Repositories list

• NucleosomePhasing

  Public
  BX methods paper

  Shell

  •

  MIT License

  •0•0•0•1•Updated Jul 14, 2025Jul 14, 2025

• yep-trackhub

  Public
  MIT License

  •0•0•0•0•Updated Jun 25, 2025Jun 25, 2025

• cegrcode.github.io

  Public
  Pugh Lab Website at Cornell.

  HTML

  •0•1•0•0•Updated Jun 4, 2025Jun 4, 2025

• plotter

  Public
  Visualization tool to plot composites at reference points & regions of interest

  visualizationbioinformatics

  JavaScript

  •0•2•23•2•Updated May 15, 2025May 15, 2025

• 2021-Rossi_Nature

  Public
  A high-resolution protein architecture of the budding yeast genome

  Rich Text Format

  •

  MIT License

  •2•4•0•0•Updated May 7, 2025May 7, 2025

• scriptmanager-docs

  Public
  website and documentation for scriptmanager

  JavaScript

  •

  MIT License

  •0•0•8•0•Updated Mar 31, 2025Mar 31, 2025

• labtutorial

  Public
  PughLab's Infrastructure and Software setup guides

  JavaScript

  •0•2•0•0•Updated Jan 29, 2025Jan 29, 2025

• ControlledAtlasPipeline_Fall2024

  Public
  Python

  •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

• scriptmanager

  Public
  genomics toolbox that supports both graphical and command-line execution

  bioinformaticsngs-analysis

  Java

  •

  MIT License

  •6•14•47•3•Updated Dec 3, 2024Dec 3, 2024

• 2023-Krebs_BenzonaseSeq

  Public
  Analysis for methods and protocol paper

  Shell

  •0•0•0•0•Updated Nov 20, 2024Nov 20, 2024

• 20XX-LastName_Journal

  Public template
  The template repo for future publication-associated repositories

  Shell

  •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

• stencil

  Public
  A web templating engine for visualizing and sharing life science datasets

  nodejsdockerbioinformatics+ 4reactjsstencilwebappbioinformatics-tool

  JavaScript

  •

  MIT License

  •2•7•0•11•Updated Oct 29, 2024Oct 29, 2024

• GenoPipe

  Public
  Toolkit for characterizing the genotype of NGS datasets

  Shell

  •

  MIT License

  •1•4•1•0•Updated Sep 30, 2024Sep 30, 2024

• 2024-Louder_Cell

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Aug 23, 2024Aug 23, 2024

• GenoPipe-docs

  Public
  website and documentation for GenoPipe

  JavaScript

  •0•0•0•0•Updated Mar 4, 2024Mar 4, 2024

• pegr-galaxy_tools

  Public
  Python

  •

  MIT License

  •0•1•0•0•Updated Dec 1, 2023Dec 1, 2023

• 2023-Breugel_JournalXXXX

  Public
  Shell

  •0•0•0•0•Updated Sep 26, 2023Sep 26, 2023

• 2022-Mittal_SAGA

  Public
  Shell

  •0•0•0•0•Updated Oct 29, 2022Oct 29, 2022

• 2018-Rossi_NatureCommunications

  Public
  Simplified ChIP-exo and ChIP-seq assays

  0•2•1•0•Updated Aug 26, 2022Aug 26, 2022

• 2018-Rossi_GenomeResearch

  Public
  Genome-wide determinants of sequence-specific DNA binding of general regulatory factors

  1•2•0•0•Updated Aug 26, 2022Aug 26, 2022

• 2021-Lai_PCRP

  Public
  MIT License

  •0•0•0•0•Updated Aug 26, 2022Aug 26, 2022

• Mittal_2021_ChEC-seq

  Public
  0•0•0•0•Updated Aug 26, 2022Aug 26, 2022

• 2020-Badjatia_peroxide_stress

  Public
  0•0•0•0•Updated Aug 26, 2022Aug 26, 2022

• 2022_EColi_John-Jabbar

  Public
  HTML

  •0•0•0•0•Updated Aug 26, 2022Aug 26, 2022

• Galaxy_Install_Ansible

  Public
  Ansible playbook to install galaxy

  Jinja

  •0•0•0•0•Updated Apr 4, 2022Apr 4, 2022

• stencil-galaxy_tools

  Public
  Galaxy tools to reformat outputs before POSTing to Stencil Website

  Python

  •0•1•0•0•Updated Mar 24, 2022Mar 24, 2022

• pegr-ngs_pipeline

  Public
  Python

  •

  MIT License

  •0•1•0•0•Updated Jul 26, 2021Jul 26, 2021

• PEGR-featureFiles

  Public
  Repo containing genomic feature files linked to PEGR

  0•0•0•0•Updated Feb 3, 2021Feb 3, 2021

• cegr-yep-qcviz

  Public
  Galaxy YEP Qc & Viz workflow invocation scripts and input datasets

  bioinformatics-pipelinengs-analysisgalaxy-workflow

  HTML

  •0•0•0•0•Updated Dec 2, 2020Dec 2, 2020

• PCRPpipeline

  Public
  Bioinformatic pipeline used to process PCRP datasets

  Perl

  •0•1•0•0•Updated May 22, 2020May 22, 2020