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    125 repositories

    • rna-seq-pipeline

      Public
      Python
      •
      MIT License
      •66•160•8•2•Updated Apr 13, 2026Apr 13, 2026

    • long-read-rna-pipeline

      Public
      ENCODE long read RNA-seq pipeline
      WDL
      •
      MIT License
      •13•51•1•1•Updated Apr 13, 2026Apr 13, 2026

    • encoded

      Public
      Metadata database for ENCODE project
      JavaScript
      •
      MIT License
      •50•114•4•55•Updated Apr 13, 2026Apr 13, 2026

    • caper

      Public
      Cromwell/WDL wrapper for Python
      Python
      •
      MIT License
      •18•58•31•2•Updated Feb 13, 2026Feb 13, 2026

    • geo-submission

      Public
      Python
      •
      MIT License
      •2•3•0•2•Updated Jan 22, 2026Jan 22, 2026

    • encode-data-usage-examples

      Public
      Jupyter Notebook
      •
      MIT License
      •9•10•0•1•Updated Sep 11, 2025Sep 11, 2025

    • cdk-kubernetes-cherry

      Public
      EKS CDK deployment and apps for cherry-lab account
      Python
      •0•0•0•0•Updated Jun 3, 2025Jun 3, 2025

    • encValData

      Public
      AngelScript
      •
      MIT License
      •6•5•0•0•Updated May 27, 2025May 27, 2025

    • genomic-data-service

      Public
      Flask based web service providing genomic region search, based on regulomedb.org
      Python
      •
      MIT License
      •2•5•1•1•Updated Feb 19, 2025Feb 19, 2025

    • regulome-encoded

      Public
      Temp repo for regulome development
      JavaScript
      •
      MIT License
      •3•1•2•16•Updated Nov 15, 2024Nov 15, 2024

    • checkfiles

      Public
      Files are checked to see if the MD5 sum (both for gzipped and ungzipped) is identical to the submitted metadata, as well as run through the validateFiles progra…
      Python
      •
      MIT License
      •0•2•0•1•Updated Oct 2, 2024Oct 2, 2024

    • kentUtils

      Public
      UCSC command line bioinformatic utilities
      C
      •96•189•15•1•Updated Jul 31, 2024Jul 31, 2024

    • atac-seq-pipeline

      Public
      ENCODE ATAC-seq pipeline
      Python
      •
      MIT License
      •170•449•91•2•Updated Jul 18, 2024Jul 18, 2024

    • snovault

      Public
      The SnoVault general purpose hybrid object-relational database
      Python
      •
      MIT License
      •8•16•2•28•Updated Mar 7, 2024Mar 7, 2024

    • chip-seq-pipeline2

      Public
      ENCODE ChIP-seq pipeline
      Python
      •
      MIT License
      •119•277•56•0•Updated Feb 15, 2024Feb 15, 2024

    • hic-pipeline

      Public
      HiC uniform processing pipeline
      WDL
      •
      MIT License
      •23•64•6•2•Updated Nov 8, 2023Nov 8, 2023

    • coalesce_s3_log_glue_spark

      Public
      Glue pyspark job to combine s3 access logs to parquet
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 19, 2023Oct 19, 2023

    • valis-hpgv

      Public
      High performance WebGL genome visualization
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •6•7•2•4•Updated Oct 17, 2023Oct 17, 2023

    • filemetadata_dynamoDB

      Public
      Load selected encode file metadata to dynamoDB
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • dnase-seq-pipeline

      Public
      ENCODE DNase-seq pipeline
      WDL
      •
      MIT License
      •4•6•1•4•Updated Sep 22, 2023Sep 22, 2023

    • autouri

      Public
      Recursive localization for various types of URIs
      Python
      •
      MIT License
      •2•0•1•0•Updated May 4, 2023May 4, 2023

    • pyencoded-tools

      Public
      Jupyter Notebook
      •
      MIT License
      •13•12•1•6•Updated Mar 17, 2023Mar 17, 2023

    • imputation_challenge

      Public
      ENCODE Imputation Challenge scoring & validation scripts
      Python
      •
      MIT License
      •0•2•1•1•Updated Mar 15, 2023Mar 15, 2023

    • segway-pipeline

      Public
      Python
      •
      MIT License
      •1•2•0•2•Updated Feb 24, 2023Feb 24, 2023

    • snovault-search

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated Feb 8, 2023Feb 8, 2023

    • accession

      Public
      Python module to upload experiment files and metadata to the ENCODE Portal
      Python
      •
      MIT License
      •0•3•0•0•Updated Feb 3, 2023Feb 3, 2023

    • ENCODE_scatac

      Public
      Python
      •
      MIT License
      •2•0•0•0•Updated Jan 31, 2023Jan 31, 2023

    • correlation_robustness

      Public
      Python
      •
      MIT License
      •1•0•0•11•Updated Dec 8, 2022Dec 8, 2022

    • ihec-processing

      Public
      IHEC processing
      WDL
      •
      MIT License
      •0•0•0•0•Updated Nov 14, 2022Nov 14, 2022

    • google-sheet-metadata-submitter

      Public
      ENCODE metadata submitter based on Google Sheet and Apps script
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Oct 21, 2022Oct 21, 2022
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