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    42 repositories

    • bird-workflow

      Public
      Repository to coordinate the effort to create a simplified workflow for running BIRD
      Python
      •
      MIT License
      •2•0•1•0•Updated Apr 17, 2026Apr 17, 2026

    • cwl-pipelines

      Public
      CWL workflows developed in the Reddy lab to process genomics and functional genomics data
      Common Workflow Language
      •
      MIT License
      •0•0•0•0•Updated Mar 19, 2026Mar 19, 2026

    • Proj_ENCODE_FCC

      Public
      Jupyter Notebook
      •0•0•25•0•Updated Dec 22, 2025Dec 22, 2025

    • Cas12a_screen_analysis

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Oct 27, 2025Oct 27, 2025

    • ggr-cwl-ipynb-gen

      Public
      Jupyter notebook generator to download and execute the processing files for GGR related datasets
      genomics-datajupyter-notebook-generator
      genomics-datajupyter-notebook-generator
      Python
      •
      MIT License
      •6•0•5•0•Updated Jul 11, 2025Jul 11, 2025

    • PMID_Scraper

      Public
      Code to scrape pubmed IDs from text files to enable generation of bibliographies
      Perl
      •0•0•0•0•Updated May 19, 2025May 19, 2025

    • IGVF-cwl

      Public
      CWL tools and workflows for IGVF and more
      Common Workflow Language
      •
      MIT License
      •17•0•0•0•Updated Apr 30, 2025Apr 30, 2025

    • CRISPR_Pipeline

      Public
      Nextflow
      •
      MIT License
      •6•0•0•0•Updated Apr 29, 2025Apr 29, 2025

    • Personal_Genomes

      Public
      Python
      •0•0•0•0•Updated Apr 7, 2025Apr 7, 2025

    • cegs-portal

      Public
      CCGR Portal
      Python
      •
      MIT License
      •0•0•2•0•Updated Mar 17, 2025Mar 17, 2025

    • ccgr_portal_data_loading

      Public
      Python
      •0•0•0•0•Updated Mar 13, 2025Mar 13, 2025

    • ccgr_portal_cov_viz

      Public
      Experiment Coverage libraries and application
      Rust
      •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

    • PyLiftRe

      Public
      A library for creating scripts to do genomic liftovers on custom file types.
      Python
      •
      Other
      •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

    • Proj_CombEffect_STARRseq

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

    • Genoverse

      Public
      HTML5 scrollable genome browser
      JavaScript
      •
      Other
      •45•0•0•0•Updated Oct 24, 2024Oct 24, 2024

    • CRADLE

      Public
      Python
      •
      MIT License
      •4•8•1•0•Updated Oct 16, 2024Oct 16, 2024

    • reddylab-dockerfiles

      Public
      Dockerfiles for bioinformatic tools used and shared at the Reddy Lab
      Dockerfile
      •
      MIT License
      •1•0•0•1•Updated Apr 25, 2024Apr 25, 2024

    • cov_viz_manifest

      Public archive
      Rust
      •0•0•0•0•Updated Dec 27, 2023Dec 27, 2023

    • cov_viz

      Public archive
      Generate data used by the CCGR Portal experiment coverage visualizer
      Rust
      •0•0•0•0•Updated Dec 27, 2023Dec 27, 2023

    • cov_viz_ds

      Public archive
      Rust
      •0•0•0•0•Updated Dec 27, 2023Dec 27, 2023

    • exp_viz

      Public archive
      Experiment coverage visualization filtering
      Rust
      •0•0•0•0•Updated Dec 27, 2023Dec 27, 2023

    • SpliceAI

      Public
      A deep learning-based tool to identify splice variants
      Python
      •
      Other
      •175•0•0•0•Updated Apr 4, 2023Apr 4, 2023

    • ProgrammingTips

      Public
      MIT License
      •0•0•0•0•Updated Oct 7, 2022Oct 7, 2022

    • jsom

      Public
      Expect script for connecting to Jupyter notebooks on DASH/SOM-HPC
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 25, 2022Aug 25, 2022

    • RegionCompare

      Public
      Compare Regions in BigWig or hdf5 files
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 1, 2022Jun 1, 2022

    • encode_cart

      Public
      Create and add items to ENCODE portal carts
      Python
      •0•0•0•0•Updated Feb 14, 2022Feb 14, 2022

    • grna_mrna_moi_exploration

      Public
      Tools for exploring grna and mrna data
      Python
      •0•0•0•0•Updated Jul 1, 2021Jul 1, 2021

    • POPSTARR2

      Public
      Pipeline for processing whole-genome Population STARR-seq data
      Python
      •
      GNU General Public License v3.0
      •1•2•1•0•Updated May 28, 2021May 28, 2021

    • gemberling-et-al-NMETH-A42509C

      Public
      Collection of notebooks associated to the NMETH-A42509C manuscript by Gemberling et al.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 20, 2021May 20, 2021

    • Proj_PROcap_analysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 22, 2021Mar 22, 2021
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