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@CCBR CCR Collaborative Bioinformatics Resource

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    97 repositories

    • actions

      Public
      🤖 GitHub Actions for CCBR repos
      Python
      •
      MIT License
      •0•0•10•1•Updated Sep 18, 2026Sep 18, 2026

    • CHAMPAGNE

      Public
      CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
      nextflowchip-seq
      nextflowchip-seq
      Nextflow
      •
      MIT License
      •5•2•62•3•Updated Sep 18, 2026Sep 18, 2026

    • nf-modules

      Public
      Reusable modules and subworkflows for CCBR nextflow pipelines
      Nextflow
      •
      MIT License
      •1•0•14•3•Updated Sep 18, 2026Sep 18, 2026

    • Tools

      Public
      Utilities for CCBR Bioinformatics Software 🛠️
      Python
      •
      MIT License
      •0•1•18•2•Updated Sep 18, 2026Sep 18, 2026

    • HowTos

      Public
      How-To Guides on CCBR ways of working
      Other
      •1•0•17•1•Updated Sep 18, 2026Sep 18, 2026

    • MOSuite

      Public
      Multi-OmicsSuite: R package for differential multi-omics analysis
      R
      •
      Other
      •0•2•39•4•Updated Sep 18, 2026Sep 18, 2026

    • RENEE

      Public
      A comprehensive quality-control and quantification RNA-seq pipeline
      Python
      •
      MIT License
      •4•8•24•2•Updated Sep 18, 2026Sep 18, 2026

    • functracer

      Public
      Trace Function Dependencies in R Code
      R
      •
      Other
      •0•0•1•0•Updated Sep 18, 2026Sep 18, 2026

    • ASPEN

      Public
      CCBR pipeline for preliminary QC, peak calling, differential chromatin accessibility analysis with ATACseq datasets 🌲
      multiqcngs-pipelinemacs2
      multiqcngs-pipelinemacs2atac-seq-pipelinegenrich
      Python
      •
      MIT License
      •2•1•19•1•Updated Sep 18, 2026Sep 18, 2026

    • CARLISLE

      Public
      Cut And Run anaLysIS pipeLinE calls peaks using MACS2, SEACR and GoPeaks on spike-in normalized input fastqs.
      workflowpipeline
      workflowpipeline
      Python
      •
      MIT License
      •4•4•23•3•Updated Sep 18, 2026Sep 18, 2026

    • syncweaver

      Public
      synchronize code and weave patches seamlessly
      Python
      •
      MIT License
      •0•0•6•2•Updated Sep 18, 2026Sep 18, 2026

    • Dockers2

      Public
      Docker container recipes for CCBR
      Python
      •
      GNU General Public License v3.0
      •2•0•9•2•Updated Sep 18, 2026Sep 18, 2026

    • .github

      Public
      organizations readme
      Python
      •0•0•3•1•Updated Sep 17, 2026Sep 17, 2026

    • CCBR_NextflowTemplate

      Public template
      CCBR template for Nextflow workflows
      nextflowtemplatestechdev
      nextflowtemplatestechdev
      Nextflow
      •
      MIT License
      •1•4•14•0•Updated Sep 15, 2026Sep 15, 2026

    • MOSuite-Galaxy

      Public
      Galaxy workflow configuration for Multi-OmicsSuite
      Python
      •
      MIT License
      •0•0•9•2•Updated Sep 14, 2026Sep 14, 2026

    • SINCLAIR

      Public
      SINgle CelL AnalysIs Resource
      R
      •
      MIT License
      •3•3•50•1•Updated Sep 14, 2026Sep 14, 2026

    • MOSuite-Nextflow

      Public
      Nextflow pipeline for Multi-OmicsSuite
      Nextflow
      •
      MIT License
      •1•0•5•2•Updated Sep 14, 2026Sep 14, 2026

    • CCBR-1326_SCLC

      Public
      integrate ATAC-seq and RNA-seq data in small cell lung cancer
      R
      •
      MIT License
      •0•0•1•0•Updated Sep 14, 2026Sep 14, 2026

    • MAFDash

      Public archive
      MAFDash: R Package to Easily Create an HTML Dashboard to Summarize and Visualize Data from Mutation Annotation Format (MAF) File
      R
      •
      MIT License
      •6•3•0•0•Updated Sep 8, 2026Sep 8, 2026

    • CRISPIN

      Public
      CRISPR screen pipeline
      Nextflow
      •
      MIT License
      •4•0•18•6•Updated Sep 8, 2026Sep 8, 2026

    • LOGAN

      Public
      whoLe genOme-sequencinG Analysis pipeliNe
      workflowbioinformaticspipeline
      workflowbioinformaticspipeline
      Nextflow
      •
      MIT License
      •6•3•19•2•Updated Sep 8, 2026Sep 8, 2026

    • METRO

      Public
      Mouse nEoanTigen pRedictOr
      bioinformaticstumormouse
      bioinformaticstumormouseneoepitopesvaccineneoantigen-prediction
      Python
      •
      MIT License
      •2•6•2•0•Updated Sep 8, 2026Sep 8, 2026

    • CHARLIE

      Public
      Circrnas in Host And viRuses anaLysis pIpEline for Detection Annotation Quantification of circRNAs
      circrnangs-analysisngs-pipeline
      circrnangs-analysisngs-pipelinecircularrna-detection
      Python
      •
      MIT License
      •3•4•11•2•Updated Sep 8, 2026Sep 8, 2026

    • CCBR_tobias

      Public
      Tobias implementation for ATAC seq data.
      Python
      •
      MIT License
      •1•1•1•2•Updated Sep 2, 2026Sep 2, 2026

    • reproducible-toolchain

      Public
      Anatomy of a modular toolchain for reproducible bioinformatics workflows
      poster
      poster
      Mermaid
      •
      MIT License
      •0•0•0•0•Updated Sep 2, 2026Sep 2, 2026

    • XAVIER

      Public
      An easy-to-use, flexible variant calling pipeline for whole exome sequencing
      Python
      •
      MIT License
      •3•6•10•2•Updated Sep 2, 2026Sep 2, 2026

    • TRANQUIL

      Public
      TRANQUIL (TRna AbundaNce QUantification pIpeLine)
      Shell
      •
      MIT License
      •1•0•2•1•Updated Sep 2, 2026Sep 2, 2026

    • MOObject

      Public
      multiOmicDataSet Object package for MOSuite
      R
      •
      Other
      •0•0•1•0•Updated Sep 2, 2026Sep 2, 2026

    • ccbr.r-universe.dev

      Public
      R Universe configuration for CCBR R packages
      0•0•0•0•Updated Sep 1, 2026Sep 1, 2026

    • SCOT

      Public
      Single Cell Omics Toolbox
      R
      •
      Other
      •0•1•15•6•Updated Aug 21, 2026Aug 21, 2026
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