Fix/tissue in files#98
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Introduces the DifferentialExpressionExperiment model, serializer, and API endpoints for listing and submitting experiments. Adds initial migration, model definition, serializer, and views for experiment management. Integrates the new app's URLs into the main project routing.
Introduces new service and task modules for differential expression, adds related Django migrations, and updates models, views, and URLs to support new experiment features. Also adds a regression example notebook and updates feature selection tasks.
Introduces a results_json JSONField to DifferentialExpressionExperiment for efficient storage of full differential expression results. Adds model methods for saving, retrieving, and filtering results, updates the serializer to expose results metadata, and modifies the service and task logic to save and handle results as JSON. Also updates .gitignore and improves mRNA data processing in the service.
Major refactor of differential expression models to use dedicated Source and ClinicalSource models, and store experiment results in a normalized table instead of JSON. Updated admin, serializers, views, and service logic to support new data model and endpoints for results and significant genes. Removed obsolete migrations and added new migration for timestamp fields. Improved mRNA/clinical data processing and result handling.
Introduces a 'top' field to DifferentialExpressionExperiment to control the number of significant results returned (max 1000). Updates model, admin, serializer, view, and service logic to support this parameter, adds validation, and improves error handling for cases with no samples or features. Also updates frontend template metadata and page title.
Dockerfile and Dockerfile-celery now install R 4.4.2 and Bioconductor limma for differential expression analysis. Updated README to list R as a requirement and document the new Celery worker queue. docker-compose_dist.yml adds a differential-expression-worker service and includes it in the backend dependencies.
Introduces DifferentialExpressionStop API view and URL to allow authenticated users to stop a running differential expression experiment. Includes permission checks, state validation, and integration with abortable Celery tasks.
Fix/prev state bug
Enhance ChatPanel with fullscreen support, MCP integration, and UI improvements
Global translations
+ Fixed others
+ Fixed others + Fixed typo
Convert various models' tissues from ManyToMany to a nullable ForeignKey (Experiment, Biomarker, CGDSStudy, DifferentialExpressionExperiment, UserFile) and add the corresponding Django migrations. Update admin classes to surface tissues in list_filter/list_display and remove M2M helper UI code. Add lightweight SimpleTissueSerializer and include tissues in multiple serializers' representations and fields. Adjust CGDSStudy serializer create/update logic to handle FK instead of M2M. Update DifferentialExpression API to accept and persist tissues and return tissues in the response. Also add a ChatWidget import/use in the frontend Base component.
Rename model field `tissues` to singular `tissue` in api_service, biomarkers, datasets_synchronization, differential_expression and user_files. Updated models, admin list_filters, serializers and views to use `tissue` and added corresponding Django rename migrations (api_service/migrations/0064_..., biomarkers/migrations/0024_..., datasets_synchronization/migrations/0040_..., differential_expression/migrations/0003_..., user_files/migrations/0019_...). Note: this changes API payloads/serializers (clients should use `tissue` now). Run `python manage.py migrate` to apply DB migrations.
…nce/multiomix into fix/tissueInFiles
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