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    39 repositories

    • ggner-3d

      Public
      Analysis code for RNAPII, nucleotide excision repair, and 3D genome dynamics after UV damage
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 23, 2026Jun 23, 2026

    • ner_rnapii_3d

      Public
      1D loop-extrusion simulation engine modeling RNAPII transcription, DNA lesions, CTCF boundaries, and repair dynamics
      Python
      •0•0•0•0•Updated Jun 23, 2026Jun 23, 2026

    • uv-3d-ddr

      Public
      Genome architecture analysis, dataset generation, and GNN training/inference from the study 'UV-induced reorganization of 3D genome mediates DNA damage response…
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Jun 5, 2026Jun 5, 2026

    • quiz-pool

      Public
      Python
      •0•0•0•0•Updated Jun 2, 2026Jun 2, 2026

    • GPCRevolution

      Public
      HTML
      •0•0•0•0•Updated May 28, 2026May 28, 2026

    • GPCR_Family_Divergence

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated May 7, 2026May 7, 2026

    • PHACE-MP

      Public
      Phylogeny-aware co-evolution
      R
      •
      MIT License
      •3•0•0•0•Updated Apr 27, 2026Apr 27, 2026

    • xr-ds-seq-snakemake

      Public
      This repository contains xr-seq and damage-seq pipelines.
      Python
      •
      MIT License
      •0•4•0•0•Updated Jan 21, 2026Jan 21, 2026

    • PHACE

      Public
      Phylogeny-aware co-evolution
      R
      •
      MIT License
      •3•12•0•0•Updated Jan 11, 2026Jan 11, 2026

    • XR-DS-seq-Tutorial

      Public
      GitHub repository tutorial for XR-Seq and Damage-Seq methodologies, providing code examples, datasets, and documentation for studying DNA damage and repair pro…
      Python
      •
      MIT License
      •1•1•0•0•Updated Dec 1, 2025Dec 1, 2025

    • B2AR_Dimer_Interface

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 23, 2025Nov 23, 2025

    • worm-UV-DR

      Public
      Worm (C. elegans) UV-induced DNA Damage and Repair
      Python
      •0•0•0•0•Updated Sep 19, 2025Sep 19, 2025

    • brendo

      Public
      CSS
      •
      MIT License
      •0•0•0•0•Updated Aug 12, 2025Aug 12, 2025

    • PHACTboost

      Public
      R
      •3•7•0•0•Updated Jul 19, 2025Jul 19, 2025

    • genome-integrity

      Public
      SCSS
      •
      Other
      •0•0•0•0•Updated Sep 4, 2024Sep 4, 2024

    • WGSpipe

      Public
      Nextflow
      •1•0•0•0•Updated Sep 2, 2024Sep 2, 2024

    • fzd7_evolution_and_structure

      Public
      Python
      •0•0•0•0•Updated Aug 2, 2024Aug 2, 2024

    • CaSR

      Public
      Python
      •1•0•0•0•Updated Jul 28, 2024Jul 28, 2024

    • PHACTboost_manuscript

      Public
      R
      •0•2•0•0•Updated Jul 3, 2024Jul 3, 2024

    • Phyloseek

      Public
      Python
      •0•0•0•0•Updated May 2, 2024May 2, 2024

    • PHYLM

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 30, 2024Apr 30, 2024

    • PHACT

      Public
      This is a phylogeny workflow for batch submission to HPC cluster built with Slurm queue manager
      R
      •7•11•0•0•Updated Mar 19, 2024Mar 19, 2024

    • XPA_evolution

      Public
      Python
      •0•0•0•0•Updated Oct 12, 2023Oct 12, 2023

    • atmm

      Public
      Python
      •0•2•0•0•Updated Jul 30, 2023Jul 30, 2023

    • missense_atlas

      Public
      Missense Atlas
      JavaScript
      •0•3•0•0•Updated Jun 19, 2023Jun 19, 2023

    • phylostat

      Public
      JavaScript
      •
      MIT License
      •0•0•0•9•Updated Mar 23, 2023Mar 23, 2023

    • boquila

      Public
      NGS read simulator to eliminate read nucleotide bias in sequence analysis.
      Rust
      •
      MIT License
      •0•6•0•0•Updated Mar 19, 2023Mar 19, 2023

    • 3D-UV

      Public
      Python
      •0•0•0•0•Updated Mar 3, 2023Mar 3, 2023

    • mdd-analysis

      Public
      HTML
      •0•0•0•0•Updated Dec 26, 2022Dec 26, 2022

    • MycoSmegmatis_TRCF

      Public
      The Mfd Protein is the Transcription-Repair Coupling Factor (TRCF) in Mycobacterium Smegmatis
      Python
      •
      MIT License
      •1•1•0•0•Updated Dec 20, 2022Dec 20, 2022
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