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/BayesPrism
A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
Danko-Lab/TED
a fully Bayesian approach to deconvolve tumor microenvironment
Danko-Lab/dREG
Detecting Regulatory Elements using GRO-seq and PRO-seq
Danko-Lab/Rgtsvm
The R package for SVM with GPU architecture based on the GTSVM software
Danko-Lab/proseq2.0
Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing
Danko-Lab/histone-mark-imputation
Repo for the histone imputation project.
Danko-Lab/utils
General utilities/ convenience scripts useful for munging genomic data.
Danko-Lab/clipnet
A deep learning approach to predicting initiation from sequence at single nucleotide resolution
Danko-Lab/tfTarget
Identify transcription factor-enhancer/promoter-gene network from run-on sequencing data
Danko-Lab/AlleleHMM
A data-driven method to identify allele-specific differences in distributed functional genomic marks
Danko-Lab/bigWig2
The extension for the bigWig package in (https://github.com/andrelmartins/bigWig)
Danko-Lab/clipnet_paper
Scripts and notebooks to reproduce figures used in the CLIPNET paper
Danko-Lab/Danko-Lab.github.io
Danko lab website
Danko-Lab/RunOnBamToBigWig
Takes bam files from Run-On sequencing data as input and writes bigWig files as output.
Danko-Lab/GLIMPSE2_setup
Scripts to create a phased reference panel from 1kGP for imputation with GLIMPSE
Danko-Lab/Hi-C_contact_caller
Program for determining the significance of interactions for pairs of points within a chromosome, using a Hi-C contact map
Danko-Lab/HS_transcription_regulation
Heat shock driven transcription regulation correlated with underlying 3D chromatin contacts
Danko-Lab/LSC-PD_analysis_pipeline
Pipeline for locus-specific xlinking pull-down analysis
Danko-Lab/stabilityHMM
Inference of transcript stability from polyA and 5' splice site sequence elements
Danko-Lab/airavata-php-gateway
Mirror of Apache Airavata PHP Gateway
Danko-Lab/ANTXR2
Analyses for Choate et al.
Danko-Lab/ChRO-seq_paper_data
Danko-Lab/dREG-Model
Models used for running dREG
Danko-Lab/dTOX
Identification of transcription factor binding patterns using genome-wide accessibility and transcription
Danko-Lab/E-P_contacts
Danko-Lab/F1_8Organs
Genetic Dissection of the RNA Polymerase II Transcription Cycle with ChRO-seq from F1 hybrid mice
Danko-Lab/HiContactCaller
Latest version of the contact caller should be updated here
Danko-Lab/polymeraseWaves
Identifies Pol II 'waves' in GRO-seq or PRO-seq with support for bigWig files.
Danko-Lab/Prophase-I-Transcription-Project
Danko-Lab/PROseq_Shapes
Use the patterns (shapes) within PRO-seq signal to call transcription element annotations