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BEDbase
BEDbase
User guides
đ Public BEDbase UI user guide
đ Public BEDbase API user guide
â Reference Genome Compatibility
đ BED Classification
đģ BBClient & caching
đ BEDbase Search
đĒŠ Embedding Visualization
âī¸ BED analyzer
Developer guides
đ Data Loading
đĻ Bulk metadata exports
đ Configuration file
Reference
Support
Contributing
Changelog
BEDhost
BEDhost overview
Building docker image
Deploy API
Changelog
BBConf
BBConf
Overview
Guide
Changelog
BEDboss
BEDboss
Tutorials
Python modules
BEDboss run-pep
BEDboss-all pipeline
BEDmaker
BEDstat
BEDbuncher
BEDindex
BEDclassifier
Ref_genome validator
Command line interface
BEDMS tutorial
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
Create config file
Install dependencies
Reference
Changelog
Geniml
Geniml
Getting Started
Module overviews
BBclient
Cache BED files with BBClient
BBClient tutorial
Use BED cache in R
Atacformer
Atacformer
Getting started
Core concepts
Quickstart
Tutorials
Generating a UMAP from fragments files
Example Brain3k Processing
Visualizing new embeddings in the latent space of a reference
Training
Pre-tokenize data for training
Train a model from scratch
Fine-tune a model
Local compute guides
Compute requirements
Using atacformer locally
Using atacformer with Apple Silicon
How-to guides
Train region2vec embeddings
Train BEDspace model
Train BEDSpace embeddings
BEDspace results notebook
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
Python API documentation
Assess
Atacformer
BBClient
BEDshift
BEDspace
Craft
Evaluation
Geneformer
I/O
Likelihood
Models
Region2Vec
scEmbed
Search
Text2BedNN
Tokenization
Universe
Utilities
Support
Contributing
Changelog
Gtars
Gtars
đŋ Install
Modules
Overview
gtars-core
Core models
gtars-overlaprs
gtars-uniwig
gtars-igd
gtars-scoring
gtars-fragsplit
gtars-tokenizers
gtars-scatrs
gtars-genomicdist
gtars-lola
gtars-refget
gtars-bbcache
Bindings
Python
Overview
Models
GenomicDist
LOLA
Digests
RefgetStore Tutorial
RefgetStore Python Reference
Refget API Reference
Wasm
Overview
Overlappers
RegionSet
Partitions
Signal
LOLA
CLI
R
R
RegionSet
GenomicDist
LOLA
IGD
RefgetStore
Reference
Changelog
Rust source API docs
Versioning policy
Manuscripts
How to cite
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
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