updates from version 1.0.0

• More data: Added new comparison tables for exploration and corrected some errors in existing comparison tables
• Upload buttons: Allow users to upload a file to the web tool directly
• Flexibility in only showing relevant visualizations
• Consistent ordering and coloring of categories and annotations across and withing visualization panels
• Many bug fixes--the only known remaining issue is bookmarking doesn't work

First ACE release: AAIC version

First release of Annotation Comparison Explorer (ACE)

ACE is A versatile tool for comparing annotations across cell types, metadata, and taxonomies! It enables researchers to:

• Compare cell types across studies: Identify consistent changes in cell types related to diseases like Alzheimer's disease.
• Convert cell type classifications: Translate cell types between different Allen Institute-hosted classifications (or 'taxonomies').
• Evaluate clustering results: Compare user-generated clusters with established cell type classifications.
• Explore spatial and functional relationships: Analyze cell type distribution in brain regions and correlate with other cell properties.
• Assess data quality: Evaluate cell type data based on quality control metrics.
• Visualize cell type abundance: Compare cell type abundance across different conditions or groups.
• Perform general data exploration: Analyze various types of data beyond cell types using visualization tools.

This is a largely stable version, with a few known issues. Future versions will:

• Add new comparison tables for exploration
• Fix bookmarking to allow one to revisit any state of the app
• Add video tutorials to complement the existing User Guide
• Allow users to upload a file to the web tool directly

Please reach out via the "Feedback" button in the tool or by submitting a GitHub Issue if you have any comments about ACE.