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    • Scripts and files for the annual Short Read Analysis Workshop
      Jupyter Notebook
      GNU General Public License v3.0
      61200Updated Mar 3, 2026Mar 3, 2026
    • Nextflow pipeline for processing RNA-seq data
      Nextflow
      MIT License
      4800Updated Feb 19, 2026Feb 19, 2026
    • AREA

      Public
      Attribute Rank Enrichment Analysis
      Jupyter Notebook
      GNU Affero General Public License v3.0
      2100Updated Feb 18, 2026Feb 18, 2026
    • Repository for all of the scripts used to make the figures in the AREA paper
      Jupyter Notebook
      0000Updated Jan 9, 2026Jan 9, 2026
    • Bidirectional transcript and gene pairs derived from nascent RNA data
      R
      GNU General Public License v3.0
      1000Updated Jan 5, 2026Jan 5, 2026
    • Jupyter Notebook
      1000Updated Dec 20, 2025Dec 20, 2025
    • TFEA

      Public
      Transcription Factor Enrichment Analysis
      Jupyter Notebook
      GNU General Public License v3.0
      83685Updated Dec 8, 2025Dec 8, 2025
    • Jupyter Notebook
      0000Updated Dec 4, 2025Dec 4, 2025
    • Arnoult Lab dual CRISPR screen for DNA damage/repair pathways
      Python
      GNU General Public License v3.0
      0000Updated Nov 24, 2025Nov 24, 2025
    • This repo includes the generalizable pipeline for identification, counting, and length assessments of Bidirectionals from nascent RNA seq data
      Jupyter Notebook
      1100Updated Sep 18, 2025Sep 18, 2025
    • Nextflow pipeline for detecting bidirectional transcripts from nascent RNA sequencing data.
      Nextflow
      GNU General Public License v3.0
      1000Updated Sep 4, 2025Sep 4, 2025
    • LIET

      Public
      Implementation of the LIET model using PyMC
      Jupyter Notebook
      GNU General Public License v3.0
      1201Updated Sep 4, 2025Sep 4, 2025
    • Nascent Transcription Processing Pipeline
      Nextflow
      MIT License
      51210Updated Aug 28, 2025Aug 28, 2025
    • codeclub

      Public
      Collected Resources for Dowell Lab Code Clubs
      HTML
      Creative Commons Attribution Share Alike 4.0 International
      3000Updated Aug 8, 2025Aug 8, 2025
    • psea

      Public
      Participant set enrichment analysis
      Jupyter Notebook
      GNU Affero General Public License v3.0
      2020Updated Jul 22, 2025Jul 22, 2025
    • Python scripts and utilities for building DBNascent in MySQL
      Python
      0000Updated Apr 11, 2025Apr 11, 2025
    • Contains meta analyses performed using data in DBNascent
      Jupyter Notebook
      GNU General Public License v3.0
      0000Updated Apr 11, 2025Apr 11, 2025
    • Generates a final merged file from bidirectionals called by Tfit and dREG across multiple samples after paper muMerge.
      Jupyter Notebook
      GNU General Public License v3.0
      1000Updated Apr 11, 2025Apr 11, 2025
    • chr21 transcrpitional regulators figures
      R
      GNU General Public License v3.0
      0000Updated Mar 20, 2025Mar 20, 2025
    • Scripts associated with Luyties 2025
      Python
      GNU General Public License v3.0
      0000Updated Mar 10, 2025Mar 10, 2025
    • Infers TF effector domain activity from nascent run-on sequencing data
      Python
      GNU General Public License v3.0
      1000Updated Mar 1, 2025Mar 1, 2025
    • These are all the scripts that are going into the rbg paper that don't belong with the stand-alone rbg workflow.
      Jupyter Notebook
      GNU General Public License v3.0
      0000Updated Mar 1, 2025Mar 1, 2025
    • Jupyter Notebook
      GNU General Public License v3.0
      1100Updated Feb 26, 2025Feb 26, 2025
    • Scripts and code used to analyze data in CDK7 inhibition project
      Shell
      1000Updated Oct 18, 2024Oct 18, 2024
    • mumerge

      Public
      muMerge tool for combining replicate bed-regions
      Python
      GNU General Public License v3.0
      1500Updated May 24, 2024May 24, 2024
    • DAStk

      Public
      Differential ATAC-seq toolkit
      Python
      BSD 3-Clause "New" or "Revised" License
      72840Updated Dec 21, 2023Dec 21, 2023
    • Method for linking GWAS SNPs to genes based on DBNascent bidirectional region and gene pairs.
      Jupyter Notebook
      GNU General Public License v3.0
      0000Updated Dec 5, 2023Dec 5, 2023
    • Code for the "virtual spike in" normalization method using the ends of long genes
      R
      GNU General Public License v3.0
      0010Updated Oct 27, 2023Oct 27, 2023
    • Scripts relating to differential expression in trisomy 21 cells
      Jupyter Notebook
      0000Updated Aug 21, 2023Aug 21, 2023
    • ChIP-Flow

      Public
      Nextflow pipeline for ChIP-seq analysis.
      Nextflow
      GNU General Public License v3.0
      0400Updated Aug 7, 2023Aug 7, 2023