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    24 repositories

    • scHiCcompare

      Public
      Differential analysis of scHi-C data. Includes imputation and normalization steps
      single-cellchromatinschi-c
      R
      •
      Other
      •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • excluderanges

      Public
      Genomic coordinates of problematic genomic regions as GRanges
      R
      •
      Other
      •3•28•1•0•Updated Nov 27, 2024Nov 27, 2024

    • deep-learning-with-r-notebooks

      Public
      HTML
      •
      MIT License
      •7•0•0•0•Updated Oct 23, 2024Oct 23, 2024

    • dozmorovlab.github.io

      Public
      GitHub pages for dozmorovlab web site
      CSS
      •0•1•0•0•Updated Oct 9, 2024Oct 9, 2024

    • BIOS524_videos

      Public
      Lectures for the BIOS-524 course
      HTML
      •0•0•0•0•Updated Aug 1, 2024Aug 1, 2024

    • DEXseq

      Public
      DEXseq analysis scripts
      R
      •
      MIT License
      •0•1•0•0•Updated Apr 20, 2024Apr 20, 2024

    • PDXHiC_supplemental

      Public
      Supplemental scripts for the PDX Hi-C paper
      R
      •3•2•0•0•Updated Apr 2, 2024Apr 2, 2024

    • deep-learning-with-R-2nd-edition-code

      Public
      Code from the book "Deep Learning with R, 2nd Edition"
      R
      •24•0•0•0•Updated Dec 3, 2023Dec 3, 2023

    • Workflows

      Public
      Shell
      •0•0•0•0•Updated Nov 6, 2023Nov 6, 2023

    • SpectralTAD

      Public
      TAD Calling using spectral clustering in R
      R
      •
      Other
      •3•8•2•0•Updated Aug 29, 2023Aug 29, 2023

    • HiCcompare

      Public
      Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices
      visualizationhi-chicnormalizationdifference-detection
      R
      •
      Other
      •3•19•1•0•Updated Jun 4, 2023Jun 4, 2023

    • CTCF

      Public
      Genomic coordinates of FIMO-predicted CTCF binding sites using JASPAR and other PWMs, human and mouse genome assemblies including mm39 and T2T. Also included experimentally derived ENCODE SCREEN CTCF-bound CREs.
      R
      •
      Other
      •1•0•0•0•Updated Dec 25, 2022Dec 25, 2022

    • CTCF.dev

      Public
      CTCF package development
      Shell
      •0•0•0•0•Updated Nov 14, 2022Nov 14, 2022

    • CTCF_orientation

      Public
      Python tool to compute distribution of Loop's CTCF orientation in a pie chart format
      Python
      •2•0•0•0•Updated Jun 2, 2022Jun 2, 2022

    • TADCompare

      Public
      Package for analysis and characterization of differential TADs
      R
      •
      Other
      •2•22•2•0•Updated Apr 25, 2022Apr 25, 2022

    • preciseTAD

      Public
      preciseTAD: A machine learning framework for precise 3D boundary prediction at base-level resolution
      R
      •
      Other
      •0•7•0•0•Updated Apr 22, 2022Apr 22, 2022

    • multiHiCcompare

      Public
      Joint normalization of multiple Hi-C matrices, visualization and detection of differential chromatin interactions, supporting covariates.
      R
      •
      Other
      •8•8•8•0•Updated Apr 22, 2022Apr 22, 2022

    • UO_project_2021

      Public
      Shared repo for the UO project
      HTML
      •1•5•0•0•Updated Mar 12, 2022Mar 12, 2022

    • preciseTADhub

      Public
      An ExperimentHub package that contains pre-trained random forest models associated with the preciseTAD R package (https://doi.org/10.1101/2020.09.03.282186)
      R
      •
      Other
      •0•0•0•0•Updated Aug 12, 2021Aug 12, 2021

    • preciseTADworkshop

      Public
      Precise prediction of TAD/loop boundaries, https://doi.org/10.1101/2020.09.03.282186
      R
      •
      Other
      •0•0•0•0•Updated Dec 8, 2020Dec 8, 2020

    • PDX-HiC_processingScripts

      Public
      PDX Hi-C data processing scripts
      Shell
      •
      Other
      •2•3•0•0•Updated Oct 18, 2020Oct 18, 2020

    • disease_coherence

      Public
      TeX
      •0•0•0•0•Updated Mar 3, 2020Mar 3, 2020

    • HMP2Data

      Public
      Integrative Human Microbiome Project (HMP2) data
      R
      •
      Other
      •1•4•0•0•Updated May 29, 2019May 29, 2019

    • HiCdiff

      Public
      Joint normalization of Hi-C matrices, visualization and detection of differential chromatin interactions
      R
      •
      Other
      •0•1•0•0•Updated Jul 11, 2017Jul 11, 2017