Danko-Lab/clipnet_paper

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Created 10 months ago
Updated 2 months ago

Danko-Lab/clipnet_paper

Danko-Lab

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Scripts and notebooks to reproduce figures used in the CLIPNET paper

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

rtfbs_db

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

tutorials

Tutorials covering various topics in genomic data analysis.

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 transcription 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

CD4-Cell-Evolution

Analyses for an initial paper on the evolutionary CD4+ T-cell PRO-seq datasets.

bigWig2

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

Danko-Lab.github.io

Danko lab website

dREG.HD

Refining TRE regions from dREG by imputing DHS.

RunOnBamToBigWig

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

Laravel-tus-server

Tus server in Laravel PHP 4.2

stabilityHMM

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

HS_transcription_regulation

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

Hi-C_contact_caller

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

polymeraseWaves

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

E-P_contacts

LSC-PD_analysis_pipeline

Pipeline for locus-specific xlinking pull-down analysis

GLIMPSE2_setup

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