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@CCBR CCR Collaborative Bioinformatics Resource

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    81 repositories

    • actions

      Public
      🤖 GitHub Actions for CCBR repos
      Python
      •
      MIT License
      •0•0•7•0•Updated Feb 18, 2025Feb 18, 2025

    • CHAMPAGNE

      Public
      CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
      nextflowchip-seq
      Nextflow
      •
      MIT License
      •2•0•58•1•Updated Feb 18, 2025Feb 18, 2025

    • .github

      Public
      organizations readme
      Python
      •0•0•0•1•Updated Feb 16, 2025Feb 16, 2025

    • XAVIER

      Public
      An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH
      Python
      •
      MIT License
      •3•3•10•1•Updated Feb 13, 2025Feb 13, 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 Feb 11, 2025Feb 11, 2025

    • MOSuite

      Public
      MultiOmicsSuite: R package for downstream multi-omics analysis
      R
      •
      Other
      •0•2•20•0•Updated Feb 11, 2025Feb 11, 2025

    • nf-modules

      Public
      Reusable modules and subworkflows for CCBR nextflow pipelines
      Nextflow
      •
      MIT License
      •0•0•10•3•Updated Feb 11, 2025Feb 11, 2025

    • Tools

      Public
      Utilities for CCBR Bioinformatics Software 🛠️
      Python
      •
      MIT License
      •4•1•8•0•Updated Feb 11, 2025Feb 11, 2025

    • LOGAN

      Public
      workflowbioinformaticspipeline
      Nextflow
      •
      MIT License
      •4•1•21•2•Updated Jan 29, 2025Jan 29, 2025

    • CARLISLE

      Public
      Cut And Run Analysis Pipeline
      workflowpipeline
      Python
      •
      MIT License
      •4•4•15•1•Updated Jan 23, 2025Jan 23, 2025

    • 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
      •
      MIT License
      •2•0•0•0•Updated Jan 22, 2025Jan 22, 2025

    • 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 Jan 21, 2025Jan 21, 2025

    • RENEE

      Public
      A comprehensive quality-control and quantification RNA-seq pipeline
      Python
      •
      MIT License
      •4•4•13•0•Updated Jan 21, 2025Jan 21, 2025

    • CRISPIN

      Public
      CRISPR screen pipeline
      Nextflow
      •
      MIT License
      •3•0•14•1•Updated Jan 21, 2025Jan 21, 2025

    • MAPLE

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Jan 21, 2025Jan 21, 2025

    • TRANQUIL

      Public
      TRANQUIL (TRna AbundaNce QUantification pIpeLine)
      Shell
      •
      MIT License
      •1•0•1•0•Updated Jan 21, 2025Jan 21, 2025

    • spacesavers2

      Public
      Python
      •1•0•5•0•Updated Jan 21, 2025Jan 21, 2025

    • MAAPster

      Public
      MAAPster is a comprehensive tool to perform transcriptome analysis of human or mouse Affymetrix gene expression data
      quality-controltranscriptomicspathway-analysisdifferential-expressionbatch-correctionmicroarray-data-analysis
      R
      •
      MIT License
      •6•9•0•0•Updated Jan 21, 2025Jan 21, 2025

    • CCBR_circRNA_AmpliconSeq

      Public
      Snakemake workflow to process circRNA AmpliconSeq datasets generated to study circRNAs in KSHV and human hosts using divergent primers.
      circrnaamplicon-sequencingamplicon-pipelinecircrna-pipelinesnakemake-workflow
      Shell
      •
      MIT License
      •1•0•0•0•Updated Jan 21, 2025Jan 21, 2025

    • ASCENT

      Public
      rMATs and IsoformSwitchAnalyeR workflow for multi-group multi-contrasts scenarios
      Python
      •
      MIT License
      •2•0•2•0•Updated Jan 21, 2025Jan 21, 2025

    • CCBR1245_Ramaswami_nCounter

      Public
      R
      •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • CCBR_tobias

      Public
      Tobias implementation for ATAC seq data.
      Python
      •
      MIT License
      •1•1•2•1•Updated Jan 13, 2025Jan 13, 2025

    • Rodrigues-TLX3-MutIL7R-Leukemia

      Public
      Code for manuscript authored by Gisele Rodrigues in the Scott Durum lab
      R
      •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

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

      Public
      R
      •1•0•0•0•Updated Jan 7, 2025Jan 7, 2025

    • DSP_Analysis

      Public
      A repository for general information and analysis templates for Nanostring's Digital Spatial Profiling
      R
      •1•0•0•0•Updated Jan 7, 2025Jan 7, 2025

    • TaskManagement

      Public
      Shell
      •0•0•0•0•Updated Dec 30, 2024Dec 30, 2024

    • Dockers

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

    • CCBR_NextflowTemplate

      Public template
      CCBR template for Nextflow workflows
      nextflowtemplatestechdev
      Nextflow
      •
      MIT License
      •1•2•14•0•Updated Nov 25, 2024Nov 25, 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