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@CCBR CCR Collaborative Bioinformatics Resource

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    80 repositories

    • .github

      Public
      organizations readme
      Python
      •0•0•0•0•Updated Oct 27, 2024Oct 27, 2024

    • RENEE

      Public
      A comprehensive quality-control and quantification RNA-seq pipeline
      Python
      •
      MIT License
      •4•3•19•0•Updated Oct 25, 2024Oct 25, 2024

    • HowTos

      Public
      How To Guides on various data management and other CCBR-related tasks.
      1•0•3•1•Updated Oct 25, 2024Oct 25, 2024

    • CHARLIE

      Public
      Circrnas in Host And viRuses anaLysis pIpEline for Detection Annotation Quantification of circRNAs
      circrnangs-analysisngs-pipelinecircularrna-detection
      Python
      •
      MIT License
      •1•2•15•2•Updated Oct 24, 2024Oct 24, 2024

    • Dockers

      Public
      A collection of Dockerfiles to facilitate reproducibility across computing environments.
      dockersingularitybiowulfsbgdnanexus
      Dockerfile
      •3•11•1•0•Updated Oct 24, 2024Oct 24, 2024

    • LOGAN

      Public
      workflowbioinformaticspipeline
      Nextflow
      •
      MIT License
      •4•1•18•0•Updated Oct 24, 2024Oct 24, 2024

    • nf-sandbox

      Public
      a repo for testing and toying with nextflow & gh actions
      Python
      •
      MIT License
      •0•0•3•0•Updated Oct 23, 2024Oct 23, 2024

    • reneeTools

      Public
      R package for downstream multi-omics analysis
      R
      •
      Other
      •0•1•31•0•Updated Oct 22, 2024Oct 22, 2024

    • CPTR-11-Beck-Canine-OsteoSarcoma-DSP-Analysis

      Public
      R
      •0•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • CRISPIN

      Public
      CRISPR screen pipeline
      Nextflow
      •
      MIT License
      •3•0•12•1•Updated Oct 16, 2024Oct 16, 2024

    • parkit

      Public
      Park folders or tarballs into HPCDME 🚙
      Python
      •
      MIT License
      •0•0•2•0•Updated Oct 16, 2024Oct 16, 2024

    • CARLISLE

      Public
      Cut And Run Analysis Pipeline
      workflowpipeline
      Python
      •
      MIT License
      •4•4•12•0•Updated Oct 14, 2024Oct 14, 2024

    • Tools

      Public
      Utilities for CCBR Bioinformatics Software ⚒️
      Python
      •
      MIT License
      •4•1•8•0•Updated Oct 10, 2024Oct 10, 2024

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

      Public
      R
      •0•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • actions

      Public
      🤖 GitHub Actions for CCBR repos
      Python
      •
      MIT License
      •0•0•5•0•Updated Oct 8, 2024Oct 8, 2024

    • XAVIER

      Public
      An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH
      Python
      •
      MIT License
      •3•1•7•0•Updated Oct 3, 2024Oct 3, 2024

    • CCBR_tobias

      Public
      Tobias implementation for ATAC seq data.
      Python
      •
      MIT License
      •1•1•2•0•Updated Oct 3, 2024Oct 3, 2024

    • CHAMPAGNE

      Public
      CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
      nextflowchip-seq
      Nextflow
      •
      MIT License
      •2•0•51•0•Updated Oct 1, 2024Oct 1, 2024

    • spacesavers2

      Public
      Python
      •1•0•4•0•Updated Oct 1, 2024Oct 1, 2024

    • CCBR_NextflowTemplate

      Public template
      CCBR template for Nextflow workflows
      nextflowtemplatestechdev
      Nextflow
      •
      MIT License
      •1•2•9•0•Updated Sep 13, 2024Sep 13, 2024

    • ASPEN

      Public
      CCBR pipeline for preliminary QC and peak calling from ATACseq datasets 🌲
      multiqcngs-pipelinemacs2atac-seq-pipelinegenrich
      Shell
      •
      MIT License
      •2•0•4•0•Updated Sep 13, 2024Sep 13, 2024

    • DSP_Analysis

      Public
      A repository for general information and analysis templates for Nanostring's Digital Spatial Profiling
      HTML
      •0•0•2•0•Updated Sep 10, 2024Sep 10, 2024

    • l2ptest

      Public
      l2p testing
      C
      •0•0•0•0•Updated Aug 30, 2024Aug 30, 2024

    • 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 Aug 23, 2024Aug 23, 2024

    • CCBR_SnakemakeTemplate

      Public template
      Barebones framework for creating new snakemake workflows.
      snakemaketemplatestechdev
      Shell
      •
      MIT License
      •1•3•1•0•Updated Aug 20, 2024Aug 20, 2024

    • build-renee-refs

      Public
      Build genome references for RENEE
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 6, 2024Aug 6, 2024

    • CCBR1245_Ramaswami_nCounter

      Public
      R
      •0•0•0•0•Updated Aug 5, 2024Aug 5, 2024

    • CPTR_5_DSP_Krug

      Public
      HTML
      •1•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • CPTR-9-Weigert-DSP-Analysis

      Public
      HTML
      •1•0•0•0•Updated Jul 24, 2024Jul 24, 2024

    • nf-modules

      Public
      Reusable modules and subworkflows for CCBR nextflow pipelines
      Nextflow
      •
      MIT License
      •0•0•10•1•Updated Jul 16, 2024Jul 16, 2024