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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 Public

    Detecting Regulatory Elements using GRO-seq and PRO-seq

    R 34 21

  2. rtfbs_db Public

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

    R 22 8

  3. tfTarget Public

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

    R 9 3

  4. proseq2.0 Public

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

    Shell 26 12

  5. Rgtsvm Public

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

    C++ 32 11

  6. BayesPrism Public

    A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

    HTML 176 49

Repositories

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

    Danko lab website

    HTML 2 2 0 0 Updated Mar 16, 2025
  • clipnet Public

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

    Python 9 MIT 3 0 0 Updated Feb 26, 2025
  • clipnet_k562 Public

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

    Jupyter Notebook 1 MIT 0 0 0 Updated Feb 15, 2025
  • clipnet_ablation Public
    Jupyter Notebook 0 0 0 0 Updated Feb 15, 2025
  • PROseq_Shapes Public

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

    R 0 0 0 0 Updated Jan 13, 2025
  • clipnet_paper Public

    Scripts and notebooks to reproduce figures used in the CLIPNET paper

    Jupyter Notebook 2 MIT 0 0 0 Updated Dec 13, 2024
  • proseq2.0 Public

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

    Shell 26 BSD-2-Clause 12 6 0 Updated Dec 13, 2024
  • BayesPrism Public

    A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

    HTML 176 49 65 0 Updated Nov 18, 2024
  • E-P_contacts Public
    Python 1 0 0 0 Updated Sep 26, 2024
  • dREG Public

    Detecting Regulatory Elements using GRO-seq and PRO-seq

    R 34 21 8 1 Updated Aug 5, 2024
View all repositories

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