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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 34 21

  2. rtfbs_db rtfbs_db Public

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

    R 22 8

  3. tfTarget tfTarget Public

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

    R 7 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 24 11

  5. Rgtsvm Rgtsvm Public

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

    C++ 32 12

  6. BayesPrism BayesPrism Public

    A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

    HTML 157 46

Repositories

Showing 10 of 43 repositories
  • BayesPrism Public

    A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

    Danko-Lab/BayesPrism’s past year of commit activity
    HTML 157 46 64 0 Updated Nov 12, 2024
  • 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
    Python 9 MIT 2 0 0 Updated Oct 29, 2024
  • 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 Oct 21, 2024
  • clipnet_k562 Public

    Transfer learning of CLIPNET (trained on LCL) to K562

    Danko-Lab/clipnet_k562’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Oct 18, 2024
  • clipnet_ablation Public
    Danko-Lab/clipnet_ablation’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Sep 30, 2024
  • E-P_contacts Public
    Danko-Lab/E-P_contacts’s past year of commit activity
    Python 1 0 0 0 Updated Sep 26, 2024
  • 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 24 BSD-2-Clause 11 6 0 Updated Sep 17, 2024
  • dREG Public

    Detecting Regulatory Elements using GRO-seq and PRO-seq

    Danko-Lab/dREG’s past year of commit activity
    R 34 21 8 1 Updated Aug 5, 2024
  • pyBayesPrism Public Forked from ziluwang829/pyBayesPrism
    Danko-Lab/pyBayesPrism’s past year of commit activity
    Python 0 MIT 2 0 0 Updated Aug 3, 2024
  • GLIMPSE2_setup Public

    Scripts to create a phased reference panel from 1kGP for imputation with GLIMPSE

    Danko-Lab/GLIMPSE2_setup’s past year of commit activity
    Python 1 MIT 1 0 1 Updated May 22, 2024
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