kota200/DEAR-OWL: DEAR-OWL v1.0.0

DEAR-OWL v1.0.0

This is the first public release of DEAR-OWL
(Differential Expression Analysis Resource on the Web, Lite), a browser-based application for differential expression analysis of RNA sequencing (RNA-seq) data.

Highlights

• Run DESeq2 directly in the browser through webR.
• Analyze hosted GExA (https://www.gexa.anesc.u-tokyo.ac.jp/) datasets or upload a raw count matrix.
• Keep uploaded count data inside the browser without sending it to a server.
• Perform two-group and one-factor multi-group comparisons.
• Use DESeq2 for standard analysis or the pairwise Z-test for fast screening.
• Generate MA plots, volcano plots, PCA plots, correlation heatmaps, and distance plots.
• Download result tables, normalized counts, plots, and analysis metadata.
• Launch DEAR-OWL locally on Windows, macOS, and Linux.

Privacy and offline analysis

Uploaded count matrices are read and processed locally in the browser. After the required runtime and input files are prepared, analysis runs with network access restricted to cached or browser-local files.

GExA mode downloads only the dataset selected by the user before analysis.

Input requirements

• Use raw, non-negative integer read counts.
• The first column must contain gene IDs.
• Each remaining column represents one sample.
• TPM values may be displayed as expression context but are not used for statistical testing.
• Current versions of Chrome or Edge are recommended.

Local use

• Windows: run start-local.cmd
• macOS or Linux: run sh start-local.sh
• macOS Finder: make start-local.command executable and open it

The local launcher is intended for uploaded count-matrix analysis. Use the hosted application for GExA datasets.

Validation

• JavaScript syntax checks passed.
• Unit tests passed.
• Offline and Service Worker tests passed.
• DESeq2 runner validation passed.

Documentation

See the repository README for usage, privacy, deployment, dataset configuration, and development information.

Acknowledgements

DEAR-OWL uses webR and DESeq2. When analyzing public datasets, please cite the corresponding source publications and database records.