Repositories list

• scATAC-reprog

  Public
  Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency" by Nair, Ameen et al.

  Jupyter Notebook

  •

  MIT License

  •1•7•0•0•Updated Nov 12, 2024Nov 12, 2024

• retina-design

  Public
  Designing AAV sequences for retinal cell types (with scATAC-seq models)

  Jupyter Notebook

  •0•1•0•0•Updated Nov 10, 2024Nov 10, 2024

• DART-Eval

  Public
  Jupyter Notebook

  •0•16•1•0•Updated Nov 6, 2024Nov 6, 2024

• ImmuneCLIP

  Public
  Repository for code and data related to ImmuneCLIP

  Python

  •

  MIT License

  •1•5•0•0•Updated Nov 1, 2024Nov 1, 2024

• variant-scorer

  Public
  A framework to score and analyze variant effects genome-wide using ChromBPNet models

  Python

  •

  MIT License

  •2•8•2•0•Updated Oct 30, 2024Oct 30, 2024

• ProCapNet

  Public
  Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.

  Jupyter Notebook

  •4•12•0•0•Updated Oct 3, 2024Oct 3, 2024

• TENet

  Public
  Python

  •0•1•0•0•Updated Sep 22, 2024Sep 22, 2024

• chrombpnet

  Public
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

  Jupyter Notebook

  •

  MIT License

  •34•123•11•1•Updated Aug 27, 2024Aug 27, 2024

• affinity_distillation

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Aug 10, 2024Aug 10, 2024

• bpnet

  Public
  Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them

  Jupyter Notebook

  •

  MIT License

  •35•142•16•1•Updated Aug 2, 2024Aug 2, 2024

• CTCFMutants

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Jul 8, 2024Jul 8, 2024

• atacseq-dnaseseq-chrombpnet-modelzoo-pipeline

  Public
  Jupyter Notebook

  •1•0•0•0•Updated May 31, 2024May 31, 2024

• synapse-backup-syncer

  Public
  Create and sync backups to Synapse

  Shell

  •0•0•0•0•Updated May 8, 2024May 8, 2024

• anvil-variant-scoring

  Public
  WDL

  •0•0•0•0•Updated May 7, 2024May 7, 2024

• bpnet-refactor

  Public
  Python

  •

  MIT License

  •0•3•5•1•Updated Apr 7, 2024Apr 7, 2024

• tfmodisco

  Public
  TF MOtif Discovery from Importance SCOres

  Jupyter Notebook

  •

  MIT License

  •29•124•22•4•Updated Jan 28, 2024Jan 28, 2024

• encode_upload_tfatlas_readmes

  Public
  0•0•0•0•Updated Aug 21, 2023Aug 21, 2023

• Cardiogenesis_Repo

  Public
  Cardiogenesis Repo

  Jupyter Notebook

  •2•9•0•0•Updated Aug 8, 2023Aug 8, 2023

• dragonn

  Public
  A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

  deep-learninggenomics

  Jupyter Notebook

  •

  MIT License

  •71•256•15•2•Updated Aug 1, 2023Aug 1, 2023

• hitcallerNet

  Public
  0•0•0•0•Updated May 25, 2023May 25, 2023

• track-hubs

  Public
  Python

  •0•0•0•0•Updated Apr 1, 2023Apr 1, 2023

• ENCODE_manual_liver

  Public
  Python

  •1•0•0•0•Updated Mar 31, 2023Mar 31, 2023

• ENCODE_manual_adrenal

  Public
  Python

  •1•0•0•0•Updated Mar 31, 2023Mar 31, 2023

• idr

  Public
  IDR

  Python

  •

  GNU General Public License v2.0

  •46•30•0•1•Updated Mar 30, 2023Mar 30, 2023

• basepairmodels

  Public
  Python

  •

  MIT License

  •6•16•18•2•Updated Mar 24, 2023Mar 24, 2023

• humbio51-student

  Public
  student files for humbio51

  Jupyter Notebook

  •0•0•0•0•Updated Mar 14, 2023Mar 14, 2023

• procapnet-modelzoo-pipeline

  Public
  Repository for the pipeline to run ProCapNet.

  0•0•0•0•Updated Mar 11, 2023Mar 11, 2023

• jamboree-toolkit

  Public
  toolkit for setting up compute environment on gcp for jamborees

  Shell

  •0•1•0•0•Updated Mar 1, 2023Mar 1, 2023

• simdna

  Public
  A python library for creating simulated regulatory DNA sequences

  Python

  •

  MIT License

  •21•38•0•2•Updated Feb 22, 2023Feb 22, 2023

• ENCODE_scatac

  Public
  Python

  •

  MIT License

  •1•8•0•0•Updated Jan 31, 2023Jan 31, 2023