Repositories list

• 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

  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

• bird-workflow

  Public
  Repository to coordinate the effort to create a simplified workflow for running BIRD

  Python

  •

  MIT License

  •2•0•1•0•Updated Mar 27, 2025Mar 27, 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

• 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 May 17, 2024May 17, 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