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    47 repositories

    • srworkshop

      Public
      Scripts and files for the annual Short Read Analysis Workshop
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •6•12•0•0•Updated Mar 3, 2026Mar 3, 2026

    • RNAseq-Flow

      Public
      Nextflow pipeline for processing RNA-seq data
      Nextflow
      •
      MIT License
      •4•8•0•0•Updated Feb 19, 2026Feb 19, 2026

    • AREA

      Public
      Attribute Rank Enrichment Analysis
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •2•1•0•0•Updated Feb 18, 2026Feb 18, 2026

    • AREA_publication_scripts

      Public
      Repository for all of the scripts used to make the figures in the AREA paper
      Jupyter Notebook
      •0•0•0•0•Updated Jan 9, 2026Jan 9, 2026

    • bidir_gene_pairs

      Public
      Bidirectional transcript and gene pairs derived from nascent RNA data
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 5, 2026Jan 5, 2026

    • Improving_tRE_Analysis_Paper

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Dec 20, 2025Dec 20, 2025

    • TFEA

      Public
      Transcription Factor Enrichment Analysis
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •8•36•8•5•Updated Dec 8, 2025Dec 8, 2025

    • Disassociation_Analysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 4, 2025Dec 4, 2025

    • CRISPR_screen_DNA_damage

      Public
      Arnoult Lab dual CRISPR screen for DNA damage/repair pathways
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 24, 2025Nov 24, 2025

    • Bidir_Counting_Analysis

      Public
      This repo includes the generalizable pipeline for identification, counting, and length assessments of Bidirectionals from nascent RNA seq data
      Jupyter Notebook
      •1•1•0•0•Updated Sep 18, 2025Sep 18, 2025

    • Bidirectional-Flow

      Public
      Nextflow pipeline for detecting bidirectional transcripts from nascent RNA sequencing data.
      Nextflow
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Sep 4, 2025Sep 4, 2025

    • LIET

      Public
      Implementation of the LIET model using PyMC
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•2•0•1•Updated Sep 4, 2025Sep 4, 2025

    • Nascent-Flow

      Public
      Nascent Transcription Processing Pipeline
      Nextflow
      •
      MIT License
      •5•12•1•0•Updated Aug 28, 2025Aug 28, 2025

    • codeclub

      Public
      Collected Resources for Dowell Lab Code Clubs
      HTML
      •
      Creative Commons Attribution Share Alike 4.0 International
      •3•0•0•0•Updated Aug 8, 2025Aug 8, 2025

    • psea

      Public
      Participant set enrichment analysis
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •2•0•2•0•Updated Jul 22, 2025Jul 22, 2025

    • DBNascent-build

      Public
      Python scripts and utilities for building DBNascent in MySQL
      Python
      •0•0•0•0•Updated Apr 11, 2025Apr 11, 2025

    • DBNascent_Analysis

      Public
      Contains meta analyses performed using data in DBNascent
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 11, 2025Apr 11, 2025

    • bidirectionals_merged

      Public
      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
      •1•0•0•0•Updated Apr 11, 2025Apr 11, 2025

    • chr21_transcrpitional_regulators

      Public
      chr21 transcrpitional regulators figures
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 20, 2025Mar 20, 2025

    • Luyties_CDK7i_5prime_3prime

      Public
      Scripts associated with Luyties 2025
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 10, 2025Mar 10, 2025

    • TF_profiler

      Public
      Infers TF effector domain activity from nascent run-on sequencing data
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 1, 2025Mar 1, 2025

    • TF_profiler_additonal_scripts

      Public
      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
      •0•0•0•0•Updated Mar 1, 2025Mar 1, 2025

    • pop_inf_beta

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Feb 26, 2025Feb 26, 2025

    • CDK7_inhibition

      Public
      Scripts and code used to analyze data in CDK7 inhibition project
      Shell
      •1•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • mumerge

      Public
      muMerge tool for combining replicate bed-regions
      Python
      •
      GNU General Public License v3.0
      •1•5•0•0•Updated May 24, 2024May 24, 2024

    • DAStk

      Public
      Differential ATAC-seq toolkit
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•28•4•0•Updated Dec 21, 2023Dec 21, 2023

    • snpconnecter

      Public
      Method for linking GWAS SNPs to genes based on DBNascent bidirectional region and gene pairs.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 5, 2023Dec 5, 2023

    • virtual_spike_in

      Public
      Code for the "virtual spike in" normalization method using the ends of long genes
      R
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Oct 27, 2023Oct 27, 2023

    • DS_Normalization

      Public
      Scripts relating to differential expression in trisomy 21 cells
      Jupyter Notebook
      •0•0•0•0•Updated Aug 21, 2023Aug 21, 2023

    • ChIP-Flow

      Public
      Nextflow pipeline for ChIP-seq analysis.
      Nextflow
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Aug 7, 2023Aug 7, 2023