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@dhslab Code and Software from David Spencer's lab

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    24 repositories

    • dragenflow

      Public
      Nextflow
      •
      MIT License
      •2•0•0•0•Updated Oct 30, 2025Oct 30, 2025

    • nf-core-scge

      Public
      Nextflow implementation of scge workflow
      Python
      •
      MIT License
      •1•1•2•2•Updated Oct 21, 2025Oct 21, 2025

    • dhslab-docker-images

      Public
      Docker images for the Spencer lab
      Dockerfile
      •
      MIT License
      •3•2•1•2•Updated Oct 6, 2025Oct 6, 2025

    • nf-core-wgsnano

      Public
      Nextflow pipeline for analysis of Nanopore Whole Genome Sequencing
      Nextflow
      •
      MIT License
      •6•6•0•0•Updated Oct 6, 2025Oct 6, 2025

    • methtools

      Public
      Python toolkit for DNA methylation analysis,
      Python
      •1•0•0•0•Updated Sep 10, 2025Sep 10, 2025

    • covfast

      Public
      Small c program to calculate coverage from a bam/cram over bed intervals
      C
      •
      MIT License
      •0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

    • dhsrmethtools

      Public
      R functions for methylation analysis
      R
      •
      Other
      •0•0•0•0•Updated Jul 11, 2025Jul 11, 2025

    • dhslab-archive

      Public
      Python scripts to perform data archiving
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 29, 2025Jun 29, 2025

    • nf-core-scge-abonney

      Public
      Nextflow implementation of scge workflow with Enhanced Reporting
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Jun 26, 2025Jun 26, 2025

    • methfast

      Public
      Simple c program for manipulating bed-like methylation files
      C
      •
      MIT License
      •0•0•0•0•Updated Jun 9, 2025Jun 9, 2025

    • peakachu-cohort

      Public
      Wraps Peakachu’s train and score_genome functions in a parallelized CLI subcommand enabling scalable analysis across cohorts without manual per-sample commands.
      Python
      •0•1•0•0•Updated Jun 5, 2025Jun 5, 2025

    • nf-chromhmm

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jun 1, 2025Jun 1, 2025

    • dhslab-website

      Public
      David Spencer Lab website
      SCSS
      •1.3k•0•0•0•Updated May 20, 2025May 20, 2025

    • cutandrun

      Public
      Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
      Nextflow
      •
      MIT License
      •62•0•0•0•Updated Mar 4, 2025Mar 4, 2025

    • cle-soma

      Public
      CLE SOMA workflow
      WDL
      •2•0•0•0•Updated Dec 11, 2024Dec 11, 2024

    • nf-core-rnanano

      Public
      Nextflow pipeline for analysis of Nanopore RNA sequencing
      Nextflow
      •
      MIT License
      •6•0•0•0•Updated Oct 7, 2024Oct 7, 2024

    • cle-myeloseqhd

      Public
      Python
      •3•0•0•0•Updated Oct 12, 2023Oct 12, 2023

    • nf-core-hic

      Public
      Pipeline for Hi-C data analysis
      workflowpipelinenextflowhi-ccapture-c
      Nextflow
      •
      MIT License
      •1•2•1•0•Updated Sep 1, 2023Sep 1, 2023

    • nf-core-hicmap

      Public
      3D genome contacts calling from HiC data
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated May 19, 2023May 19, 2023

    • nf-chicago

      Public
      Pipeline for detection of DNA looping interactions in capture Hi-C data
      Nextflow
      •0•0•0•0•Updated Mar 18, 2023Mar 18, 2023

    • nextflow-nanopore

      Public
      Nextflow pipeline for analysis of Nanopore Whole Genome Sequencing
      Nextflow
      •1•1•0•0•Updated Dec 15, 2022Dec 15, 2022

    • wdlworkflows

      Public
      Spencer lab WDL workflows for genomic analysis
      WDL
      •
      MIT License
      •1•0•3•0•Updated Aug 24, 2022Aug 24, 2022

    • sv_merge

      Public
      Python script to merge and/or annotate SVs encoded in a VCF file
      Python
      •1•0•0•1•Updated Jun 29, 2022Jun 29, 2022

    • tagbam

      Public
      C program to add a tag to reads in a bam file from amplicon sequencing with an ID for each amplicon.
      C
      •
      MIT License
      •1•0•0•0•Updated Apr 7, 2022Apr 7, 2022