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    73 repositories

    • tool-Nextflow-action

      Public
      Python
      •
      GNU General Public License v2.0
      •0•0•7•2•Updated Jan 27, 2025Jan 27, 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 subclonal reconstruction
      pipeline
      Groovy
      •
      GNU General Public License v2.0
      •0•6•36•0•Updated Jan 25, 2025Jan 25, 2025

    • package-NanoStringNorm

      Public
      NanoStringNorm
      R
      •
      GNU General Public License v2.0
      •0•0•1•1•Updated Jan 25, 2025Jan 25, 2025

    • Ligare

      Public
      Python
      •
      GNU General Public License v2.0
      •0•0•17•1•Updated Jan 24, 2025Jan 24, 2025

    • package-CancerEvolutionVisualization

      Public
      Publication Quality Phylogenetic Tree Plots
      R
      •
      GNU General Public License v2.0
      •0•2•17•4•Updated Jan 24, 2025Jan 24, 2025

    • docker-Delly

      Public
      Docker repository for Delly
      Dockerfile
      •
      GNU General Public License v2.0
      •0•0•1•1•Updated Jan 23, 2025Jan 23, 2025

    • package-moPepGen

      Public
      Multi-Omics Peptide Generator
      genomicscancer-genomicsproteomicsproteogenomicsneoantigen
      Python
      •
      GNU General Public License v2.0
      •1•8•20•0•Updated Jan 20, 2025Jan 20, 2025

    • docker-SAMtools

      Public
      Dockerfile for samtools - a tools for "Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format".
      docker
      Dockerfile
      •0•0•0•1•Updated Jan 15, 2025Jan 15, 2025

    • prostate-cancer-m6a-paper

      Public
      Code for "The Landscape of N6-Methyladenosine in Localized Primary Prostate Cancer"
      R
      •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

    • tool-PlantUML-action

      Public
      Shell
      •
      GNU General Public License v2.0
      •0•1•1•3•Updated Jan 13, 2025Jan 13, 2025

    • pipeline-call-gSNP

      Public
      Nextflow pipeline to call germline short variants using GATK
      pipelinenextflow
      Nextflow
      •
      GNU General Public License v2.0
      •1•1•22•4•Updated Jan 10, 2025Jan 10, 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•16•0•Updated Jan 6, 2025Jan 6, 2025

    • package-iSubGen

      Public
      R
      •
      GNU General Public License v2.0
      •0•1•4•0•Updated Dec 27, 2024Dec 27, 2024

    • 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•0•6•0•Updated Dec 26, 2024Dec 26, 2024

    • pipeline-recalibrate-BAM

      Public
      Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration
      Nextflow
      •
      GNU General Public License v2.0
      •1•1•9•1•Updated Dec 20, 2024Dec 20, 2024

    • pipeline-call-sSNV

      Public
      Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.
      pipeline
      Nextflow
      •
      GNU General Public License v2.0
      •2•6•34•2•Updated Dec 18, 2024Dec 18, 2024

    • pipeline-Nextflow-config

      Public
      Set of commonly used Nextflow configs
      Groovy
      •
      GNU General Public License v2.0
      •0•1•16•1•Updated Dec 17, 2024Dec 17, 2024

    • pipeline-StableLift

      Public
      Nextflow pipeline for predicting variant stability across reference genome builds.
      R
      •
      GNU General Public License v2.0
      •0•0•0•1•Updated Dec 17, 2024Dec 17, 2024

    • pipeline-call-sSV

      Public
      Nextflow pipeline to call somatic structural variants using DELLY and Manta
      pipeline
      Groovy
      •
      GNU General Public License v2.0
      •0•2•17•2•Updated Dec 16, 2024Dec 16, 2024

    • pipeline-align-DNA

      Public
      Nextflow pipeline to align paired DNA FASTQs and sort, mark duplicates, and index resulting alignment
      pipeline
      Nextflow
      •
      GNU General Public License v2.0
      •1•4•25•1•Updated Dec 16, 2024Dec 16, 2024

    • pipeline-call-gSV

      Public
      Nextflow pipeline to call germline structural variants and copy number variants using DELLY and Manta
      pipeline
      Nextflow
      •
      GNU General Public License v2.0
      •1•2•10•2•Updated Dec 16, 2024Dec 16, 2024

    • pipeline-calculate-targeted-coverage

      Public
      Nextflow pipeline to calculate read-depth related stats for targeted sequencing experiments
      Nextflow
      •
      GNU General Public License v2.0
      •0•0•10•1•Updated Dec 16, 2024Dec 16, 2024

    • package-PipeVal

      Public
      An easy to use CLI tool that can be used to validate different parameters in your NF script/pipeline.
      Python
      •
      GNU General Public License v2.0
      •1•5•16•5•Updated Dec 14, 2024Dec 14, 2024

    • project-CancerBiology-OutlierAnalysis

      Public
      R
      •
      GNU General Public License v2.0
      •0•1•0•0•Updated Dec 13, 2024Dec 13, 2024

    • tool-static-analysis

      Public
      GitHub composite Action to perform static code analysis
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • megalinter

      Public
      🦙 MegaLinter analyzes 50 languages, 22 formats, 21 tooling formats, excessive copy-pastes, spelling mistakes and security issues in your repository sources with a GitHub Action, other CI tools or locally.
      Dockerfile
      •
      GNU Affero General Public License v3.0
      •244•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • package-VennDiagram

      Public
      Generate High-Resolution Venn and Euler Plots
      R
      •
      GNU General Public License v2.0
      •1•2•6•1•Updated Nov 20, 2024Nov 20, 2024

    • tool-NFTest

      Public
      CLI to automate Nextflow pipeline testing
      Python
      •
      GNU General Public License v2.0
      •1•12•13•0•Updated Nov 19, 2024Nov 19, 2024

    • package-OutSeekR

      Public
      R
      •
      GNU General Public License v2.0
      •0•0•2•0•Updated Nov 15, 2024Nov 15, 2024

    • pipeline-call-NonCanonicalPeptide

      Public
      Nextflow pipeline to call non-canonical peptides as custom databases for proteogenomic analysis
      Nextflow
      •
      GNU General Public License v2.0
      •1•0•3•1•Updated Nov 15, 2024Nov 15, 2024