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@AMSSwanglab The Wang lab at AMSS

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    16 repositories

    • cRegulon

      Public
      cRegulon is an optimization model to identify combinatorial regulon from single cell expression and chromatin accessibility data.
      combinatorial-regulationtf-modulecell-type-annotationtf-combination
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jul 9, 2024Jul 9, 2024

    • cTOP

      Public
      Python
      •0•1•0•0•Updated Jun 24, 2024Jun 24, 2024

    • scPECA

      Public
      Python
      •0•0•0•0•Updated Apr 10, 2024Apr 10, 2024

    • ClusterMatch

      Public
      R
      •0•3•0•0•Updated Dec 18, 2023Dec 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
      R
      •0•0•0•0•Updated Nov 29, 2023Nov 29, 2023

    • SpecLoop

      Public
      SpecLoop is a method for predicting cell type-specific chromatin loops via transcription factor cooperation.
      R
      •0•1•0•0•Updated Aug 14, 2023Aug 14, 2023

    • MutNet

      Public
      A heterogeneous network embedding based method by integrating genomic data with genes’ biological processes including protein-protein interactions and pathways.
      Jupyter Notebook
      •1•0•0•0•Updated Jul 28, 2023Jul 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
      gwasvariant-interpretationregulatory-networksrelevant-tissuephenotopic-correlation
      Shell
      •
      GNU General Public License v3.0
      •0•7•0•0•Updated May 8, 2023May 8, 2023

    • RE-GOA

      Public
      A tool for non-coding genomic regions function enrichment analysis based on Regulatory Elements Gene Ontology Annotation (RE-GOA)
      gene-ontologynetwork-embeddingregulatory-elements
      Python
      •1•5•0•0•Updated Sep 6, 2021Sep 6, 2021

    • MIMIC

      Public
      MATLAB
      •0•0•0•0•Updated Sep 1, 2021Sep 1, 2021

    • CNEReg

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 1, 2021Sep 1, 2021

    • hReg-CNCC

      Public
      hReg-CNCC is a high-quality Regulatory network of Cranial Neural Crest Cell (CNCC), built by consensus optimization.
      variant-interpretationregulatory-network-constructionconsensus-optimizationhreg-cncc
      Python
      •0•6•0•0•Updated Aug 5, 2021Aug 5, 2021

    • 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
      •2•8•0•0•Updated Dec 31, 2020Dec 31, 2020

    • GuidingNet

      Public
      GuidingNet is a method to reveal transcriptional cofactor and predict binding for DNA methyltransferase by network regularization.
      methylation
      R
      •1•0•0•0•Updated Aug 9, 2020Aug 9, 2020

    • 3SCover

      Public
      3SCover is a method to identify safeguard TF from cell type -TF network by an extended mimimum set cover model.
      R
      •0•2•0•0•Updated Jun 10, 2020Jun 10, 2020

    • scTIM

      Public
      scTIM is a convenient tool for cell-type indicative marker detection based on single cell RNA-seq data
      single-cell-rna-seqcell-type-indicative-markermarker-detection
      Python
      •0•5•0•0•Updated Jun 3, 2020Jun 3, 2020