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@CCBR CCR Collaborative Bioinformatics Resource

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    84 repositories

    • .github

      Public
      organizations readme
      Python
      •0•0•0•0•Updated Feb 22, 2026Feb 22, 2026

    • Dockers2

      Public
      Docker container recipes for CCBR
      Shell
      •
      GNU General Public License v3.0
      •2•0•5•1•Updated Feb 20, 2026Feb 20, 2026

    • CARLISLE

      Public
      Cut And Run anaLysIS pipeLinE calls peaks using MACS2, SEACR and GoPeaks on spike-in normalized input fastqs.
      workflowpipeline
      Python
      •
      MIT License
      •4•4•27•0•Updated Feb 20, 2026Feb 20, 2026

    • RENEE

      Public
      A comprehensive quality-control and quantification RNA-seq pipeline
      Python
      •
      MIT License
      •4•7•23•1•Updated Feb 20, 2026Feb 20, 2026

    • HowTos

      Public
      How-To Guides on CCBR ways of working
      Other
      •1•0•15•0•Updated Feb 20, 2026Feb 20, 2026

    • SINCLAIR

      Public
      SINgle CelL AnalysIs Resource
      R
      •
      MIT License
      •3•1•50•1•Updated Feb 20, 2026Feb 20, 2026

    • parkit

      Public
      Park folders or tarballs into HPCDME 🚙
      Python
      •
      MIT License
      •0•0•0•2•Updated Feb 19, 2026Feb 19, 2026

    • MOSuite-Galaxy

      Public
      Galaxy workflow configuration for Multi-OmicsSuite
      Python
      •
      MIT License
      •0•0•9•0•Updated Feb 19, 2026Feb 19, 2026

    • MOSuite

      Public
      Multi-OmicsSuite: R package for differential multi-omics analysis
      R
      •
      Other
      •0•1•28•2•Updated Feb 19, 2026Feb 19, 2026

    • Tools

      Public
      Utilities for CCBR Bioinformatics Software 🛠️
      Python
      •
      MIT License
      •0•1•6•1•Updated Feb 18, 2026Feb 18, 2026

    • CHAMPAGNE

      Public
      CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
      nextflowchip-seq
      Nextflow
      •
      MIT License
      •3•0•53•1•Updated Feb 16, 2026Feb 16, 2026

    • actions

      Public
      🤖 GitHub Actions for CCBR repos
      Python
      •
      MIT License
      •0•0•11•0•Updated Feb 13, 2026Feb 13, 2026

    • DSP_Analysis

      Public
      A repository for general information and analysis templates for Nanostring's Digital Spatial Profiling
      R
      •1•0•3•0•Updated Feb 12, 2026Feb 12, 2026

    • LOGAN

      Public
      whoLe genOme-sequencinG Analysis pipeliNe
      workflowbioinformaticspipeline
      Nextflow
      •
      MIT License
      •5•3•18•0•Updated Feb 12, 2026Feb 12, 2026

    • MOSuite-Nextflow

      Public
      Nextflow pipeline for Multi-OmicsSuite
      Nextflow
      •
      MIT License
      •1•0•5•0•Updated Feb 10, 2026Feb 10, 2026

    • XAVIER

      Public
      An easy-to-use, flexible variant calling pipeline for whole exome sequencing
      Python
      •
      MIT License
      •3•6•9•0•Updated Feb 5, 2026Feb 5, 2026

    • TRANQUIL

      Public
      TRANQUIL (TRna AbundaNce QUantification pIpeLine)
      Shell
      •
      MIT License
      •1•0•2•0•Updated Feb 5, 2026Feb 5, 2026

    • spacesavers2

      Public
      Python
      •1•0•6•0•Updated Feb 5, 2026Feb 5, 2026

    • nf-modules

      Public
      Reusable modules and subworkflows for CCBR nextflow pipelines
      Nextflow
      •
      MIT License
      •0•0•10•3•Updated Feb 5, 2026Feb 5, 2026

    • CHARLIE

      Public
      Circrnas in Host And viRuses anaLysis pIpEline for Detection Annotation Quantification of circRNAs
      circrnangs-analysisngs-pipelinecircularrna-detection
      Python
      •
      MIT License
      •3•3•11•1•Updated Feb 5, 2026Feb 5, 2026

    • CCBR_tobias

      Public
      Tobias implementation for ATAC seq data.
      Python
      •
      MIT License
      •1•1•1•1•Updated Feb 5, 2026Feb 5, 2026

    • ASPEN

      Public
      CCBR pipeline for preliminary QC, peak calling, differential chromatin accessibility analysis with ATACseq datasets 🌲
      multiqcngs-pipelinemacs2atac-seq-pipelinegenrich
      Python
      •
      MIT License
      •2•0•12•0•Updated Feb 5, 2026Feb 5, 2026

    • shiny-example

      Public
      An example shiny app that provides a template for creating and publishing apps internally to NCI or publicly outside of NCI.
      R
      •
      MIT License
      •1•0•3•0•Updated Jan 13, 2026Jan 13, 2026

    • CCBR_SnakemakeTemplate

      Public template
      Barebones framework for creating new snakemake workflows.
      snakemaketemplatestechdev
      Shell
      •
      MIT License
      •1•3•2•2•Updated Jan 12, 2026Jan 12, 2026

    • SpITR-CPTR--15-DSP-Analysis-Deborah-Citrin

      Public
      R
      •0•0•0•0•Updated Dec 22, 2025Dec 22, 2025

    • DoubletFinder

      Public
      R package for detecting doublets in single-cell RNA sequencing data
      R
      •125•0•0•0•Updated Nov 10, 2025Nov 10, 2025

    • ccbr.r-universe.dev

      Public
      R Universe configuration for CCBR R packages
      0•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • CPTR-10-Tosato-Mouse-WTA-DSP-Analysis

      Public
      R
      •1•0•0•0•Updated Sep 8, 2025Sep 8, 2025

    • rNA

      Public
      Interactive report to assess the quality of large RNA-seq cohorts
      quality-controlrna-seqdashboardinteractivermarkdownfiltering
      R
      •
      MIT License
      •2•1•0•0•Updated Aug 18, 2025Aug 18, 2025

    • CCBR_NextflowTemplate

      Public template
      CCBR template for Nextflow workflows
      nextflowtemplatestechdev
      Nextflow
      •
      MIT License
      •1•2•12•0•Updated Jul 7, 2025Jul 7, 2025