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    123 repositories

    • encoded

      Public
      Metadata database for ENCODE project
      JavaScript
      •
      MIT License
      •51•110•4•56•Updated Nov 8, 2024Nov 8, 2024

    • regulome-encoded

      Public
      Temp repo for regulome development
      JavaScript
      •
      MIT License
      •4•1•2•17•Updated Nov 4, 2024Nov 4, 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 program from jksrc.
      Python
      •
      MIT License
      •0•2•0•1•Updated Oct 2, 2024Oct 2, 2024

    • kentUtils

      Public
      UCSC command line bioinformatic utilities
      C
      •95•168•15•1•Updated Jul 31, 2024Jul 31, 2024

    • genomic-data-service

      Public
      Flask based web service providing genomic region search, based on regulomedb.org
      Python
      •
      MIT License
      •2•4•1•0•Updated Jul 23, 2024Jul 23, 2024

    • atac-seq-pipeline

      Public
      ENCODE ATAC-seq pipeline
      Python
      •
      MIT License
      •172•385•86•2•Updated Jul 18, 2024Jul 18, 2024

    • geo-submission

      Public
      Python
      •
      MIT License
      •2•3•0•1•Updated May 16, 2024May 16, 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
      •123•245•49•0•Updated Feb 15, 2024Feb 15, 2024

    • hic-pipeline

      Public
      HiC uniform processing pipeline
      WDL
      •
      MIT License
      •24•57•5•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
      •5•5•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

    • caper

      Public
      Cromwell/WDL wrapper for Python
      Python
      •
      MIT License
      •18•54•28•1•Updated Jul 21, 2023Jul 21, 2023

    • autouri

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

    • pyencoded-tools

      Public
      Jupyter Notebook
      •
      MIT License
      •13•10•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

    • long-read-rna-pipeline

      Public
      ENCODE long read RNA-seq pipeline
      WDL
      •
      MIT License
      •13•44•1•0•Updated Jan 9, 2023Jan 9, 2023

    • correlation_robustness

      Public
      Python
      •
      MIT License
      •2•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

    • rna-seq-pipeline

      Public
      Python
      •
      MIT License
      •62•141•7•1•Updated Nov 3, 2022Nov 3, 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

    • d3-sequence-logo

      Public
      Sequence Logo generation in d3.js
      JavaScript
      •
      MIT License
      •3•1•0•0•Updated Sep 19, 2022Sep 19, 2022

    • kentUtils_bin_v381

      Public
      kentUtils_bin_v381 (binary from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/)
      Shell
      •0•0•0•0•Updated Jul 20, 2022Jul 20, 2022

    • wgbs-pipeline

      Public
      ENCODE whole-genome bisulfite sequencing (WGBS) pipeline
      bioinformaticspipelinengsmethylationwgbs
      Python
      •
      MIT License
      •14•29•4•0•Updated Feb 15, 2022Feb 15, 2022

    • encValData

      Public
      AngelScript
      •
      MIT License
      •6•5•0•0•Updated Feb 10, 2022Feb 10, 2022