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BEDbase: a unified platform for genomic regions
Region2Vec
BEDbase
BEDboss
Geniml
Gtars
Manuscripts
BEDbase: a unified platform for genomic regions
BEDbase
BEDbase
User guides
User guides
Public BEDbase UI user guide
Public BEDbase API user guide
✅ Reference Genome Compatibility
📝 BED Classification
💻 BBClient
🔍 BEDbase Search
Developer guides
Developer guides
📇 BEDhost API server
📇 BEDhost API server
Building docker image
Deploy API
Changelog
🔌 BBConf configuration
🔌 BBConf configuration
Overview
Guide
Changelog
🧰 BEDBoss processing pipeline
🔄 BEDbase auto uploader
📜 Configuration file
Reference
Reference
How to cite
Support
Contributing
Changelog
BEDboss
BEDboss
Tutorials
Tutorials
Python modules
Python modules
BEDboss run-pep
BEDboss-all pipeline
BEDmaker
BEDstat
BEDbuncher
BEDindex
BEDclassifier
Ref_genome validator
Command line interface
BEDMS tutorial
How to guides
How to guides
Plot GEO BED files number
Upload GEO data
Upload BED from PEP
Reindex vector store
Generate UMAP
Create BEDbase database
Run BEDboss in Docker
📜 Configuration file
Install dependencies
Reference
Reference
How to cite
Changelog
Geniml
Geniml
Getting Started
Getting Started
Module overviews
BBclient
BBclient
Cache BED files with BBClient
Use BED cache in R
Atacformer
Atacformer
Getting started
Getting started
Core concepts
Quickstart
Tutorials
Tutorials
Generating a UMAP from fragments files
Example Brain3k Processing
Visualizing new embeddings in the latent space of a reference
Training
Training
Pre-tokenize data for training
Train a model from scratch
Fine-tune a model
Local compute guides
Local compute guides
Compute requirements
Using atacformer locally
Using atacformer with Apple Silicon
How-to guides
How-to guides
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
How to cite
Python API documentation
Python API documentation
Assess
Atacformer
BBClient
BEDshift
BEDspace
Craft
Evaluation
Geneformer
I/O
Likelihood
Models
Region2Vec
Region2Vec
Table of contents
region2vec
scEmbed
Search
Text2BedNN
Tokenization
Universe
Utilities
Support
Contributing
Changelog
Gtars
Gtars
💿 Install
Modules
Modules
Overview
gtars-core
gtars-overlaprs
gtars-uniwig
gtars-igd
gtars-scoring
gtars-fragsplit
gtars-tokenizers
gtars-scatrs
gtars-refget
gtars-bbcache
Bindings
Bindings
Python
Python
Python
Digests
RegionSet
RefgetStore
Tokenizers
Wasm
Wasm
Overview
Overlappers
CLI
R
Reference
Reference
Changelog
Rust source API docs
Manuscripts
Manuscripts
How to cite
Published manuscripts
Published manuscripts
Gharavi et al. 2021
Gu et al. 2021
Rymuza et al. 2024
Gharavi et al. 2024
LeRoy et al. 2024
Zheng et al. 2024
Table of contents
region2vec
Region2Vec Module
region2vec
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