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    186 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.
      Shell
      •0•0•0•0•Updated Jan 23, 2025Jan 23, 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 Jan 17, 2025Jan 17, 2025

    • CAENDR

      Public
      HTML
      •
      MIT License
      •3•4•0•9•Updated Jan 15, 2025Jan 15, 2025

    • wi-gatk

      Public
      The new GATK-based pipeline for wild isolate C. elegans strains
      Nextflow
      •3•1•6•0•Updated Jan 15, 2025Jan 15, 2025

    • cellprofiler-nf

      Public
      A nextflow pipeline to run CellProfiler pipelines on raw images and process output
      Nextflow
      •
      MIT License
      •2•1•6•1•Updated Jan 15, 2025Jan 15, 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 Jan 14, 2025Jan 14, 2025

    • pathogenDiscovery-sh

      Public
      C. elegans pathogen discovery through taxonomic classification from unaligned wild strains reads
      Shell
      •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

    • andersenlab.github.io

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

    • cv

      Public
      Andersen Curriculum Vitae
      1•0•0•0•Updated Dec 20, 2024Dec 20, 2024

    • alignment-nf

      Public
      A nextflow pipeline for genome sequences alignment
      nextflowcelegans
      Nextflow
      •
      MIT License
      •0•1•1•0•Updated Dec 18, 2024Dec 18, 2024

    • 2024_cyp35D1_TBZ_manuscript

      Public
      All code, data, and plots from 2024 TBZ manuscript
      R
      •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • easyXpress

      Public
      easyXpress is an R package for the analysis and visualization of high-throughput image-based nematode data
      HTML
      •
      MIT License
      •2•2•11•0•Updated Dec 5, 2024Dec 5, 2024

    • post-gatk-nf

      Public
      Subset isotype-only vcf, build tree etc. steps after variant calling and isotype assignment
      Nextflow
      •1•2•0•0•Updated Dec 5, 2024Dec 5, 2024

    • NemaScan

      Public
      GWA Mapping and Simulation with C. elegans, C. tropicalis, and C. briggsae
      R
      •4•2•8•0•Updated Dec 5, 2024Dec 5, 2024

    • nil-ril-nf

      Public
      Nextflow pipeline for calling NILs and RILs
      nextflow
      Nextflow
      •
      MIT License
      •2•0•0•0•Updated Dec 2, 2024Dec 2, 2024

    • miRNA_variant_filter-sh

      Public
      Tabor Roderiques Rotation Project, filtering C elegans WI.20231213.hard-filter.isotype.vcf.gz for variants in miRNA genes and 3' UTR mRNA predicted binding sites
      Shell
      •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

    • HDR_haplotypePlotter

      Public
      R script that generates gene-level visualization of hyper-divergent haplotypes using G2G alignments
      R
      •1•0•0•0•Updated Nov 6, 2024Nov 6, 2024

    • noaa-nf

      Public
      R
      •
      MIT License
      •1•1•0•0•Updated Oct 14, 2024Oct 14, 2024

    • trim-fq-nf

      Public
      Nextflow
      •
      MIT License
      •1•0•2•0•Updated Oct 4, 2024Oct 4, 2024

    • concordance-nf

      Public
      nextflow
      R
      •
      MIT License
      •2•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • delly-nf

      Public
      Nextflow workflow for calling INDELs with delly
      Nextflow
      •0•0•0•0•Updated Sep 23, 2024Sep 23, 2024

    • low_coverage_concordance

      Public
      Code to analyze concordance of a sequenced strain to an isotype reference strain
      Shell
      •0•1•0•0•Updated Sep 13, 2024Sep 13, 2024

    • impute-nf

      Public
      Nextflow
      •0•1•0•0•Updated Aug 30, 2024Aug 30, 2024

    • genomes-nf

      Public
      scripts and tools for managing genomes
      Nextflow
      •
      MIT License
      •2•0•0•0•Updated Aug 30, 2024Aug 30, 2024

    • annotation-nf

      Public
      Annotate VCF with snpeff and bcsq
      Nextflow
      •1•1•4•0•Updated Aug 30, 2024Aug 30, 2024

    • dry-guide

      Public
      The Guide to Computing in the Andersen Lab
      MIT License
      •6•5•1•0•Updated Aug 30, 2024Aug 30, 2024

    • VCF-kit

      Public
      VCF-kit: Assorted utilities for the variant call format
      vcfpython
      Python
      •
      MIT License
      •25•126•19•0•Updated Aug 5, 2024Aug 5, 2024

    • Ct_pop_gen_project

      Public
      R
      •0•0•0•0•Updated Jul 30, 2024Jul 30, 2024

    • bam-toolbox

      Public
      A bam toolbox
      Python
      •
      MIT License
      •1•1•0•0•Updated Jul 30, 2024Jul 30, 2024

    • cegwas2-nf

      Public
      GWA mapping with C. elegans
      nextflow
      R
      •
      MIT License
      •6•8•7•0•Updated Jun 3, 2024Jun 3, 2024