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    36 repositories

    • MINTsC

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Apr 10, 2026Apr 10, 2026

    • GLEAM

      Public
      GLEAM is a graph-based method for integrating multi-modal single-cell data and predicting missing modalities
      Python
      •0•0•0•0•Updated Feb 2, 2026Feb 2, 2026

    • BasCoD

      Public
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jan 20, 2026Jan 20, 2026

    • CMAPS

      Public
      Causal Mediation Analysis of Perturbation Screens
      R
      •1•0•0•0•Updated Jan 20, 2026Jan 20, 2026

    • BandNorm

      Public
      Simple Normalization Method for single-cell Hi-C
      R
      •
      GNU General Public License v3.0
      •4•4•0•0•Updated Aug 5, 2025Aug 5, 2025

    • Dozer

      Public
      HTML
      •2•1•0•0•Updated Aug 2, 2024Aug 2, 2024

    • GEEES

      Public
      GEEES: Inferring Cell-specific Gene-Enhancer Interactions from Multi-modal Single Cell Data
      R
      •1•1•0•0•Updated Dec 12, 2023Dec 12, 2023

    • Muscle

      Public
      R
      •0•4•0•0•Updated Dec 5, 2023Dec 5, 2023

    • INCA

      Public
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Nov 3, 2023Nov 3, 2023

    • INCAData

      Public
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 11, 2023Oct 11, 2023

    • MuDCoD

      Public
      MuDCoD: Multi-subject Dynamic Community Detection
      Python
      •
      MIT License
      •3•0•0•0•Updated May 20, 2023May 20, 2023

    • AdaLiftOver

      Public
      Adaptive LiftOver
      R
      •
      GNU General Public License v3.0
      •3•1•0•0•Updated Apr 3, 2023Apr 3, 2023

    • BandNorm_and_scVI-3D_manuscript

      Public
      Code for generating figures and tables from "Normalization and De-noising of Single-cell Hi-C Data with BandNorm and scVI-3D"
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Sep 16, 2022Sep 16, 2022

    • scVI-3D

      Public
      Python
      •
      GNU General Public License v3.0
      •3•3•0•0•Updated Sep 14, 2022Sep 14, 2022

    • scRNAzirf

      Public
      This repository contains the code base for zero inflated random forests.
      R
      •1•0•0•0•Updated Oct 30, 2021Oct 30, 2021

    • INFIMA-paper

      Public
      The source codes for the INFIMA paper
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jul 14, 2021Jul 14, 2021

    • INFIMA

      Public
      Integrative Fine-mapping with Model Organism Multi-Omics Data
      R
      •
      MIT License
      •1•1•0•0•Updated Jul 14, 2021Jul 14, 2021

    • mbasic

      Public
      Matrix Based Analysis for State-space Inference and Clustering.
      R
      •5•1•0•0•Updated Jul 13, 2021Jul 13, 2021

    • dpeak

      Public
      High resolution identification of protein binding sites using PET and SET ChIP-Seq and ChIP-exo data
      R
      •2•0•0•0•Updated Jul 13, 2021Jul 13, 2021

    • mosaics

      Public
      MOdel-based one and two Sample Analysis and Inference for ChIP-Seq
      R
      •5•1•0•0•Updated Jul 13, 2021Jul 13, 2021

    • ChIPUtils

      Public
      A package with basic utilities for ChIP analysis (both ChIPseq and ChIPexo)
      R
      •2•0•0•0•Updated Jul 13, 2021Jul 13, 2021

    • permseq

      Public
      Prior-enhanced read mapping for ChIP-seq
      R
      •2•6•0•0•Updated Jul 13, 2021Jul 13, 2021

    • ChIPexoQualExample

      Public
      Example data for the ChIPexoQual pacakge
      R
      •1•0•0•0•Updated Jul 13, 2021Jul 13, 2021

    • atSNP

      Public
      High speed p-value computation for regulatory SNP detection using Motif information
      R
      •7•5•0•0•Updated Jul 13, 2021Jul 13, 2021

    • iFunMed

      Public
      Integrative functional mediation: example and usage
      R
      •
      MIT License
      •3•1•0•0•Updated Jul 13, 2021Jul 13, 2021

    • surf

      Public
      The statistical utility for RBP functions (SURF)
      R
      •
      GNU General Public License v3.0
      •3•1•0•0•Updated Jul 13, 2021Jul 13, 2021

    • FreeHiC

      Public
      FreeHi-C pipeline for high fidelity Hi-C data simulation.
      Python
      •
      MIT License
      •10•12•0•0•Updated Jul 13, 2021Jul 13, 2021

    • mlg

      Public
      R
      •2•2•0•0•Updated Oct 19, 2020Oct 19, 2020

    • mHiC

      Public
      mhi-cmulti-reads
      mhi-cmulti-reads
      Python
      •
      MIT License
      •11•12•0•1•Updated May 26, 2020May 26, 2020

    • surf-paper

      Public
      This repository makes available the source code of our SURF paper(s).
      R
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated May 4, 2020May 4, 2020
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