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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•2•0•0•Updated Apr 10, 2024Apr 10, 2024

    • ClusterMatch

      Public
      R
      •0•5•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
      •1•1•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 n…
      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-interpretationconsensus-optimizationhreg-cnccregulatory-network-construction
      Python
      •0•7•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 element…
      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•1•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-seqmarker-detectioncell-type-indicative-marker
      Python
      •0•5•0•0•Updated Jun 3, 2020Jun 3, 2020