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@CCBR CCR Collaborative Bioinformatics Resource

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    88 repositories

    • .github

      Public
      organizations readme
      Python
      •0•0•3•3•Updated Apr 26, 2026Apr 26, 2026

    • Dockers2

      Public
      Docker container recipes for CCBR
      Python
      •
      GNU General Public License v3.0
      •2•0•4•4•Updated Apr 25, 2026Apr 25, 2026

    • SINCLAIR

      Public
      SINgle CelL AnalysIs Resource
      R
      •
      MIT License
      •3•2•56•3•Updated Apr 24, 2026Apr 24, 2026

    • actions

      Public
      🤖 GitHub Actions for CCBR repos
      Python
      •
      MIT License
      •0•0•11•0•Updated Apr 24, 2026Apr 24, 2026

    • MOSuite

      Public
      Multi-OmicsSuite: R package for differential multi-omics analysis
      R
      •
      Other
      •0•1•29•3•Updated Apr 23, 2026Apr 23, 2026

    • DSP_Analysis

      Public
      A repository for general information and analysis templates for Nanostring's Digital Spatial Profiling
      R
      •1•0•3•0•Updated Apr 22, 2026Apr 22, 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•19•2•Updated Apr 22, 2026Apr 22, 2026

    • Tools

      Public
      Utilities for CCBR Bioinformatics Software 🛠️
      Python
      •
      MIT License
      •0•1•7•1•Updated Apr 22, 2026Apr 22, 2026

    • LOGAN

      Public
      whoLe genOme-sequencinG Analysis pipeliNe
      workflowbioinformaticspipeline
      workflowbioinformaticspipeline
      Nextflow
      •
      MIT License
      •5•3•19•2•Updated Apr 21, 2026Apr 21, 2026

    • CHAMPAGNE

      Public
      CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
      nextflowchip-seq
      nextflowchip-seq
      Nextflow
      •
      MIT License
      •3•0•52•1•Updated Apr 21, 2026Apr 21, 2026

    • CCBR_Website_Redesign

      Public
      HTML
      •1•0•0•0•Updated Apr 20, 2026Apr 20, 2026

    • CCBR1007-Multimodal-identification-of-HCC-Markers

      Public
      R
      •0•0•0•0•Updated Apr 20, 2026Apr 20, 2026

    • CCBR_NextflowTemplate

      Public template
      CCBR template for Nextflow workflows
      nextflowtemplatestechdev
      nextflowtemplatestechdev
      Nextflow
      •
      MIT License
      •1•2•12•0•Updated Apr 20, 2026Apr 20, 2026

    • MOSuite-Galaxy

      Public
      Galaxy workflow configuration for Multi-OmicsSuite
      Python
      •
      MIT License
      •0•0•9•1•Updated Apr 20, 2026Apr 20, 2026

    • MOSuite-Nextflow

      Public
      Nextflow pipeline for Multi-OmicsSuite
      Nextflow
      •
      MIT License
      •1•0•5•2•Updated Apr 20, 2026Apr 20, 2026

    • RENEE

      Public
      A comprehensive quality-control and quantification RNA-seq pipeline
      Python
      •
      MIT License
      •4•7•21•2•Updated Apr 20, 2026Apr 20, 2026

    • HowTos

      Public
      How-To Guides on CCBR ways of working
      Other
      •1•0•15•0•Updated Apr 7, 2026Apr 7, 2026

    • CCBR1321-Antibody-based-TCR-signaling-overcomes-antigen-heterogeneity

      Public
      Manuscript Submission
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 2, 2026Apr 2, 2026

    • CCBR-1432-A-bispecific-antibody-targeting-a-non-shed-epitope-of-mesothelin-redirects-T-cells

      Public
      Manuscript Submission
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 2, 2026Apr 2, 2026

    • CCBR_SnakemakeTemplate

      Public template
      Barebones framework for creating new snakemake workflows.
      snakemaketemplatestechdev
      snakemaketemplatestechdev
      Shell
      •
      MIT License
      •1•3•2•2•Updated Mar 31, 2026Mar 31, 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•17•0•Updated Mar 24, 2026Mar 24, 2026

    • nf-modules

      Public
      Reusable modules and subworkflows for CCBR nextflow pipelines
      Nextflow
      •
      MIT License
      •0•0•10•3•Updated Mar 24, 2026Mar 24, 2026

    • CRISPIN

      Public
      CRISPR screen pipeline
      Nextflow
      •
      MIT License
      •3•0•13•3•Updated Mar 23, 2026Mar 23, 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•3•11•3•Updated Mar 16, 2026Mar 16, 2026

    • XAVIER

      Public
      An easy-to-use, flexible variant calling pipeline for whole exome sequencing
      Python
      •
      MIT License
      •3•6•9•2•Updated Mar 16, 2026Mar 16, 2026

    • CCBR_tobias

      Public
      Tobias implementation for ATAC seq data.
      Python
      •
      MIT License
      •1•1•1•2•Updated Mar 13, 2026Mar 13, 2026

    • TRANQUIL

      Public
      TRANQUIL (TRna AbundaNce QUantification pIpeLine)
      Shell
      •
      MIT License
      •1•0•2•1•Updated Mar 13, 2026Mar 13, 2026

    • parkit

      Public
      Park folders or tarballs into HPCDME 🚙
      Python
      •
      MIT License
      •0•0•0•3•Updated Mar 13, 2026Mar 13, 2026

    • spacesavers2

      Public
      Python
      •1•0•6•1•Updated Mar 13, 2026Mar 13, 2026

    • HERVx

      Public
      Pipeline to characterize Human Endogenous Retrovirus (HERV) expression
      dockertelescopeherv
      dockertelescopehervwdl-workflow
      Shell
      •
      MIT License
      •3•5•0•0•Updated Feb 25, 2026Feb 25, 2026
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