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BEDbase: a unified platform for genomic regions

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BEDbase: a unified platform for genomic regions

Home
BEDbase
BEDbase
- User guides
  User guides
  - Public BEDbase UI user guide
  - Public BEDbase API user guide
- Developer guides
  Developer guides
  - BEDhost API server
    
    BEDhost API server
    
    Building docker image
    
    Deploy API
    
    Changelog
  - BBConf configuration
    
    BBConf configuration
    
    Configuring
    
    Overview
    
    Guide
    
    Changelog
  - BEDBoss processing pipeline
- Reference
  Reference
  - How to cite
  - Usage
  - Support
  - Contributing
  - Changelog
BEDboss
BEDboss
- Tutorials
  Tutorials
- How to guides
  How to guides
- Reference
  Reference
Geniml
Geniml
- Getting Started
  Getting Started
  - Module overviews
- How-to guides
  How-to guides
  - Cache BED files with BBClient
  - Use BED cache in R
  - Tokenization
  - Tokenize a BED file with CLI
  - Train region2vec embeddings
  - Train BEDspace model
    Train BEDspace model
    
    Train BEDSpace embeddings
    
    BEDspace results notebook
  - Use scEmbed model
    Use scEmbed model
    
    Train single-cell embeddings
    
    Populate a vector store
    
    Predict cell-types using KNN
  - Evaluate embeddings
  - Create consensus peaks with CLI
  - Create consensus peaks with Python
  - Assess universe fit
  - Fine-tune embeddings
  - Randomize bed files
  - Create evaluation dataset with bedshift
  - Create search backend
- Reference
  Reference
Gtars
Gtars
- Install
- Modules
  Modules
  - Digests
- Reference
  Reference
  - Changelog
Manuscripts
Manuscripts
- How to cite
- Published manuscripts
  Published manuscripts

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API documentation