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@CCBR CCR Collaborative Bioinformatics Resource

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    81 repositories

    • .github

      Public
      organizations readme
      Python
      •0•0•1•0•Updated Dec 15, 2024Dec 15, 2024

    • actions

      Public
      🤖 GitHub Actions for CCBR repos
      Python
      •
      MIT License
      •0•0•7•0•Updated Dec 13, 2024Dec 13, 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•11•1•Updated Dec 13, 2024Dec 13, 2024

    • DSP_Analysis

      Public
      A repository for general information and analysis templates for Nanostring's Digital Spatial Profiling
      R
      •1•0•3•0•Updated Dec 13, 2024Dec 13, 2024

    • nf-modules

      Public
      Reusable modules and subworkflows for CCBR nextflow pipelines
      Nextflow
      •
      MIT License
      •0•0•10•2•Updated Dec 11, 2024Dec 11, 2024

    • RECAP

      Public
      RECAP for RE-CAlibration of P-values from ChIP-seq peak calling, by method of RE-sampling reads and re-CAlling Peaks.
      Shell
      •2•0•0•0•Updated Dec 11, 2024Dec 11, 2024

    • LOGAN

      Public
      workflowbioinformaticspipeline
      Nextflow
      •
      MIT License
      •4•1•19•1•Updated Dec 11, 2024Dec 11, 2024

    • RENEE

      Public
      A comprehensive quality-control and quantification RNA-seq pipeline
      Python
      •
      MIT License
      •4•4•15•1•Updated Dec 3, 2024Dec 3, 2024

    • Dockers

      Public
      A collection of Dockerfiles to facilitate reproducibility across computing environments.
      dockersingularitybiowulfsbgdnanexus
      Dockerfile
      •3•11•2•0•Updated Dec 3, 2024Dec 3, 2024

    • MOSuite

      Public
      MultiOmicsSuite: R package for downstream multi-omics analysis
      R
      •
      Other
      •0•1•34•0•Updated Dec 3, 2024Dec 3, 2024

    • Tools

      Public
      Utilities for CCBR Bioinformatics Software ⚒️
      Python
      •
      MIT License
      •4•1•8•0•Updated Dec 2, 2024Dec 2, 2024

    • CRISPIN

      Public
      CRISPR screen pipeline
      Nextflow
      •
      MIT License
      •3•0•14•1•Updated Dec 2, 2024Dec 2, 2024

    • CHAMPAGNE

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

    • XAVIER

      Public
      An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH
      Python
      •
      MIT License
      •3•1•8•1•Updated Dec 2, 2024Dec 2, 2024

    • CCBR_NextflowTemplate

      Public template
      CCBR template for Nextflow workflows
      nextflowtemplatestechdev
      Nextflow
      •
      MIT License
      •1•2•9•0•Updated Nov 25, 2024Nov 25, 2024

    • CCBR1245_Ramaswami_nCounter

      Public
      R
      •0•0•0•0•Updated Nov 22, 2024Nov 22, 2024

    • nf-sandbox

      Public
      a repo for testing and toying with nextflow & gh actions
      Python
      •
      MIT License
      •0•0•3•0•Updated Nov 20, 2024Nov 20, 2024

    • mim-tRNAseq

      Public
      Modification-induced misincorporation tRNA sequencing
      Scheme
      •
      GNU General Public License v3.0
      •14•0•0•0•Updated Nov 19, 2024Nov 19, 2024

    • TRANQUIL

      Public
      TRANQUIL (TRna AbundaNce QUantification pIpeLine)
      Shell
      •
      MIT License
      •1•0•1•0•Updated Nov 19, 2024Nov 19, 2024

    • CCBR_tobias

      Public
      Tobias implementation for ATAC seq data.
      Python
      •
      MIT License
      •1•1•3•0•Updated Nov 12, 2024Nov 12, 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 Nov 7, 2024Nov 7, 2024

    • CPTR-12-Wang-DSP-Analysis

      Public
      R
      •1•0•0•0•Updated Oct 31, 2024Oct 31, 2024

    • HowTos

      Public
      How To Guides on various data management and other CCBR-related tasks.
      1•0•2•0•Updated Oct 30, 2024Oct 30, 2024

    • parkit

      Public
      Park folders or tarballs into HPCDME 🚙
      Python
      •
      MIT License
      •0•0•2•0•Updated Oct 30, 2024Oct 30, 2024

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

      Public
      R
      •1•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • CARLISLE

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

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

      Public
      R
      •1•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • spacesavers2

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