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OPEN RESEARCH

Software & data

Open-source software, reproducible workflows, and expression resources.

OPEN DATA RESOURCE

Expression atlas

Explore gene expression across bulk, single-cell, and spatial datasets, with cross-species ortholog mapping.

Open atlas ↗

Research software

All repositories ↗
Biomedical research

Biomed Workbench

A research workflow connecting scientific questions, multi-omics analysis, evidence interpretation, and publication deliverables.

Apache-2.0 · Original repository

View on GitHub ↗
Literature & accessibility

Paper Voice

Offline paper narration and synchronized translation for Zotero, with multilingual reading support.

MIT · Original repository

View on GitHub ↗Releases ↗
Regulatory genomics

SCENIC+ GRN Workflow

Reproducible SCENIC+ workflows for matched snRNA/snATAC and scMultiome data, including environment setup, motif resources, and network analysis.

MIT · Original repository

View on GitHub ↗
Spatial image analysis

SpatialPlexomera

Guided multiplex spatial image analysis, from composite visualization and cell typing to spatial measurements and figure exports.

MIT · Fork · Original project

View on GitHub ↗
Behavioral phenotyping

MouseScope

A desktop platform for mouse behavioral video analysis, including open field, object recognition, maze, swim, and suspension assays.

GPL-3.0 · Fork · Original project

View on GitHub ↗
Document workflows

MarkItDown

Convert documents and other file formats into Markdown for downstream research workflows.

MIT · Fork · Original project

View on GitHub ↗