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    38 repositories

    • K2Taxonomer

      Public
      A tool for the multi-resolution characterization of molecular taxonomies in bulk and single-cell omics data
      visualizationannotationshiny-appsunsupervised-learning
      R
      •
      GNU General Public License v3.0
      •1•4•3•0•Updated Dec 19, 2024Dec 19, 2024

    • OmicSignature

      Public
      R
      •
      GNU General Public License v3.0
      •0•3•1•0•Updated Dec 18, 2024Dec 18, 2024

    • CaDrA

      Public
      Candidate Drivers Analysis: Multi-Omic Search for Candidate Drivers of Functional Signatures
      R
      •
      GNU General Public License v3.0
      •1•24•8•0•Updated Sep 21, 2024Sep 21, 2024

    • LSD1_Antitumor_Immunity

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

    • BS831

      Public
      Course Materials for Genomics Data Mining
      HTML
      •
      GNU General Public License v3.0
      •9•22•9•1•Updated Sep 2, 2024Sep 2, 2024

    • hypeR

      Public
      An R Package for Geneset Enrichment Workflows
      bioinformaticscomputational-biologygeneset-enrichment-analysis
      R
      •
      GNU General Public License v3.0
      •11•76•9•0•Updated May 29, 2024May 29, 2024

    • nf-gwas-pipeline

      Public
      A Nextflow Genome-Wide Association Study (GWAS) Pipeline
      nextflowbioinformatics-pipeline
      R
      •
      GNU General Public License v3.0
      •20•31•1•0•Updated May 7, 2024May 7, 2024

    • evalGSVAsig

      Public
      Evaluate genes driving signature
      R
      •
      GNU General Public License v3.0
      •1•1•2•0•Updated Apr 18, 2024Apr 18, 2024

    • yQTLpipeline

      Public
      R
      •
      GNU General Public License v3.0
      •0•1•1•0•Updated Apr 12, 2024Apr 12, 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•0•0•Updated Mar 29, 2024Mar 29, 2024

    • bieulergy

      Public
      Interactive analysis of multi-omics regulatory networks
      network-analysisshiny-apps
      R
      •
      GNU General Public License v3.0
      •0•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

    • hypeR-next

      Public
      Network enrichment through random walks
      network-biology
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 2, 2023Mar 2, 2023

    • Xposome

      Public
      Chemical Screenings using high-throughput transcriptomics assays
      R
      •
      MIT License
      •2•2•9•0•Updated Sep 19, 2022Sep 19, 2022

    • ConAn

      Public
      Resampling-Based Differential Network Connectivity Analysis
      R
      •
      GNU General Public License v3.0
      •4•2•4•0•Updated Jul 12, 2022Jul 12, 2022

    • hypeR-db

      Public
      A hypeR repository for relational and flat genesets
      hyper-repository
      GNU General Public License v3.0
      •0•0•1•0•Updated May 17, 2022May 17, 2022

    • shine-nf

      Public
      A Collection of Nextflow Modules for Bayesian Structure Learning
      nextflownetwork-biologygraphical-modeling
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated May 1, 2022May 1, 2022

    • rpkgs

      Public
      A skeleton for R packages + Docker / Pkgdown / Pages aimed for Bioconductor
      dockergh-pagesexamplebioconductorr-package
      R
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Mar 26, 2022Mar 26, 2022

    • hypeR-modules

      Public
      Integration of hypeR modules in Shiny applications
      R
      •0•0•0•0•Updated Jul 16, 2021Jul 16, 2021

    • hypeR-shiny

      Public
      A web interface for interacting with the R package hypeR
      rshiny
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 16, 2021Jul 16, 2021

    • omics-network

      Public
      An R6 data representation of biological networks and accessory omics data
      network-biology
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 6, 2021Jul 6, 2021

    • hypeR-docs

      Public
      Documentation for hypeR
      hyper-repository
      0•0•0•0•Updated Jul 1, 2021Jul 1, 2021

    • ProteomicsSignaturesCentenarians

      Public
      Analysis scripts associated to Sebastiani et al., Aging Cell 20(2):e13290, 2021
      R
      •1•2•0•0•Updated May 20, 2021May 20, 2021

    • shine

      Public
      Structure Learning for Hierarchical Networks
      structure-learningnetworks-biologygraphical-modeling
      R
      •
      GNU General Public License v3.0
      •2•4•0•0•Updated May 18, 2021May 18, 2021

    • ppi-context

      Public
      Contextualization of protein-protein interaction databases by cell line
      proteomicsnetworks-biology
      Python
      •
      GNU General Public License v3.0
      •0•5•2•0•Updated Mar 3, 2021Mar 3, 2021

    • Adipogen2020

      Public
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jan 20, 2021Jan 20, 2021

    • carcinogenome

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Oct 13, 2020Oct 13, 2020

    • bands

      Public
      Simple interactive chromosome maps written in R
      visualizationrgenomics
      R
      •
      GNU General Public License v3.0
      •3•7•0•0•Updated Aug 19, 2020Aug 19, 2020