Databio

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101 repositories

bedboss
Public
Python pipeline for processing BED files for BEDbase
geo bed-files bed-format genomic-intervals
Python
•
BSD 2-Clause "Simplified" License
•0•2•12•1•Updated Jan 30, 2026Jan 30, 2026
bedhost
Public
API and UI for BEDbase
bioinformatics server genomics rest-api bed fastapi genomic-intervals
TypeScript
•
BSD 2-Clause "Simplified" License
•1•2•13•1•Updated Jan 29, 2026Jan 29, 2026
renin_atac
Public
Jupyter Notebook
•0•0•0•0•Updated Jan 28, 2026Jan 28, 2026
bedbase
Public
Aggregate, analyze, and serve genomic regions.
genomic-intervals
Jupyter Notebook
•0•4•6•0•Updated Jan 28, 2026Jan 28, 2026
gtars
Public
Performance-critical tools to manipulate, analyze, and process genomic interval data
Rust
•
BSD 2-Clause "Simplified" License
•4•23•36•1•Updated Jan 27, 2026Jan 27, 2026
bedbase-loader
Public
BEDbase GEO bed file uploading
bioinformatics-pipeline
Python
•0•0•0•0•Updated Jan 26, 2026Jan 26, 2026
ai-sandbox
Public
a basic sandbox to collect some AI resources and example projects
Python
•0•0•0•0•Updated Jan 23, 2026Jan 23, 2026
bbconf
Public
Configuration package for bedbase project
config-management python-api genomic-intervals
Python
•
BSD 2-Clause "Simplified" License
•2•0•2•1•Updated Jan 21, 2026Jan 21, 2026
geniml
Public
Genomic interval machine learning
machine-learning representation-learning genomic-intervals
Python
•
BSD 2-Clause "Simplified" License
•3•21•10•0•Updated Jan 14, 2026Jan 14, 2026
markmeld
Public
A Python package for melding markdown content and YAML structured data
markdown yaml jinja2 pandoc
Python
•
BSD 2-Clause "Simplified" License
•2•7•3•1•Updated Dec 18, 2025Dec 18, 2025
yacman
Public
YAML configuration manager
Python
•
BSD 2-Clause "Simplified" License
•2•6•10•1•Updated Dec 3, 2025Dec 3, 2025
uniwig_paper_scripts
Public
Research applications using uniwig
Python
•0•0•0•0•Updated Nov 8, 2025Nov 8, 2025
seqcol_paper_scripts
Public
Scripts used for analysis to write seq col paper.
Python
•0•0•0•0•Updated Nov 6, 2025Nov 6, 2025
astro-reveal
Public
A template for combining Astro and Reveal.js to build and deploy beautiful presentation websites.
Astro
•0•0•0•0•Updated Nov 6, 2025Nov 6, 2025
pypiper
Public
Python toolkit for building restartable pipelines
python bioinformatics pipeline bioinformatics-pipeline python-toolkit
Python
•
BSD 2-Clause "Simplified" License
•9•45•56•0•Updated Nov 6, 2025Nov 6, 2025
sciquill
Public
Author academic documents in markdown
markdown academic-publishing cv-template
TeX
•5•12•4•0•Updated Oct 17, 2025Oct 17, 2025
mm_templates
Public
Jinja
•0•3•0•0•Updated Oct 6, 2025Oct 6, 2025
schema.databio.org
Public
Repository of JSON-schemas
JavaScript
•
BSD 2-Clause "Simplified" License
•1•2•1•2•Updated Oct 2, 2025Oct 2, 2025
bedshift
Public
Bedfile perturbation tool
region-of-interest genomic-regions genomic-intervals
Python
•
BSD 2-Clause "Simplified" License
•3•17•5•0•Updated Sep 29, 2025Sep 29, 2025
mouse_sciATAC_atlas
Public
Python
•8•0•0•0•Updated Sep 26, 2025Sep 26, 2025
pepatac
Public
A modular, containerized pipeline for ATAC-seq data processing
Python
•
BSD 2-Clause "Simplified" License
•16•61•53•2•Updated Sep 23, 2025Sep 23, 2025
hub.bulker.io
Public
Bulker registry
HTML
•
BSD 2-Clause "Simplified" License
•1•5•3•0•Updated Apr 29, 2025Apr 29, 2025
GenomicDistributions
Public
Calculate and plot distributions of genomic ranges
R
•
Other
•10•27•9•1•Updated Apr 23, 2025Apr 23, 2025
henge
Public
Keeper of DRUIDs: a Python interface to Decomposable Recursive UIDs
Python
•
BSD 2-Clause "Simplified" License
•0•2•1•0•Updated Mar 15, 2025Mar 15, 2025
gtokenizers-bench
Public
Benchmark various implementations of genomic overlap methods (tokenizers) in a controlled environment.
Rust
•0•0•0•0•Updated Feb 12, 2025Feb 12, 2025
uniwig
Public
C
•0•1•5•0•Updated Feb 10, 2025Feb 10, 2025
COCOA
Public
Annotating epigenetic variation among samples with region sets in R
pca dna-methylation
R
•
Other
•0•11•2•1•Updated Jan 18, 2025Jan 18, 2025
rust-gc-count
Public
A tool for generating wiggle files of GC from DNA written in Rust.
Rust
•
Apache License 2.0
•2•0•0•1•Updated Dec 13, 2024Dec 13, 2024
bedms
Public
Tool for standardization of genomics/epigenomics metadata
metadata genetics genomic-intervals
Python
•
BSD 2-Clause "Simplified" License
•0•3•1•1•Updated Dec 10, 2024Dec 10, 2024
bulker
Public
Manager for multi-container computing environments
docker reproducible-research containers environments
Jupyter Notebook
•
BSD 2-Clause "Simplified" License
•2•25•21•2•Updated Oct 20, 2024Oct 20, 2024