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    96 repositories

    • gtars

      Public
      Performance-critical tools to manipulate, analyze, and process genomic interval data. Primarily focused on building tools for geniml - our genomic machine learning python package.
      Rust
      •
      BSD 2-Clause "Simplified" License
      •3•5•34•1•Updated Mar 25, 2025Mar 25, 2025

    • bedboss

      Public
      Python pipeline for processing BED files for BEDbase
      genomic-intervals
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•1•23•1•Updated Mar 24, 2025Mar 24, 2025

    • bbconf

      Public
      Configuration package for bedbase project
      config-managementpython-apigenomic-intervals
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•0•1•1•Updated Mar 24, 2025Mar 24, 2025

    • pepatac

      Public
      A modular, containerized pipeline for ATAC-seq data processing
      Python
      •
      BSD 2-Clause "Simplified" License
      •16•55•52•3•Updated Mar 24, 2025Mar 24, 2025

    • bedbase

      Public
      Aggregate, analyze, and serve genomic regions.
      genomic-intervals
      Jupyter Notebook
      •0•4•6•1•Updated Mar 24, 2025Mar 24, 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

    • mm_templates

      Public
      Jinja
      •0•3•0•0•Updated Mar 15, 2025Mar 15, 2025

    • bedhost

      Public
      API and UI for BEDbase
      serverrest-apibedjinja2-templatesfastapigenomic-intervals
      TypeScript
      •
      BSD 2-Clause "Simplified" License
      •1•1•14•0•Updated Mar 12, 2025Mar 12, 2025

    • GenomicDistributions

      Public
      Calculate and plot distributions of genomic ranges
      R
      •
      Other
      •10•26•9•1•Updated Mar 11, 2025Mar 11, 2025

    • pypiper

      Public
      Python toolkit for building restartable pipelines
      bioinformaticsbioinformatics-pipelinepythonpipelinepython-toolkit
      Python
      •
      BSD 2-Clause "Simplified" License
      •9•44•56•0•Updated Feb 25, 2025Feb 25, 2025

    • bedbase-loader

      Public
      Tests for GEO bed file uploading
      Shell
      •0•0•0•0•Updated Feb 18, 2025Feb 18, 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
      pcadna-methylation
      R
      •
      Other
      •0•10•2•1•Updated Jan 18, 2025Jan 18, 2025

    • hub.bulker.io

      Public
      Bulker registry
      HTML
      •
      BSD 2-Clause "Simplified" License
      •1•5•3•1•Updated Jan 16, 2025Jan 16, 2025

    • markmeld

      Public
      A Python package for melding markdown content and YAML structured data
      markdownyamljinja2pandoc
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•6•3•1•Updated Jan 15, 2025Jan 15, 2025

    • geniml

      Public
      Genomic interval machine learning
      machine-learningrepresentation-learninggenomic-intervals
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•18•3•0•Updated Jan 3, 2025Jan 3, 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
      metadatageneticsgenomic-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
      dockerreproducible-researchcontainersenvironments
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •2•24•21•2•Updated Oct 20, 2024Oct 20, 2024

    • yacman

      Public
      YAML configuration manager
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•6•10•0•Updated Oct 9, 2024Oct 9, 2024

    • pararead

      Public
      Simplifies parallel processing of DNA sequencing reads
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•9•2•0•Updated Oct 3, 2024Oct 3, 2024

    • schema.databio.org

      Public
      Repository of JSON-schemas
      JavaScript
      •
      BSD 2-Clause "Simplified" License
      •1•2•1•2•Updated Sep 10, 2024Sep 10, 2024

    • dockerfiles

      Public
      Sheffield lab dockerfiles
      Shell
      •
      BSD 2-Clause "Simplified" License
      •0•1•1•0•Updated Jul 5, 2024Jul 5, 2024

    • region2vec_eval

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 14, 2024Jun 14, 2024

    • fasta-id

      Public
      JavaScript
      •0•1•0•0•Updated May 10, 2024May 10, 2024

    • sciquill

      Public
      Author academic documents in markdown
      markdownacademic-publishingcv-template
      TeX
      •5•12•4•1•Updated May 10, 2024May 10, 2024

    • logmuse

      Public
      Small logging setup package
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•3•8•0•Updated Apr 4, 2024Apr 4, 2024

    • bedhost-ui

      Public archive
      JavaScript
      •1•0•0•0•Updated Mar 14, 2024Mar 14, 2024

    • bedmaker

      Public archive
      pipeline to convert bigWig, bedGraph and other file types into BED format
      Python
      •1•0•1•0•Updated Dec 19, 2023Dec 19, 2023