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    40 repositories

    • clipnet

      Public
      A deep learning approach to predicting transcription initiation from sequence at single nucleotide resolution
      Python
      •
      MIT License
      •2•9•0•0•Updated Jan 27, 2025Jan 27, 2025

    • Danko-Lab.github.io

      Public
      Danko lab website
      HTML
      •
      Other
      •2•2•0•0•Updated Jan 27, 2025Jan 27, 2025

    • clipnet_k562

      Public
      Transfer learning of CLIPNET (trained on LCL) to K562
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jan 27, 2025Jan 27, 2025

    • clipnet_ablation

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • PROseq_Shapes

      Public
      Use the patterns (shapes) within PRO-seq signal to call transcription element annotations
      R
      •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

    • clipnet_paper

      Public
      Scripts and notebooks to reproduce figures used in the CLIPNET paper
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Dec 13, 2024Dec 13, 2024

    • proseq2.0

      Public
      Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing
      Shell
      •
      BSD 2-Clause "Simplified" License
      •12•24•6•0•Updated Dec 13, 2024Dec 13, 2024

    • BayesPrism

      Public
      A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
      HTML
      •46•170•65•0•Updated Nov 18, 2024Nov 18, 2024

    • E-P_contacts

      Public
      Python
      •0•1•0•0•Updated Sep 26, 2024Sep 26, 2024

    • GLIMPSE2_setup

      Public
      Scripts to create a phased reference panel from 1kGP for imputation with GLIMPSE
      Python
      •
      MIT License
      •1•1•0•1•Updated May 22, 2024May 22, 2024

    • ChRO-seq_paper_data

      Public
      R
      •0•0•0•0•Updated Apr 17, 2024Apr 17, 2024

    • dREG

      Public
      Detecting Regulatory Elements using GRO-seq and PRO-seq
      gene-regulationpro-seqchro-seqtranscription-regulatory-elementsgro-seq
      R
      •21•34•8•1•Updated Aug 5, 2024Aug 5, 2024

    • histone-mark-imputation

      Public
      Repo for the histone imputation project.
      R
      •3•10•3•0•Updated Dec 7, 2023Dec 7, 2023

    • RunOnBamToBigWig

      Public
      Takes bam files from Run-On sequencing data as input and writes bigWig files as output.
      Shell
      •
      BSD 2-Clause "Simplified" License
      •4•2•0•0•Updated Sep 13, 2023Sep 13, 2023

    • Prophase-I-Transcription-Project

      Public
      Shell
      •0•0•0•0•Updated Feb 9, 2023Feb 9, 2023

    • tfTarget

      Public
      Identify transcription factor-enhancer/promoter-gene network from run-on sequencing data
      transcriptional-regulatory-networkenhancer-predictionpro-seqchro-seq
      R
      •3•8•1•2•Updated Aug 27, 2022Aug 27, 2022

    • TED

      Public
      a fully Bayesian approach to deconvolve tumor microenvironment
      scrna-seqdeconvolutionbulk-rna-seqtumor-cellsstromal-cellsexpression-profiletumor-expression
      R
      •10•60•12•0•Updated Jun 20, 2022Jun 20, 2022

    • dREG-Model

      Public
      Models used for running dREG
      1•0•0•0•Updated Oct 11, 2021Oct 11, 2021

    • dTOX

      Public
      Identification of transcription factor binding patterns using genome-wide accessibility and transcription
      R
      •
      GNU Lesser General Public License v3.0
      •1•0•0•0•Updated Oct 9, 2021Oct 9, 2021

    • ANTXR2

      Public
      Analyses for Choate et al.
      Shell
      •0•0•0•0•Updated Aug 9, 2021Aug 9, 2021

    • Rgtsvm

      Public
      The R package for SVM with GPU architecture based on the GTSVM software
      rsvre1071-compatibilitygpusvmgt-svmgpu-architecture
      C++
      •12•32•12•0•Updated Aug 4, 2021Aug 4, 2021

    • F1_8Organs

      Public
      Genetic Dissection of the RNA Polymerase II Transcription Cycle with ChRO-seq from F1 hybrid mice
      R
      •0•0•0•0•Updated May 10, 2021May 10, 2021

    • utils

      Public
      General utilities/ convenience scripts useful for munging genomic data.
      Shell
      •4•8•0•0•Updated Aug 4, 2020Aug 4, 2020

    • stabilityHMM

      Public
      Inference of transcript stability from polyA and 5' splice site sequence elements
      R
      •
      BSD 2-Clause "Simplified" License
      •1•2•0•0•Updated Jun 10, 2020Jun 10, 2020

    • polymeraseWaves

      Public
      Identifies Pol II 'waves' in GRO-seq or PRO-seq with support for bigWig files.
      R
      •3•1•0•1•Updated Apr 21, 2020Apr 21, 2020

    • bigWig2

      Public
      The extension for the bigWig package in (https://github.com/andrelmartins/bigWig)
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Mar 22, 2020Mar 22, 2020

    • HiContactCaller

      Public
      Latest version of the contact caller should be updated here
      Python
      •0•0•0•0•Updated Jan 24, 2020Jan 24, 2020

    • AlleleHMM

      Public
      A data-driven method to identify allele-specific differences in distributed functional genomic marks
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•5•0•0•Updated Oct 9, 2019Oct 9, 2019

    • HS_transcription_regulation

      Public
      Heat shock driven transcription regulation correlated with underlying 3D chromatin contacts
      R
      •1•1•0•0•Updated Sep 16, 2019Sep 16, 2019

    • Hi-C_contact_caller

      Public
      Program for determining the significance of interactions for pairs of points within a chromosome, using a Hi-C contact map
      Python
      •2•1•0•0•Updated Jul 3, 2019Jul 3, 2019