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    24 repositories

    • ActiveDriverWGSR

      Public
      ActiveDriverWGSR is an R package for discovery of cancer driver genes and non-coding elements in whole genome sequencing data
      R
      •8•9•5•0•Updated Mar 9, 2026Mar 9, 2026

    • RM2

      Public
      Regression Models for Localised Mutations
      R
      •3•1•1•0•Updated Feb 13, 2026Feb 13, 2026

    • PACIFIC

      Public
      R
      •0•1•0•0•Updated Feb 8, 2026Feb 8, 2026

    • MIMP_V2

      Public
      R
      •0•0•0•0•Updated Feb 3, 2026Feb 3, 2026

    • IGX_publication_code

      Public
      R
      •0•0•0•0•Updated Aug 29, 2025Aug 29, 2025

    • ActivePathways

      Public
      Integrative pathway enrichment analysis of multivariate omics data
      R
      •26•120•1•0•Updated Jul 11, 2025Jul 11, 2025

    • DPM_publication_code

      Public
      DPM: code and input files for the publication
      R
      •0•7•0•0•Updated Jun 20, 2024Jun 20, 2024

    • reimandlab.github.io

      Public
      Ruby
      •1•0•0•0•Updated Oct 14, 2023Oct 14, 2023

    • PPI_network_based_gene_type_prediction_model

      Public
      This is the repository for Reagan (Gen) LI's BCB430 summer project.
      R
      •1•0•0•0•Updated Aug 18, 2023Aug 18, 2023

    • ActiveDriverDB

      Public
      ActiveDriverDB
      Python
      •
      GNU Lesser General Public License v2.1
      •3•12•7•3•Updated May 1, 2023May 1, 2023

    • CA2M_v2

      Public
      CA2M: chromatin accessibility and mutations in cancer genomes
      R
      •2•4•0•0•Updated May 18, 2022May 18, 2022

    • ShinyActivePathways

      Public
      A shiny web server that performs ActivePathways and display results in Enrichment map
      R
      •1•0•0•0•Updated Apr 8, 2022Apr 8, 2022

    • lncRNAs_TCGA

      Public
      Code I have used throughout my Masters analyzing TCGA clinical and RNA-Seq datasets to discover lncRNA prognostic markers
      R
      •4•2•0•0•Updated Sep 9, 2021Sep 9, 2021

    • CNNClassifier

      Public
      Convolutional Neural Net for Sequence Classification
      R
      •1•1•0•0•Updated Jun 15, 2021Jun 15, 2021

    • CA2M

      Public
      Chromatin accessibility of primary human cancers ties regional mutational processes with tissues of origin (repository for paper)
      R
      •1•1•0•0•Updated May 20, 2021May 20, 2021

    • simpsonlab.github.io

      Public
      HTML
      •
      Other
      •8•0•0•0•Updated Nov 30, 2020Nov 30, 2020

    • needleplot

      Public
      Another needleplot for mutation data, used by ActiveDriverDB
      visualizationbioinformaticsplot
      visualizationbioinformaticsplotproteinprotein-interactionptmmutation-analysismutation-data
      JavaScript
      •
      GNU Lesser General Public License v2.1
      •1•2•0•0•Updated Nov 1, 2020Nov 1, 2020

    • plotwistR

      Public
      R
      •
      MIT License
      •1•0•0•0•Updated Aug 17, 2018Aug 17, 2018

    • rmimp2018

      Public
      Predicting the impact of mutations on kinase–substrate phosphorylation
      R
      •8•0•0•0•Updated Mar 15, 2018Mar 15, 2018

    • ActiveDriver

      Public
      R
      •7•0•0•1•Updated Jan 18, 2018Jan 18, 2018

    • mExplorer

      Public
      R
      •1•0•0•0•Updated Aug 24, 2017Aug 24, 2017

    • GEP

      Public
      R
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Sep 2, 2016Sep 2, 2016

    • shiny-web-form

      Public
      A web form created as a shiny app for literature analysis
      R
      •3•1•0•0•Updated Aug 30, 2016Aug 30, 2016

    • muts-needle-plot

      Public
      A needle plot for mutation data
      JavaScript
      •26•0•0•0•Updated Nov 10, 2015Nov 10, 2015
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