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    54 repositories

    • SigRepo

      Public
      SigRepo: An R package for storing and processing omic signatures
      R
      •
      GNU General Public License v3.0
      •1•3•22•0•Updated Mar 11, 2026Mar 11, 2026

    • sigrecon

      Public
      Benchmarking tasks for the recontextualization of gene expression signatures
      R
      •
      GNU General Public License v3.0
      •0•0•10•0•Updated Mar 11, 2026Mar 11, 2026

    • SigRepo_Server

      Public
      Server Architecture of SigRepo Database
      HTML
      •
      GNU General Public License v3.0
      •0•0•3•0•Updated Mar 3, 2026Mar 3, 2026

    • RSNet

      Public
      Resampling-based Network Structure Inference
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 24, 2026Feb 24, 2026

    • sigProCon

      Public
      Evaluate genes driving signature
      R
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Feb 24, 2026Feb 24, 2026

    • brcasurv

      Public
      Age-adjusted survival associations of gene signatures in TCGA/METABRIC/SCANB
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 18, 2026Feb 18, 2026

    • li_et_al_llfs_transcriptomics

      Public
      Analysis scripts associated to the manuscript "Whole blood transcriptional signatures of age and survival identified in Long Life Family and Integrative Longevi…
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 21, 2026Jan 21, 2026

    • kroehling_et_al_hpvneg_hnscc_atlas

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 9, 2026Jan 9, 2026

    • OmicSignature

      Public
      R
      •
      GNU General Public License v3.0
      •0•3•4•0•Updated Dec 16, 2025Dec 16, 2025

    • hypeR-GEM

      Public
      A R Package For Connecting Metabolic Signatures to Enzyme-coding Genes
      R
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Dec 13, 2025Dec 13, 2025

    • hypeR

      Public
      An R Package for Geneset Enrichment Workflows
      bioinformaticscomputational-biologygeneset-enrichment-analysis
      bioinformaticscomputational-biologygeneset-enrichment-analysis
      R
      •
      GNU General Public License v3.0
      •14•79•10•0•Updated Dec 11, 2025Dec 11, 2025

    • brca_atlas

      Public
      Integrated scRNAseq atlas of Breast Cancer
      HTML
      •1•3•3•0•Updated Dec 4, 2025Dec 4, 2025

    • huang_hypeR.GEM_analysis

      Public
      R
      •0•0•0•0•Updated Nov 27, 2025Nov 27, 2025

    • CaDrA

      Public
      Candidate Drivers Analysis: Multi-Omic Search for Candidate Drivers of Functional Signatures
      R
      •
      GNU General Public License v3.0
      •1•24•9•0•Updated Oct 13, 2025Oct 13, 2025

    • .github

      Public
      0•0•0•0•Updated Sep 26, 2025Sep 26, 2025

    • BS831

      Public
      Course Materials for Genomics Data Mining
      HTML
      •
      GNU General Public License v3.0
      •11•22•9•1•Updated Sep 18, 2025Sep 18, 2025

    • monti_et_al_necs_metabolomics

      Public
      HTML
      •0•0•0•0•Updated Sep 12, 2025Sep 12, 2025

    • BrCaExoPDO

      Public
      R
      •0•2•0•0•Updated Aug 26, 2025Aug 26, 2025

    • SerineStarvation

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • nf-gwas-pipeline

      Public
      A Nextflow Genome-Wide Association Study (GWAS) Pipeline
      nextflowbioinformatics-pipeline
      nextflowbioinformatics-pipeline
      R
      •
      GNU General Public License v3.0
      •22•36•1•0•Updated Jun 26, 2025Jun 26, 2025

    • yQTLpipeline

      Public
      R
      •
      GNU General Public License v3.0
      •0•1•1•0•Updated May 7, 2025May 7, 2025

    • K2Taxonomer

      Public
      A tool for the multi-resolution characterization of molecular taxonomies in bulk and single-cell omics data
      visualizationannotationshiny-apps
      visualizationannotationshiny-appsunsupervised-learning
      R
      •
      GNU General Public License v3.0
      •2•4•3•0•Updated Mar 31, 2025Mar 31, 2025

    • 4T1_brainmets

      Public
      HTML
      •0•0•0•0•Updated Mar 13, 2025Mar 13, 2025

    • LSD1_Antitumor_Immunity

      Public
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Sep 17, 2024Sep 17, 2024

    • pipeliner-2

      Public
      Pipeliner upgraded for Nextflow DSL2 modules
      Nextflow
      •
      GNU General Public License v3.0
      •1•3•1•0•Updated Apr 9, 2024Apr 9, 2024

    • knnmi

      Public
      k-nearest neighbor mutual information estimator
      C++
      •
      GNU General Public License v3.0
      •0•1•1•0•Updated Mar 29, 2024Mar 29, 2024

    • best-practices

      Public
      Software engineering best practices for bioinformatics
      0•0•0•0•Updated Mar 13, 2024Mar 13, 2024

    • bieulergy

      Public
      Interactive analysis of multi-omics regulatory networks
      network-analysisshiny-apps
      network-analysisshiny-apps
      R
      •
      GNU General Public License v3.0
      •1•1•3•0•Updated Dec 18, 2023Dec 18, 2023

    • CaDrA.shiny

      Public
      A web interface for interacting with the R package CaDrA
      HTML
      •
      GNU General Public License v3.0
      •0•0•2•0•Updated Dec 11, 2023Dec 11, 2023

    • pml_analysis

      Public
      A code repo for the PML project.
      HTML
      •1•0•0•0•Updated Jun 29, 2023Jun 29, 2023