Repositories list

• HowTos

  Public
  How-To Guides on CCBR ways of working

  Shell

  •

  Other

  •11 fork in CCBR/HowTos•00 stars in CCBR/HowTos•1717 issues in CCBR/HowTos•00 pull requests in CCBR/HowTos•Updated Oct 29, 2026Oct 29, 2026

• Tools

  Public
  Utilities for CCBR Bioinformatics Software 🛠️

  Python

  •

  MIT License

  •00 forks in CCBR/Tools•11 star in CCBR/Tools•1919 issues in CCBR/Tools•22 pull requests in CCBR/Tools•Updated Oct 28, 2026Oct 28, 2026

• parkit

  Public
  Park folders or tarballs into HPCDME 🚙

  Python

  •

  MIT License

  •00 forks in CCBR/parkit•00 stars in CCBR/parkit•00 issues in CCBR/parkit•22 pull requests in CCBR/parkit•Updated Oct 28, 2026Oct 28, 2026

• CCBR_SnakemakeTemplate

  Public template
  Barebones framework for creating new snakemake workflows.

  snakemaketemplatestechdev

  snakemaketemplatestechdev

  Shell

  •

  MIT License

  •11 fork in CCBR/CCBR_SnakemakeTemplate•33 stars in CCBR/CCBR_SnakemakeTemplate•22 issues in CCBR/CCBR_SnakemakeTemplate•22 pull requests in CCBR/CCBR_SnakemakeTemplate•Updated Oct 27, 2026Oct 27, 2026

• CCBR_NextflowTemplate

  Public template
  CCBR template for Nextflow workflows

  nextflowtemplatestechdev

  nextflowtemplatestechdev

  Nextflow

  •

  MIT License

  •11 fork in CCBR/CCBR_NextflowTemplate•44 stars in CCBR/CCBR_NextflowTemplate•1414 issues in CCBR/CCBR_NextflowTemplate•00 pull requests in CCBR/CCBR_NextflowTemplate•Updated Oct 27, 2026Oct 27, 2026

• quarto-version-selector

  Public
  Website versions for Quarto

  quartoquarto-extensionquarto-template+ 2

  quartoquarto-extensionquarto-templatequarto-filterquarto-website

  Python

  •

  MIT License

  •00 forks in CCBR/quarto-version-selector•00 stars in CCBR/quarto-version-selector•00 issues in CCBR/quarto-version-selector•22 pull requests in CCBR/quarto-version-selector•Updated Oct 27, 2026Oct 27, 2026

• CHAMPAGNE

  Public
  CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline

  nextflowchip-seq

  nextflowchip-seq

  Nextflow

  •

  MIT License

  •55 forks in CCBR/CHAMPAGNE•22 stars in CCBR/CHAMPAGNE•6161 issues in CCBR/CHAMPAGNE•33 pull requests in CCBR/CHAMPAGNE•Updated Oct 27, 2026Oct 27, 2026

• actions

  Public
  🤖 GitHub Actions for CCBR repos

  Python

  •

  MIT License

  •00 forks in CCBR/actions•00 stars in CCBR/actions•1010 issues in CCBR/actions•11 pull request in CCBR/actions•Updated Oct 27, 2026Oct 27, 2026

• SINCLAIR

  Public
  SINgle CelL AnalysIs Resource

  R

  •

  MIT License

  •33 forks in CCBR/SINCLAIR•33 stars in CCBR/SINCLAIR•5151 issues in CCBR/SINCLAIR•00 pull requests in CCBR/SINCLAIR•Updated Oct 26, 2026Oct 26, 2026

• MOSuite-Nextflow

  Public
  Nextflow pipeline for Multi-OmicsSuite

  Nextflow

  •

  MIT License

  •11 fork in CCBR/MOSuite-Nextflow•00 stars in CCBR/MOSuite-Nextflow•55 issues in CCBR/MOSuite-Nextflow•33 pull requests in CCBR/MOSuite-Nextflow•Updated Oct 26, 2026Oct 26, 2026

