Projects in Awesome Lists by Danko-Lab
A curated list of projects in awesome lists by Danko-Lab .
https://github.com/danko-lab/bayesprism
A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
Last synced: 10 Feb 2026
https://github.com/danko-lab/ted
a fully Bayesian approach to deconvolve tumor microenvironment
bulk-rna-seq deconvolution expression-profile scrna-seq stromal-cells tumor-cells tumor-expression
Last synced: 16 Aug 2025
https://github.com/danko-lab/dreg
Detecting Regulatory Elements using GRO-seq and PRO-seq
chro-seq gene-regulation gro-seq pro-seq transcription-regulatory-elements
Last synced: 16 Aug 2025
https://github.com/Danko-Lab/dREG
Detecting Regulatory Elements using GRO-seq and PRO-seq
chro-seq gene-regulation gro-seq pro-seq transcription-regulatory-elements
Last synced: 10 May 2025
https://github.com/danko-lab/rgtsvm
The R package for SVM with GPU architecture based on the GTSVM software
e1071-compatibility gpu gpu-architecture gt-svm r svm svr
Last synced: 16 Aug 2025
https://github.com/danko-lab/proseq2.0
Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing
Last synced: 16 Aug 2025
https://github.com/Danko-Lab/proseq2.0
Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing
Last synced: 10 May 2025
https://github.com/danko-lab/rtfbs_db
Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
cis-bp enrichment-analysis motif r tfbs-discovery transcription-factor-binding transcription-factors
Last synced: 01 Aug 2025
https://github.com/danko-lab/tutorials
Tutorials covering various topics in genomic data analysis.
Last synced: 06 Mar 2026
https://github.com/danko-lab/clipnet
A deep learning approach to predicting transcription initiation from sequence at single nucleotide resolution
Last synced: 08 Sep 2025
https://github.com/danko-lab/histone-mark-imputation
Repo for the histone imputation project.
Last synced: 16 Aug 2025
https://github.com/danko-lab/tftarget
Identify transcription factor-enhancer/promoter-gene network from run-on sequencing data
chro-seq enhancer-prediction pro-seq transcriptional-regulatory-network
Last synced: 14 Mar 2026
https://github.com/danko-lab/utils
General utilities/ convenience scripts useful for munging genomic data.
Last synced: 16 Aug 2025
https://github.com/Danko-Lab/tfTarget
Identify transcription factor-enhancer/promoter-gene network from run-on sequencing data
chro-seq enhancer-prediction pro-seq transcriptional-regulatory-network
Last synced: 10 May 2025
https://github.com/danko-lab/allelehmm
A data-driven method to identify allele-specific differences in distributed functional genomic marks
Last synced: 16 Aug 2025
https://github.com/danko-lab/cd4-cell-evolution
Analyses for an initial paper on the evolutionary CD4+ T-cell PRO-seq datasets.
Last synced: 31 Aug 2025
https://github.com/danko-lab/runonbamtobigwig
Takes bam files from Run-On sequencing data as input and writes bigWig files as output.
Last synced: 16 Aug 2025
https://github.com/danko-lab/clipnet_paper
Scripts and notebooks to reproduce figures used in the CLIPNET paper
Last synced: 20 Feb 2026
https://github.com/danko-lab/bigwig2
The extension for the bigWig package in (https://github.com/andrelmartins/bigWig)
Last synced: 16 Aug 2025
https://github.com/danko-lab/dreg.hd
Refining TRE regions from dREG by imputing DHS.
Last synced: 16 Aug 2025
https://github.com/danko-lab/stabilityhmm
Inference of transcript stability from polyA and 5' splice site sequence elements
Last synced: 18 Oct 2025
https://github.com/danko-lab/glimpse2_setup
Scripts to create a phased reference panel from 1kGP for imputation with GLIMPSE
Last synced: 16 Aug 2025
https://github.com/danko-lab/lsc-pd_analysis_pipeline
Pipeline for locus-specific xlinking pull-down analysis
Last synced: 01 Sep 2025
https://github.com/danko-lab/laravel-tus-server
Tus server in Laravel PHP 4.2
Last synced: 16 Aug 2025
https://github.com/danko-lab/hs_transcription_regulation
Heat shock driven transcription regulation correlated with underlying 3D chromatin contacts
Last synced: 16 Aug 2025
https://github.com/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
Last synced: 24 Oct 2025
https://github.com/danko-lab/polymerasewaves
Identifies Pol II 'waves' in GRO-seq or PRO-seq with support for bigWig files.
Last synced: 16 Aug 2025
https://github.com/danko-lab/dtox
Identification of transcription factor binding patterns using genome-wide accessibility and transcription
Last synced: 16 Aug 2025
https://github.com/danko-lab/proseq_shapes
Use the patterns (shapes) within PRO-seq signal to call transcription element annotations
Last synced: 30 Aug 2025
https://github.com/danko-lab/f1_8organs
Genetic Dissection of the RNA Polymerase II Transcription Cycle with ChRO-seq from F1 hybrid mice
Last synced: 16 Aug 2025
https://github.com/danko-lab/hicontactcaller
Latest version of the contact caller should be updated here
Last synced: 16 Aug 2025
https://github.com/danko-lab/mcf7tamres
Analyze mechanisms of tamoxifen resistence in MCF-7 subclones
Last synced: 16 Aug 2025