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    77 repositories

    • RENEE

      Public
      A comprehensive quality-control and quantification RNA-seq pipeline
      Python
      •
      MIT License
      •4•0•0•0•Updated Dec 23, 2025Dec 23, 2025

    • Dockers2

      Public
      Revamp of Dockers
      Shell
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • Oncogenomics_NF_WF

      Public
      Nextflow
      •1•0•0•0•Updated Dec 4, 2025Dec 4, 2025

    • CHAMPAGNE

      Public
      CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
      Nextflow
      •
      MIT License
      •3•0•0•0•Updated Dec 3, 2025Dec 3, 2025

    • non-B_gfa

      Public
      Identify non-B forming motifs
      C
      •
      MIT License
      •10•10•2•0•Updated Nov 26, 2025Nov 26, 2025

    • bss-tracker

      Public
      BSS Tracker is a hierarchical laboratory information management system designed to track and manage Investigators, Projects, Biosamples, Samples, and Specimens.
      JavaScript
      •2•0•0•2•Updated Nov 21, 2025Nov 21, 2025

    • CARLISLE

      Public
      Cut And Run Analysis Pipeline
      Python
      •
      MIT License
      •4•0•0•0•Updated Nov 20, 2025Nov 20, 2025

    • ASPEN

      Public
      CCBR pipeline for preliminary QC, peak calling, differential chromatin accessibility analysis with ATACseq datasets 🌲
      Python
      •
      MIT License
      •2•0•0•0•Updated Oct 2, 2025Oct 2, 2025

    • abcsFrederick.github.io

      Public
      This is the repo for the official abcsFrederick IO webpage.
      0•0•10•0•Updated Sep 30, 2025Sep 30, 2025

    • SINCLAIR

      Public
      scRNASeq pipeline
      R
      •
      MIT License
      •3•0•0•0•Updated Sep 20, 2025Sep 20, 2025

    • NCI-RBL-Dockers

      Public
      A repository of recipes for Docker containers built for the NCI-RBL
      C
      •3•0•0•0•Updated Sep 20, 2025Sep 20, 2025

    • LOGAN

      Public
      Nextflow
      •
      MIT License
      •4•0•0•0•Updated Sep 11, 2025Sep 11, 2025

    • scRNA_pipeline

      Public
      Single Cell RNA-seq Analysis Pipeline
      R
      •
      Apache License 2.0
      •1•4•0•0•Updated Aug 22, 2025Aug 22, 2025

    • NGS_SV_CNV_Pipeline

      Public
      Genome Structural Variants Detection and Annotation Pipeline. Functions include NGS data QC, both germline and somatic SVs and CNVs detections, SVs and CNVs annotation and visualization.
      Python
      •
      MIT License
      •2•6•0•0•Updated Aug 22, 2025Aug 22, 2025

    • rNA

      Public
      Interactive report to assess the quality of large RNA-seq cohorts
      R
      •
      MIT License
      •2•0•0•0•Updated Aug 19, 2025Aug 19, 2025

    • XAVIER

      Public
      An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH
      Python
      •
      MIT License
      •3•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • spacesavers2

      Public
      Python
      •1•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • FIBSEM

      Public
      Run Time Augmentation System
      Python
      •1•0•0•0•Updated Jul 9, 2025Jul 9, 2025

    • CCBR_NextflowTemplate

      Public template
      CCBR template for Nextflow workflows
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Jul 8, 2025Jul 8, 2025

    • TRANQUIL

      Public
      TRANQUIL (TRna AbundaNce QUantification pIpeLine)
      Shell
      •
      MIT License
      •1•0•0•0•Updated Jun 17, 2025Jun 17, 2025

    • CRISPIN

      Public
      Crispr scReen seqUencIng analySis pipEline
      Nextflow
      •
      MIT License
      •3•0•0•0•Updated Jun 4, 2025Jun 4, 2025

    • l2p

      Public
      List to pathway, or l2p, is an R package for gene set enrichment analysis that is optimized for speed.
      C
      •
      MIT License
      •2•0•0•0•Updated May 22, 2025May 22, 2025

    • Archive

      Public
      Python
      •0•0•0•1•Updated Apr 23, 2025Apr 23, 2025

    • MAPLE

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 9, 2025Apr 9, 2025

    • METRO

      Public
      Mouse nEoanTigen pRedictOr
      Python
      •
      MIT License
      •2•0•0•0•Updated Apr 9, 2025Apr 9, 2025

    • CCBR_SnakemakeTemplate

      Public template
      Barebones framework for creating new snakemake workflows.
      Shell
      •
      MIT License
      •1•0•0•0•Updated Apr 9, 2025Apr 9, 2025

    • ABCS-pydicom-split

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Feb 25, 2025Feb 25, 2025

    • MAAPster

      Public
      MAAPster is a comprehensive tool to perform transcriptome analysis of human or mouse Affymetrix gene expression data
      R
      •
      MIT License
      •6•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•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.
      Shell
      •
      MIT License
      •1•0•0•0•Updated Jan 21, 2025Jan 21, 2025