@Danko-Lab

Danko Lab @Cornell

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

Pinned repositories

  1. rtfbs_db

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

    R 15 5

  2. dREG

    Detecting Regulatory Elements using GRO-seq and PRO-seq

    R 11 11

  3. Rgtsvm

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

    C++ 15 9

  4. utils

    General utilities/ convenience scripts useful for munging genomic data.

    Shell 5 2

  5. dREG.HD

    Refining TRE regions from dREG by imputing DHS.

    R 1 1

  6. Laravel-tus-server

    Tus server in Laravel PHP 4.2

    PHP 1

  • General utilities/ convenience scripts useful for munging genomic data.

    Shell 5 2 Updated Aug 17, 2018
  • A data-driven method to identify allele-specific differences in distributed functional genomic marks

    Python 2 BSD-2-Clause Updated Aug 15, 2018
  • Identify transcription factor-enhancer/promoter-gene network from run-on sequencing data

    R 1 Updated Aug 12, 2018
  • The R package for SVM with GPU architecture based on the GTSVM software

    C++ 15 9 Updated Aug 6, 2018
  • Refining TRE regions from dREG by imputing DHS.

    R 1 1 Updated Jul 19, 2018
  • Mirror of Apache Airavata PHP Gateway

    PHP 29 Updated Jun 25, 2018
  • Tutorials covering various topics in genomic data analysis.

    3 3 Updated Jun 7, 2018
  • Detecting Regulatory Elements using GRO-seq and PRO-seq

    R 11 11 Updated Jun 6, 2018
  • Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.

    R 15 5 GPL-3.0 Updated May 11, 2018
  • Danko lab website

    HTML 1 Updated Apr 15, 2018
  • Analyses for an initial paper on the evolutionary CD4+ T-cell PRO-seq datasets.

    R 2 2 Updated Mar 28, 2018
  • R Updated Mar 15, 2018
  • Tus server in Laravel PHP 4.2

    PHP 1 MIT Updated Mar 21, 2017
  • Shell MIT Updated Feb 15, 2017
  • Analyze mechanisms of tamoxifen resistence in MCF-7 subclones

    R Updated Jan 4, 2017
  • 4DN web site

    HTML Updated May 31, 2016
  • Inference of transcript stability from polyA and 5' splice site sequence elements

    R BSD-2-Clause Updated Feb 19, 2016
  • Calculate a sort of 'information content' for data in bed format, by seeing how many unique positions are recovered as a function of the total read depth.

    R 1 MIT Updated Sep 27, 2015
  • Identifies Pol II 'waves' in GRO-seq or PRO-seq with support for bigWig files.

    R 2 Updated Apr 30, 2015
  • Models used for running dREG

    Updated Feb 26, 2015