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    196 repositories

    • Ce_geneAnno-sh

      Public
      This repository contains the scripts used to assess the presence/absence of Caenorhabditis elegans ref genome genes across all wild strains. Genes are classified as "core", "soft-core", "rare", or "private" based on the frequency at which they occur in wild strains.
      Jupyter Notebook
      •0•0•0•0•Updated Jan 3, 2026Jan 3, 2026

    • ce_cb_ct_betatubulin

      Public
      PostScript
      •0•0•0•0•Updated Jan 2, 2026Jan 2, 2026

    • nemascan-sims-nf

      Public
      Nextflow workflow for running GWA simulations
      Nextflow
      •0•0•6•0•Updated Dec 16, 2025Dec 16, 2025

    • andersenlab.github.io

      Public
      Andersen Lab Website
      HTML
      •
      MIT License
      •3•2•0•2•Updated Dec 14, 2025Dec 14, 2025

    • fq-processing-nf

      Public
      A nextflow pipeline for taking raw sequenced reads (fastqs) and performing trimming, species check, alignment, and genotype checking
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Nov 18, 2025Nov 18, 2025

    • NemaScan

      Public
      GWA Mapping and Simulation with C. elegans, C. tropicalis, and C. briggsae
      R
      •3•3•11•0•Updated Nov 11, 2025Nov 11, 2025

    • ToxinGWAS_Manuscript

      Public
      Repository for Manuscript
      Jupyter Notebook
      •0•0•0•0•Updated Nov 6, 2025Nov 6, 2025

    • annotation-nf

      Public
      Annotate VCF with snpeff and bcsq
      Perl
      •2•1•4•0•Updated Oct 27, 2025Oct 27, 2025

    • pathogenDiscovery-sh

      Public
      C. elegans pathogen discovery through taxonomic classification from unaligned wild strains reads
      Shell
      •0•0•0•0•Updated Oct 25, 2025Oct 25, 2025

    • cv

      Public
      Andersen Curriculum Vitae
      1•0•0•0•Updated Oct 16, 2025Oct 16, 2025

    • variantanno-sh

      Public
      Shells scripts to run tools (SIFT, VEP, ANNOVAR) to annotate variants in selfing Caenorhabditis WI VCFs
      Shell
      •0•0•0•0•Updated Oct 13, 2025Oct 13, 2025

    • trim-fq-nf

      Public
      Nextflow
      •
      MIT License
      •1•0•2•0•Updated Oct 9, 2025Oct 9, 2025

    • CAENDR

      Public
      HTML
      •
      MIT License
      •3•4•0•9•Updated Oct 8, 2025Oct 8, 2025

    • calc_heritability

      Public
      R
      •1•0•0•0•Updated Sep 30, 2025Sep 30, 2025

    • nil-ril-nf

      Public
      Nextflow pipeline for calling NILs and RILs
      nextflow
      Nextflow
      •
      MIT License
      •2•0•0•0•Updated Sep 12, 2025Sep 12, 2025

    • EHP_manuscript

      Public
      This repository holds data, code, and plots for the Environmental Health Perspectives manuscript written with Dr. Scott Glaberman
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 28, 2025Jul 28, 2025

    • caenorhabditis_colors

      Public
      Color codes for Caenorhabditis species and strains
      0•0•0•0•Updated Jul 20, 2025Jul 20, 2025

    • isotype-nf

      Public
      Nextflow pipeline for calling isotype groups
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 18, 2025Jul 18, 2025

    • VCF-kit

      Public
      VCF-kit: Assorted utilities for the variant call format
      pythonvcf
      Python
      •
      MIT License
      •27•132•19•0•Updated Jul 10, 2025Jul 10, 2025

    • cellprofiler-nf

      Public
      A nextflow pipeline to run CellProfiler pipelines on raw images and process output
      Nextflow
      •
      MIT License
      •3•2•6•1•Updated Jun 3, 2025Jun 3, 2025

    • noaa-nf

      Public
      R
      •
      MIT License
      •1•1•0•0•Updated May 16, 2025May 16, 2025

    • variation_orthology_vis

      Public
      Josh Bauman rotation spring 2025 - wrote bash scripts to filter GATK and PAV VCFs, R scripts for visualizing this variation, and worked on validating BRAKER gene model calls between N2 and WS using BLASTP
      R
      •0•0•0•0•Updated May 12, 2025May 12, 2025

    • finemap_qtl_overlap

      Public
      Simple NF workflow to finemmap the same genomic regions for a pair of traits
      Nextflow
      •0•0•1•0•Updated May 8, 2025May 8, 2025

    • Caeno_Scan

      Public
      Repository to do GWAS simulations across selfing Caenorhabditis species
      R
      •0•0•1•0•Updated May 5, 2025May 5, 2025

    • gtcheck-nf

      Public
      Nextflow workflow for checking sample variants against known variants to verify identity
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Apr 25, 2025Apr 25, 2025

    • caendrprep-nf

      Public
      A Nextflow workflow for performing all of the analyses downstream of variant and isotype calling in preparation for a CaeNDR data release
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Apr 9, 2025Apr 9, 2025

    • wi-gatk

      Public
      The new GATK-based pipeline for wild isolate C. elegans strains
      Nextflow
      •3•1•6•0•Updated Apr 7, 2025Apr 7, 2025

    • alignment-nf

      Public
      A nextflow pipeline for genome sequences alignment
      nextflowcelegans
      Nextflow
      •
      MIT License
      •0•1•1•0•Updated Mar 14, 2025Mar 14, 2025

    • delly-nf

      Public
      Nextflow workflow for calling INDELs with delly
      Nextflow
      •0•0•0•0•Updated Feb 26, 2025Feb 26, 2025

    • NAR_CaeNDR_manuscript

      Public
      Code and data used in the Nucleic Acids Research manuscript describing CaeNDR
      R
      •
      MIT License
      •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025