Danko Lab @Cornell
We study how gene expression is encoded in DNA, and how this process contributes to evolution, development, and disease.
Cornell University
Pinned Repositories
BayesPrism
A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
dREG
Detecting Regulatory Elements using GRO-seq and PRO-seq
histone-mark-imputation
Repo for the histone imputation project.
proseq2.0
Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing
Rgtsvm
The R package for SVM with GPU architecture based on the GTSVM software
rtfbs_db
Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
TED
a fully Bayesian approach to deconvolve tumor microenvironment
tfTarget
Identify transcription factor-enhancer/promoter-gene network from run-on sequencing data
tutorials
Tutorials covering various topics in genomic data analysis.
utils
General utilities/ convenience scripts useful for munging genomic data.
Danko Lab @Cornell's Repositories
Danko-Lab/rtfbs_db
Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
Danko-Lab/tutorials
Tutorials covering various topics in genomic data analysis.
Danko-Lab/CD4-Cell-Evolution
Analyses for an initial paper on the evolutionary CD4+ T-cell PRO-seq datasets.
Danko-Lab/dREG.HD
Refining TRE regions from dREG by imputing DHS.
Danko-Lab/Laravel-tus-server
Tus server in Laravel PHP 4.2
Danko-Lab/4DN
4DN web site
Danko-Lab/bed-metric
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.
Danko-Lab/callerSquad
Danko-Lab/dreg-gateway-app
Danko-Lab/mcf7tamres
Analyze mechanisms of tamoxifen resistence in MCF-7 subclones