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@Danko-Lab

Danko Lab @Cornell

We study how gene expression is encoded in DNA, and how this process contributes to evolution, development, and disease.

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  1. dREG dREG Public

    Detecting Regulatory Elements using GRO-seq and PRO-seq

    R 41 20

  2. rtfbs_db rtfbs_db Public

    Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.

    R 23 8

  3. tfTarget tfTarget Public

    Identify transcription factor-enhancer/promoter-gene network from run-on sequencing data

    R 9 3

  4. proseq2.0 proseq2.0 Public

    Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing

    Shell 30 15

  5. Rgtsvm Rgtsvm Public

    The R package for SVM with GPU architecture based on the GTSVM software

    C++ 32 11

  6. BayesPrism BayesPrism Public

    A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

    HTML 242 59

Repositories

Showing 10 of 43 repositories
  • Danko-Lab.github.io Public

    Danko lab website

    Danko-Lab/Danko-Lab.github.io’s past year of commit activity
    HTML 2 1 0 0 Updated Jun 22, 2026
  • clipnet_ablation Public
    Danko-Lab/clipnet_ablation’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Jun 20, 2026
  • clipnet Public

    A deep learning approach to predicting transcription initiation from sequence at single nucleotide resolution

    Danko-Lab/clipnet’s past year of commit activity
    Jupyter Notebook 14 MIT 3 0 0 Updated May 20, 2026
  • clipnet_finetuning Public

    Fine tuning CLIPNET models to predict K562 PRO-cap and PRO-seq profiles

    Danko-Lab/clipnet_finetuning’s past year of commit activity
    Jupyter Notebook 2 MIT 0 0 0 Updated May 19, 2026
  • PROseq_Shapes Public

    Use the patterns (shapes) within PRO-seq signal to call transcription element annotations

    Danko-Lab/PROseq_Shapes’s past year of commit activity
    R 0 0 0 0 Updated May 15, 2026
  • BayesPrism Public

    A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

    Danko-Lab/BayesPrism’s past year of commit activity
    HTML 242 59 77 0 Updated Apr 3, 2026
  • clipnet_paper Public

    Scripts and notebooks to reproduce figures used in the CLIPNET paper

    Danko-Lab/clipnet_paper’s past year of commit activity
    Jupyter Notebook 2 MIT 0 0 0 Updated Feb 20, 2026
  • dREG Public

    Detecting Regulatory Elements using GRO-seq and PRO-seq

    Danko-Lab/dREG’s past year of commit activity
    R 41 20 10 0 Updated Apr 30, 2025
  • proseq2.0 Public

    Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing

    Danko-Lab/proseq2.0’s past year of commit activity
    Shell 30 BSD-2-Clause 15 7 0 Updated Dec 13, 2024
  • E-P_contacts Public
    Danko-Lab/E-P_contacts’s past year of commit activity
    Python 3 0 0 0 Updated Sep 26, 2024
View all repositories

Most used topics

chro-seq pro-seq r