Repositories list

• methyl-microc

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 21, 2026Apr 21, 2026

• topology-tools

  Public
  Processing pipelines for HiC and other 3D genome tools

  WDL

  •11 fork•44 stars•33 issues•00 pull requests•Updated Apr 19, 2026Apr 19, 2026

• bwa

  Public
  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

  C

  •

  GNU General Public License v3.0

  •579579 forks•00 stars•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.9k3.9k forks•00 stars•00 issues•00 pull requests•Updated Apr 5, 2026Apr 5, 2026

• igv

  Public
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

  Java

  •

  MIT License

  •407407 forks•00 stars•00 issues•00 pull requests•Updated Apr 4, 2026Apr 4, 2026

• foci-3d

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 3, 2026Apr 3, 2026

• codex-agent-project-skeleton

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Apr 1, 2026Apr 1, 2026

• agent-skills

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• footprint-tools

  Public
  Jupyter Notebook

  •00 forks•00 stars•22 issues•00 pull requests•Updated Mar 5, 2026Mar 5, 2026

• aryeelab.dfci.harvard.edu

  Public
  Aryee Lab Webpage

  JavaScript

  •

  MIT License

  •9999 forks•00 stars•00 issues•00 pull requests•Updated Oct 2, 2025Oct 2, 2025

• diffusion-walks

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 10, 2025Jun 10, 2025

• cohesin_extrusion_reproducibility

  Public
  Code repository to reproduce all results for Sept, et al. 2023

  R

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Oct 14, 2024Oct 14, 2024

• nanopore-tools

  Public
  Tools for Oxford Nanopore

  WDL

  •11 fork•22 stars•33 issues•00 pull requests•Updated Aug 21, 2024Aug 21, 2024

• extrusion-sim

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 12, 2024Feb 12, 2024

• neochromatin

  Public
  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Nov 5, 2023Nov 5, 2023

• guideseq

  Public
  Analysis pipeline for the GUIDE-seq assay.

  Python

  •

  GNU Affero General Public License v3.0

  •6161 forks•8181 stars•3939 issues•00 pull requests•Updated Jun 14, 2023Jun 14, 2023

• population-offtargets

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Jun 4, 2023Jun 4, 2023

• block_methylation

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated May 22, 2023May 22, 2023

• encode-chip-seq-pipeline2

  Public
  ENCODE ChIP-seq pipeline

  Python

  •

  MIT License

  •119119 forks•00 stars•00 issues•00 pull requests•Updated May 18, 2023May 18, 2023

• umi

  Public
  Preprocessing tools for unique molecular index (UMI) sequencing reads

  Python

  •

  MIT License

  •2727 forks•3131 stars•1010 issues•00 pull requests•Updated Apr 25, 2023Apr 25, 2023

• encode-hic-pipeline

  Public
  HiC uniform processing pipeline

  WDL

  •

  MIT License

  •2323 forks•00 stars•00 issues•00 pull requests•Updated Feb 3, 2023Feb 3, 2023

• knock-knock

  Public
  toolkit for analyzing genome editing experiments

  Python

  •

  GNU General Public License v3.0

  •1010 forks•00 stars•00 issues•00 pull requests•Updated Jan 25, 2023Jan 25, 2023

• broad-epi-cut-n-run

  Public
  Porting the 4d nucleosome Cut-and-Run pipeline to WDL

  WDL

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 3, 2023Jan 3, 2023

• seaseq

  Public
  Abraham's lab - ChipSeq Pipeline

  WDL

  •

  Apache License 2.0

  •55 forks•00 stars•00 issues•00 pull requests•Updated Dec 20, 2022Dec 20, 2022

• pairtools

  Public
  CLI tools to process mapped Hi-C data

  Python

  •

  MIT License

  •3636 forks•00 stars•00 issues•00 pull requests•Updated Dec 8, 2022Dec 8, 2022

• nanoHiMe

  Public
  C

  •44 forks•00 stars•00 issues•00 pull requests•Updated Nov 4, 2022Nov 4, 2022

• nanopolish

  Public
  Signal-level algorithms for MinION data

  C++

  •

  MIT License

  •160160 forks•00 stars•00 issues•00 pull requests•Updated Jul 29, 2022Jul 29, 2022

• hichipper

  Public
  A preprocessing and QC pipeline for HiChIP data

  bioinformaticsepigeneticschromatin-interaction+ 1

  bioinformaticsepigeneticschromatin-interactionhichip

  HTML

  •

  MIT License

  •1515 forks•4040 stars•4848 issues•11 pull request•Updated Jul 11, 2022Jul 11, 2022

• cas-designer

  Public
  WDL

  •00 forks•11 star•11 issue•00 pull requests•Updated Jul 23, 2021Jul 23, 2021

• cromwell-monitor

  Public
  Generate stats for Cromwell task calls including resource utilization & estimated costs

  Python

  •99 forks•00 stars•00 issues•00 pull requests•Updated Jun 26, 2021Jun 26, 2021