• .github

  Public
  organizations readme

  Python

  •00 forks in CCBR/.github•00 stars in CCBR/.github•33 issues in CCBR/.github•11 pull request in CCBR/.github•Updated Oct 26, 2026Oct 26, 2026

• MOSuite-Galaxy

  Public
  Galaxy workflow configuration for Multi-OmicsSuite

  Python

  •

  MIT License

  •00 forks in CCBR/MOSuite-Galaxy•00 stars in CCBR/MOSuite-Galaxy•99 issues in CCBR/MOSuite-Galaxy•33 pull requests in CCBR/MOSuite-Galaxy•Updated Oct 26, 2026Oct 26, 2026

• RENEE

  Public
  A comprehensive quality-control and quantification RNA-seq pipeline (Snakemake)

  Python

  •

  MIT License

  •55 forks in CCBR/RENEE•88 stars in CCBR/RENEE•2525 issues in CCBR/RENEE•33 pull requests in CCBR/RENEE•Updated Oct 26, 2026Oct 26, 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

  •44 forks in CCBR/CARLISLE•44 stars in CCBR/CARLISLE•2424 issues in CCBR/CARLISLE•44 pull requests in CCBR/CARLISLE•Updated Oct 26, 2026Oct 26, 2026

• Dockers2

  Public
  Docker container recipes for CCBR

  Python

  •

  GNU General Public License v3.0

  •22 forks in CCBR/Dockers2•00 stars in CCBR/Dockers2•99 issues in CCBR/Dockers2•22 pull requests in CCBR/Dockers2•Updated Oct 26, 2026Oct 26, 2026

• syncweaver

  Public
  synchronize code and weave patches seamlessly

  Python

  •

  MIT License

  •00 forks in CCBR/syncweaver•00 stars in CCBR/syncweaver•66 issues in CCBR/syncweaver•22 pull requests in CCBR/syncweaver•Updated Oct 24, 2026Oct 24, 2026

• RENEE_NF

  Public
  A comprehensive quality-control and quantification RNA-seq pipeline (Nextflow)

  nextflowbulk-rna-seq

  nextflowbulk-rna-seq

  Nextflow

  •

  MIT License

  •00 forks in CCBR/RENEE_NF•00 stars in CCBR/RENEE_NF•1919 issues in CCBR/RENEE_NF•22 pull requests in CCBR/RENEE_NF•Updated Oct 24, 2026Oct 24, 2026

• quarto-fnl

  Public
  FNL Themes for Quarto

  quartoquarto-extensionquarto-template

  quartoquarto-extensionquarto-template

  SCSS

  •

  MIT License

  •00 forks in CCBR/quarto-fnl•00 stars in CCBR/quarto-fnl•00 issues in CCBR/quarto-fnl•00 pull requests in CCBR/quarto-fnl•Updated Oct 23, 2026Oct 23, 2026

• MOSuite

  Public
  Multi-OmicsSuite: R package for differential multi-omics analysis

  R

  •

  Other

  •00 forks in CCBR/MOSuite•33 stars in CCBR/MOSuite•3939 issues in CCBR/MOSuite•33 pull requests in CCBR/MOSuite•Updated Oct 21, 2026Oct 21, 2026

• BTEP2026

  Public
  Wilfried Guiblet repository for presentation on LLM integration into bioinformatic pipelines.

