# labrat

> A Python framework designed to improve reproducibility, simplify laboratory management, and support common biomedical research tasks.

## Docs

### API Reference

#### Query models and clients
> Shared results and clients for external biological resources.

- [query.QueryResult](https://www.shauritahutchins.com/labrat/reference/query.QueryResult.html)
- [query.QueryError](https://www.shauritahutchins.com/labrat/reference/query.QueryError.html)
- [query.PubTatorClient](https://www.shauritahutchins.com/labrat/reference/query.PubTatorClient.html)

#### Biological queries
> Gene, variant, and biomedical literature queries.

- [query.query_gene](https://www.shauritahutchins.com/labrat/reference/query.query_gene.html)
- [query.query_variant](https://www.shauritahutchins.com/labrat/reference/query.query_variant.html)
- [query.query_literature](https://www.shauritahutchins.com/labrat/reference/query.query_literature.html)

#### Project and file management
> Classes for projects, archives, and scientific files.

- [project.ProjectManager](https://www.shauritahutchins.com/labrat/reference/project.ProjectManager.html)
- [filemanager.Archiver](https://www.shauritahutchins.com/labrat/reference/filemanager.Archiver.html)
- [filemanager.FileOrganizer](https://www.shauritahutchins.com/labrat/reference/filemanager.FileOrganizer.html)

#### ProjectManager methods

- [project.ProjectManager.new_project](https://www.shauritahutchins.com/labrat/reference/project.ProjectManager.new_project.html)
- [project.ProjectManager.list_projects](https://www.shauritahutchins.com/labrat/reference/project.ProjectManager.list_projects.html)
- [project.ProjectManager.update_project](https://www.shauritahutchins.com/labrat/reference/project.ProjectManager.update_project.html)
- [project.ProjectManager.list_project_files](https://www.shauritahutchins.com/labrat/reference/project.ProjectManager.list_project_files.html)
- [project.ProjectManager.archive_project](https://www.shauritahutchins.com/labrat/reference/project.ProjectManager.archive_project.html)
- [project.ProjectManager.add_template](https://www.shauritahutchins.com/labrat/reference/project.ProjectManager.add_template.html)
- [project.ProjectManager.delete_project](https://www.shauritahutchins.com/labrat/reference/project.ProjectManager.delete_project.html)

#### FileOrganizer methods

- [filemanager.FileOrganizer.move_file](https://www.shauritahutchins.com/labrat/reference/filemanager.FileOrganizer.move_file.html)
- [filemanager.FileOrganizer.organize_by_year](https://www.shauritahutchins.com/labrat/reference/filemanager.FileOrganizer.organize_by_year.html)
- [filemanager.FileOrganizer.organize_documents](https://www.shauritahutchins.com/labrat/reference/filemanager.FileOrganizer.organize_documents.html)
- [filemanager.FileOrganizer.organize_archives](https://www.shauritahutchins.com/labrat/reference/filemanager.FileOrganizer.organize_archives.html)
- [filemanager.FileOrganizer.organize_files](https://www.shauritahutchins.com/labrat/reference/filemanager.FileOrganizer.organize_files.html)
- [filemanager.FileOrganizer.move_specific_files](https://www.shauritahutchins.com/labrat/reference/filemanager.FileOrganizer.move_specific_files.html)
- [filemanager.FileOrganizer.organize_science_files](https://www.shauritahutchins.com/labrat/reference/filemanager.FileOrganizer.organize_science_files.html)
- [filemanager.FileOrganizer.organize_all](https://www.shauritahutchins.com/labrat/reference/filemanager.FileOrganizer.organize_all.html)

#### Genetics
> DNA and protein sequence utilities.

- [genetics.atgc_content](https://www.shauritahutchins.com/labrat/reference/genetics.atgc_content.html)
- [genetics.complementary_dna](https://www.shauritahutchins.com/labrat/reference/genetics.complementary_dna.html)
- [genetics.dna2aminoacid](https://www.shauritahutchins.com/labrat/reference/genetics.dna2aminoacid.html)

#### Laboratory math
> Common concentration and optical calculations.

- [math.calculate_molarity](https://www.shauritahutchins.com/labrat/reference/math.calculate_molarity.html)
- [math.dilute_stock](https://www.shauritahutchins.com/labrat/reference/math.dilute_stock.html)
- [math.mass_recorder](https://www.shauritahutchins.com/labrat/reference/math.mass_recorder.html)
- [math.refractive_index_prism](https://www.shauritahutchins.com/labrat/reference/math.refractive_index_prism.html)
- [math.transmittance_to_absorbance](https://www.shauritahutchins.com/labrat/reference/math.transmittance_to_absorbance.html)