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@AMSSwanglab

The Wang lab at AMSS

Optimization and Computational Systems Biology

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  1. vPECA vPECA Public

    vPECA is a Variants interpretation method by Paired Expression and Chromatin Accessibility data which can identify active and active selected regulatory elements and their gene regulatory network.

    MATLAB 8 2

  2. SpecVar SpecVar Public

    SpecVar is a convenient tool for estimating interpretable genetic correlation of human complex traits and annotating the SNPs with context specific regulatory networks

    Shell 7

  3. hReg-CNCC hReg-CNCC Public

    hReg-CNCC is a high-quality Regulatory network of Cranial Neural Crest Cell (CNCC), built by consensus optimization.

    Python 6

  4. scTIM scTIM Public

    scTIM is a convenient tool for cell-type indicative marker detection based on single cell RNA-seq data

    Python 5

  5. RE-GOA RE-GOA Public

    A tool for non-coding genomic regions function enrichment analysis based on Regulatory Elements Gene Ontology Annotation (RE-GOA)

    Python 5 1

  6. 3SCover 3SCover Public

    3SCover is a method to identify safeguard TF from cell type -TF network by an extended mimimum set cover model.

    R 2

Repositories

Showing 10 of 16 repositories
  • cRegulon Public

    cRegulon is an optimization model to identify combinatorial regulon from single cell expression and chromatin accessibility data.

    AMSSwanglab/cRegulon’s past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Jul 9, 2024
  • cTOP Public
    AMSSwanglab/cTOP’s past year of commit activity
    Python 1 0 0 0 Updated Jun 24, 2024
  • scPECA Public
    AMSSwanglab/scPECA’s past year of commit activity
    Python 0 0 0 0 Updated Apr 10, 2024
  • ClusterMatch Public
    AMSSwanglab/ClusterMatch’s past year of commit activity
    R 1 0 0 0 Updated Dec 18, 2023
  • RP3 Public

    RP3 (RNA Polymerase II Pausing Prediction) is a method for predicting transcriptional elongation Pol II pausing by integrating multi-omics data

    AMSSwanglab/RP3’s past year of commit activity
    R 0 0 0 0 Updated Nov 29, 2023
  • SpecLoop Public

    SpecLoop is a method for predicting cell type-specific chromatin loops via transcription factor cooperation.

    AMSSwanglab/SpecLoop’s past year of commit activity
    R 1 0 0 0 Updated Aug 14, 2023
  • MutNet Public Forked from YurunLu/MutNet

    A heterogeneous network embedding based method by integrating genomic data with genes’ biological processes including protein-protein interactions and pathways.

    AMSSwanglab/MutNet’s past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated Jul 28, 2023
  • SpecVar Public

    SpecVar is a convenient tool for estimating interpretable genetic correlation of human complex traits and annotating the SNPs with context specific regulatory networks

    AMSSwanglab/SpecVar’s past year of commit activity
    Shell 7 GPL-3.0 0 0 0 Updated May 8, 2023
  • RE-GOA Public

    A tool for non-coding genomic regions function enrichment analysis based on Regulatory Elements Gene Ontology Annotation (RE-GOA)

    AMSSwanglab/RE-GOA’s past year of commit activity
    Python 5 1 0 0 Updated Sep 6, 2021
  • MIMIC Public
    AMSSwanglab/MIMIC’s past year of commit activity
    MATLAB 0 0 0 0 Updated Sep 1, 2021
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