  HTML

  •11 fork in CCBR/BTEP2026•00 stars in CCBR/BTEP2026•00 issues in CCBR/BTEP2026•00 pull requests in CCBR/BTEP2026•Updated Oct 20, 2026Oct 20, 2026

• MOObject

  Public
  multiOmicDataSet Object package for MOSuite

  R

  •

  Other

  •00 forks in CCBR/MOObject•00 stars in CCBR/MOObject•11 issue in CCBR/MOObject•00 pull requests in CCBR/MOObject•Updated Oct 20, 2026Oct 20, 2026

• SCOT

  Public
  Single Cell Omics Toolbox

  R

  •

  Other

  •00 forks in CCBR/SCOT•11 star in CCBR/SCOT•1515 issues in CCBR/SCOT•55 pull requests in CCBR/SCOT•Updated Oct 19, 2026Oct 19, 2026

• CHARLIE

  Public
  Circrnas in Host And viRuses anaLysis pIpEline for Detection Annotation Quantification of circRNAs

  circrnangs-analysisngs-pipeline+ 1

  circrnangs-analysisngs-pipelinecircularrna-detection

  Python

  •

  MIT License

  •33 forks in CCBR/CHARLIE•44 stars in CCBR/CHARLIE•1212 issues in CCBR/CHARLIE•33 pull requests in CCBR/CHARLIE•Updated Oct 19, 2026Oct 19, 2026

• LOGAN

  Public
  whoLe genOme-sequencinG Analysis pipeliNe

  workflowbioinformaticspipeline

  workflowbioinformaticspipeline

  Nextflow

  •

  MIT License

  •66 forks in CCBR/LOGAN•33 stars in CCBR/LOGAN•2020 issues in CCBR/LOGAN•33 pull requests in CCBR/LOGAN•Updated Oct 19, 2026Oct 19, 2026

• CRISPIN

  Public
  CRISPR screen pipeline

  Nextflow

  •

  MIT License

  •44 forks in CCBR/CRISPIN•00 stars in CCBR/CRISPIN•1919 issues in CCBR/CRISPIN•77 pull requests in CCBR/CRISPIN•Updated Oct 19, 2026Oct 19, 2026

• XAVIER

  Public
  An easy-to-use, flexible variant calling pipeline for whole exome sequencing

  Python

  •

  MIT License

  •44 forks in CCBR/XAVIER•88 stars in CCBR/XAVIER•1111 issues in CCBR/XAVIER•33 pull requests in CCBR/XAVIER•Updated Oct 19, 2026Oct 19, 2026

• nf-modules

  Public
  Reusable modules and subworkflows for CCBR nextflow pipelines

  Nextflow

  •

  MIT License

  •11 fork in CCBR/nf-modules•00 stars in CCBR/nf-modules•1414 issues in CCBR/nf-modules•33 pull requests in CCBR/nf-modules•Updated Oct 14, 2026Oct 14, 2026

• vscode-ghcopilot-superpowers

  Public
  Install superpowers in any repo when coding on biowulf to use them via VSCode

  Shell

  •00 forks in CCBR/vscode-ghcopilot-superpowers•00 stars in CCBR/vscode-ghcopilot-superpowers•11 issue in CCBR/vscode-ghcopilot-superpowers•00 pull requests in CCBR/vscode-ghcopilot-superpowers•Updated Oct 13, 2026Oct 13, 2026

• ASPEN

  Public
  CCBR pipeline for preliminary QC, peak calling, differential chromatin accessibility analysis with ATACseq datasets 🌲

  multiqcngs-pipelinemacs2+ 2

  multiqcngs-pipelinemacs2atac-seq-pipelinegenrich

  Python

  •

  MIT License

  •22 forks in CCBR/ASPEN•11 star in CCBR/ASPEN•99 issues in CCBR/ASPEN•00 pull requests in CCBR/ASPEN•Updated Oct 13, 2026Oct 13, 2026

• TRANQUIL

  Public
  TRANQUIL (TRna AbundaNce QUantification pIpeLine)

  Shell

  •

  MIT License

  •11 fork in CCBR/TRANQUIL•00 stars in CCBR/TRANQUIL•22 issues in CCBR/TRANQUIL•22 pull requests in CCBR/TRANQUIL•Updated Oct 8, 2026Oct 8, 2026