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@dhslab Code and Software from David Spencer's lab

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    18 repositories

    • 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
      •47•0•0•0•Updated Oct 23, 2024Oct 23, 2024

    • dhslab-docker-images

      Public
      Docker images for the Spencer lab
      Dockerfile
      •
      MIT License
      •1•1•1•0•Updated Oct 19, 2024Oct 19, 2024

    • dhsrmethtools

      Public
      R functions for methylation analysis
      R
      •
      Other
      •0•0•0•0•Updated Oct 17, 2024Oct 17, 2024

    • dragenflow

      Public
      Nextflow
      •
      MIT License
      •2•0•0•0•Updated Oct 17, 2024Oct 17, 2024

    • nf-core-scge

      Public
      Nextflow implementation of scge workflow
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • methfast

      Public
      Simple c program for manipulating bed-like methylation files
      C
      •
      MIT License
      •0•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • nf-core-rnanano

      Public
      Nextflow pipeline for analysis of Nanopore RNA sequencing
      Nextflow
      •
      MIT License
      •4•0•0•0•Updated Oct 7, 2024Oct 7, 2024

    • nf-core-wgsnano

      Public
      Nextflow pipeline for analysis of Nanopore Whole Genome Sequencing
      Nextflow
      •
      MIT License
      •4•4•0•0•Updated Oct 2, 2024Oct 2, 2024

    • cle-soma

      Public
      CLE SOMA workflow
      WDL
      •2•0•0•0•Updated Aug 12, 2024Aug 12, 2024

    • dhslab-website

      Public
      David Spencer Lab website
      SCSS
      •1.2k•0•0•0•Updated May 29, 2024May 29, 2024

    • cle-myeloseqhd

      Public
      Python
      •4•0•0•0•Updated Oct 12, 2023Oct 12, 2023

    • nf-core-hic

      Public
      Pipeline for Hi-C data analysis
      nextflowhi-ccapture-cworkflowpipeline
      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•0•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
      •0•0•0•0•Updated Apr 7, 2022Apr 7, 2022