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@CCBR CCR Collaborative Bioinformatics Resource

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    78 repositories

    • SINCLAIR

      Public
      scRNASeq pipeline
      R
      •
      MIT License
      •3•1•49•3•Updated Aug 22, 2025Aug 22, 2025

    • Tools

      Public
      Utilities for CCBR Bioinformatics Software 🛠️
      Python
      •
      MIT License
      •0•1•4•1•Updated Aug 22, 2025Aug 22, 2025

    • RENEE

      Public
      A comprehensive quality-control and quantification RNA-seq pipeline
      Python
      •
      MIT License
      •5•7•21•0•Updated Aug 22, 2025Aug 22, 2025

    • 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•19•0•Updated Aug 22, 2025Aug 22, 2025

    • MOSuite

      Public
      Multi-OmicsSuite: R package for differential multi-omics analysis
      R
      •
      Other
      •0•1•23•1•Updated Aug 22, 2025Aug 22, 2025

    • rNA

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

    • .github

      Public
      organizations readme
      Python
      •0•0•0•0•Updated Aug 17, 2025Aug 17, 2025

    • CHAMPAGNE

      Public
      CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
      nextflowchip-seq
      Nextflow
      •
      MIT License
      •2•0•54•0•Updated Aug 15, 2025Aug 15, 2025

    • Dockers2

      Public
      Revamp of Dockers
      Shell
      •
      GNU General Public License v3.0
      •1•0•4•1•Updated Aug 13, 2025Aug 13, 2025

    • actions

      Public
      🤖 GitHub Actions for CCBR repos
      Python
      •
      MIT License
      •0•0•10•0•Updated Jul 29, 2025Jul 29, 2025

    • DSP_Analysis

      Public
      A repository for general information and analysis templates for Nanostring's Digital Spatial Profiling
      R
      •1•0•0•0•Updated Jul 25, 2025Jul 25, 2025

    • 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 Jul 21, 2025Jul 21, 2025

    • XAVIER

      Public
      An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH
      Python
      •
      MIT License
      •3•6•11•0•Updated Jul 15, 2025Jul 15, 2025

    • spacesavers2

      Public
      Python
      •1•0•6•0•Updated Jul 15, 2025Jul 15, 2025

    • parkit

      Public
      Park folders or tarballs into HPCDME 🚙
      Python
      •
      MIT License
      •0•0•2•0•Updated Jul 12, 2025Jul 12, 2025

    • CCBR_NextflowTemplate

      Public template
      CCBR template for Nextflow workflows
      nextflowtemplatestechdev
      Nextflow
      •
      MIT License
      •1•2•10•0•Updated Jul 7, 2025Jul 7, 2025

    • LOGAN

      Public
      workflowbioinformaticspipeline
      Nextflow
      •
      MIT License
      •4•2•21•0•Updated Jun 26, 2025Jun 26, 2025

    • CCBR_tobias

      Public
      Tobias implementation for ATAC seq data.
      Python
      •
      MIT License
      •1•1•1•1•Updated Jun 23, 2025Jun 23, 2025

    • TRANQUIL

      Public
      TRANQUIL (TRna AbundaNce QUantification pIpeLine)
      Shell
      •
      MIT License
      •1•0•2•0•Updated Jun 16, 2025Jun 16, 2025

    • CRISPIN

      Public
      CRISPR screen pipeline
      Nextflow
      •
      MIT License
      •3•0•13•1•Updated Jun 3, 2025Jun 3, 2025

    • CHARLIE

      Public
      Circrnas in Host And viRuses anaLysis pIpEline for Detection Annotation Quantification of circRNAs
      circrnangs-analysisngs-pipelinecircularrna-detection
      Python
      •
      MIT License
      •3•2•11•1•Updated May 27, 2025May 27, 2025

    • l2p

      Public
      List to pathway, or l2p, is an R package for gene set enrichment analysis that is optimized for speed.
      cr-packagefunctional-enrichment-analysisover-representation-analysisl2p
      C
      •
      MIT License
      •2•0•0•0•Updated May 21, 2025May 21, 2025

    • A-Pan-Cancer-Comparative-Analysis-of-The-Cancer-Genome-Atlas-Transcriptomic-TIL-Immune-Signatures

      Public
      0•0•0•0•Updated May 19, 2025May 19, 2025

    • ccbr1271_ERVpipeline

      Public
      ERV pipeline based of scripts from NCI Yasmine Belkaid Lab
      Python
      •
      MIT License
      •0•2•1•0•Updated May 15, 2025May 15, 2025

    • pipeliner-docs

      Public archive
      Documentation for users and developers working with or contributing to Pipeliner.
      documentationpipeliner
      MIT License
      •2•4•0•0•Updated May 15, 2025May 15, 2025

    • build-renee-refs

      Public
      Build genome references for RENEE
      Python
      •
      MIT License
      •0•0•0•0•Updated May 13, 2025May 13, 2025

    • hTLX3_mutIL7R_leukemia_Rodrigues

      Public
      Code used to process data for manuscript on leukemia produced by human TLX3 and mutant IL7R-alpha (Rodrigues et al.)
      R
      •
      MIT License
      •0•0•0•0•Updated May 12, 2025May 12, 2025

    • HowTos

      Public
      How To Guides on various data management and other CCBR-related tasks.
      1•0•3•0•Updated Apr 24, 2025Apr 24, 2025

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

      Public
      R
      •1•0•0•0•Updated Apr 24, 2025Apr 24, 2025

    • mim-tRNAseq

      Public
      Modification-induced misincorporation tRNA sequencing
      Scheme
      •
      GNU General Public License v3.0
      •14•0•0•0•Updated Apr 8, 2025Apr 8, 2025