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    81 repositories

    • package-ApplyPolygenicScore

      Public
      Utilities for matching a polygenic score coordinate file to a VCF input and the subsequent calculation of the provided polygenic score in each individual.
      R
      •
      GNU General Public License v2.0
      •0•4•8•0•Updated Feb 26, 2026Feb 26, 2026

    • public-R-CancerEvolutionVisualization

      Public
      Publication Quality Phylogenetic Tree Plots
      R
      •
      GNU General Public License v2.0
      •0•2•20•2•Updated Jan 29, 2026Jan 29, 2026

    • public-R-NanoStringNormCNV

      Public
      Helper Functions to Normalize NanoString CNV Data
      R
      •
      GNU General Public License v2.0
      •0•0•0•1•Updated Jan 23, 2026Jan 23, 2026

    • package-iSubGen

      Public
      R
      •
      GNU General Public License v2.0
      •0•1•5•1•Updated Jan 23, 2026Jan 23, 2026

    • public-R-SeqKat

      Public
      Detection of Kataegis
      R
      •0•0•1•0•Updated Jan 23, 2026Jan 23, 2026

    • package-OmicsQC

      Public
      Aggregation of QC metrics and outlier nomination for multi-sample studies
      quality-controlrgenomics
      quality-controlrgenomicscosine-similarityngs-analysis
      R
      •
      GNU General Public License v2.0
      •0•1•5•1•Updated Jan 23, 2026Jan 23, 2026

    • public-R-HistogramZoo

      Public
      HistogramZoo - A set of methods for histogram segmentation and characterization
      R
      •
      GNU General Public License v3.0
      •0•3•35•0•Updated Jan 22, 2026Jan 22, 2026

    • package-BoutrosLab-plotting-general

      Public
      Functions to Create Publication-Quality Plots
      R
      •4•17•61•2•Updated Jan 21, 2026Jan 21, 2026

    • package-VennDiagram

      Public
      Generate High-Resolution Venn and Euler Plots
      R
      •
      GNU General Public License v2.0
      •2•8•6•2•Updated Jan 14, 2026Jan 14, 2026

    • Ligare

      Public
      Python
      •
      GNU General Public License v2.0
      •0•1•16•7•Updated Jan 8, 2026Jan 8, 2026

    • tool-PlantUML-action

      Public
      Shell
      •
      GNU General Public License v2.0
      •1•1•1•2•Updated Dec 22, 2025Dec 22, 2025

    • tool-create-release

      Public
      GitHub reusable workflows to manage the release process
      release-automationgithub-actions
      release-automationgithub-actions
      Python
      •
      GNU General Public License v2.0
      •1•0•0•3•Updated Dec 15, 2025Dec 15, 2025

    • tool-NFTest

      Public
      CLI to automate Nextflow pipeline testing
      Python
      •
      GNU General Public License v2.0
      •2•12•16•3•Updated Dec 15, 2025Dec 15, 2025

    • pipeline-StableLift

      Public
      Nextflow pipeline for predicting variant stability across reference genome builds.
      R
      •
      GNU General Public License v2.0
      •1•0•0•2•Updated Nov 24, 2025Nov 24, 2025

    • tool-Docker-action

      Public
      An Action to automatically build and push images to the GitHub Container registry. Includes automatic building of images for development.
      dockercicdgithub-actions
      dockercicdgithub-actions
      JavaScript
      •
      GNU General Public License v2.0
      •2•0•3•3•Updated Nov 24, 2025Nov 24, 2025

    • pipeline-call-sSNV

      Public
      Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.
      pipeline
      pipeline
      Nextflow
      •
      GNU General Public License v2.0
      •3•6•36•5•Updated Nov 24, 2025Nov 24, 2025

    • pipeline-call-gSNP

      Public
      Nextflow pipeline to call germline short variants using GATK
      pipelinenextflow
      pipelinenextflow
      Nextflow
      •
      GNU General Public License v2.0
      •2•1•21•4•Updated Nov 24, 2025Nov 24, 2025

    • metapipeline-DNA

      Public
      Nextflow pipeline to convert BAM to FASTQ, align, perform QC, assess targeted coverage, call gSNP, call sSNV, call mtSNV, call SVs, call sCNA, and perform subcl…
      pipeline
      pipeline
      Groovy
      •
      GNU General Public License v2.0
      •1•17•35•1•Updated Nov 24, 2025Nov 24, 2025

    • tool-static-analysis

      Public
      GitHub composite Action to perform static code analysis
      Python
      •
      GNU General Public License v2.0
      •1•0•1•2•Updated Nov 24, 2025Nov 24, 2025

    • pipeline-call-sSV

      Public
      Nextflow pipeline to call somatic structural variants using DELLY, GRIDSS2 and Manta
      pipeline
      pipeline
      Nextflow
      •
      GNU General Public License v2.0
      •1•2•15•2•Updated Nov 24, 2025Nov 24, 2025

    • pipeline-align-DNA

      Public
      Nextflow pipeline to align paired DNA FASTQs and sort, mark duplicates, and index resulting alignment
      pipeline
      pipeline
      Nextflow
      •
      GNU General Public License v2.0
      •2•4•26•3•Updated Nov 24, 2025Nov 24, 2025

    • pipeline-call-gSV

      Public
      Nextflow pipeline to call germline structural variants and copy number variants using DELLY and Manta
      pipeline
      pipeline
      R
      •
      GNU General Public License v2.0
      •2•3•11•2•Updated Nov 24, 2025Nov 24, 2025

    • pipeline-calculate-mtDNA-CopyNumber

      Public
      Nextflow pipeline to calculate mitochondrial DNA copy number
      Groovy
      •
      GNU General Public License v2.0
      •0•0•0•2•Updated Nov 24, 2025Nov 24, 2025

    • pipeline-generate-SQC-BAM

      Public
      Nextflow pipeline to generate sample level QC data from BAM files
      Groovy
      •
      GNU General Public License v2.0
      •0•0•17•3•Updated Nov 24, 2025Nov 24, 2025

    • package-moPepGen

      Public
      Multi-Omics Peptide Generator
      genomicscancer-genomicsproteomics
      genomicscancer-genomicsproteomicsproteogenomicsneoantigen
      Python
      •
      GNU General Public License v2.0
      •5•30•27•1•Updated Nov 6, 2025Nov 6, 2025

    • tool-Nextflow-action

      Public
      Python
      •
      GNU General Public License v2.0
      •1•0•6•5•Updated Oct 27, 2025Oct 27, 2025

    • package-PrCaMethy

      Public
      R
      •
      GNU General Public License v2.0
      •0•0•1•1•Updated Oct 17, 2025Oct 17, 2025

    • project-CancerBiology-OutlierAnalysis

      Public
      R
      •
      GNU General Public License v2.0
      •0•1•0•0•Updated Oct 13, 2025Oct 13, 2025

    • package-PCaModelSystemRNA

      Public
      A transcriptomic compendium for a variety of current and upcoming models used to study Prostate cancer.
      rna
      rna
      R
      •
      GNU General Public License v2.0
      •0•0•11•3•Updated Sep 8, 2025Sep 8, 2025

    • pipeline-recalibrate-BAM

      Public
      Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration
      Nextflow
      •
      GNU General Public License v2.0
      •2•1•14•2•Updated Sep 2, 2025Sep 2, 2025
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