Danko Lab @Cornell

BayesPrism

A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

TED

a fully Bayesian approach to deconvolve tumor microenvironment

dREG

Detecting Regulatory Elements using GRO-seq and PRO-seq

Rgtsvm

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

proseq2.0

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

histone-mark-imputation

Repo for the histone imputation project.

utils

General utilities/ convenience scripts useful for munging genomic data.

clipnet

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

tfTarget

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

AlleleHMM

A data-driven method to identify allele-specific differences in distributed functional genomic marks

bigWig2

The extension for the bigWig package in (https://github.com/andrelmartins/bigWig)

clipnet_paper

Scripts and notebooks to reproduce figures used in the CLIPNET paper

Danko-Lab.github.io

Danko lab website

RunOnBamToBigWig

Takes bam files from Run-On sequencing data as input and writes bigWig files as output.

GLIMPSE2_setup

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

Hi-C_contact_caller

Program for determining the significance of interactions for pairs of points within a chromosome, using a Hi-C contact map

HS_transcription_regulation

Heat shock driven transcription regulation correlated with underlying 3D chromatin contacts

LSC-PD_analysis_pipeline

Pipeline for locus-specific xlinking pull-down analysis

stabilityHMM

Inference of transcript stability from polyA and 5' splice site sequence elements

airavata-php-gateway

Mirror of Apache Airavata PHP Gateway

ANTXR2

Analyses for Choate et al.

ChRO-seq_paper_data

dREG-Model

Models used for running dREG

dTOX

Identification of transcription factor binding patterns using genome-wide accessibility and transcription

E-P_contacts

F1_8Organs

Genetic Dissection of the RNA Polymerase II Transcription Cycle with ChRO-seq from F1 hybrid mice

HiContactCaller

Latest version of the contact caller should be updated here

polymeraseWaves

Identifies Pol II 'waves' in GRO-seq or PRO-seq with support for bigWig files.

Prophase-I-Transcription-Project

PROseq_Shapes

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