Repositories list

• Ce_pangenome_MS

  Public
  Scripts, data, figures, and tables for the Caenorhabditis elegans pangenome manuscript.

  R

  •00 forks in AndersenLab/Ce_pangenome_MS•00 stars in AndersenLab/Ce_pangenome_MS•00 issues in AndersenLab/Ce_pangenome_MS•00 pull requests in AndersenLab/Ce_pangenome_MS•Updated Nov 12, 2026Nov 12, 2026

• linkagemapping

  Public
  R

  •11 fork in AndersenLab/linkagemapping•11 star in AndersenLab/linkagemapping•11 issue in AndersenLab/linkagemapping•00 pull requests in AndersenLab/linkagemapping•Updated Nov 12, 2026Nov 12, 2026

• caenorhabditis_colors

  Public
  Color codes for Caenorhabditis species and strains

  00 forks in AndersenLab/caenorhabditis_colors•00 stars in AndersenLab/caenorhabditis_colors•00 issues in AndersenLab/caenorhabditis_colors•00 pull requests in AndersenLab/caenorhabditis_colors•Updated Nov 12, 2026Nov 12, 2026

• 2026_counting_broodsize_images_YOLO

  Public
  Scripts used to count number of animals on a 6 cm NGMA plate using Tau Scientific developed YOLO platform

  Python

  •00 forks in AndersenLab/2026_counting_broodsize_images_YOLO•00 stars in AndersenLab/2026_counting_broodsize_images_YOLO•00 issues in AndersenLab/2026_counting_broodsize_images_YOLO•00 pull requests in AndersenLab/2026_counting_broodsize_images_YOLO•Updated Nov 12, 2026Nov 12, 2026

• andersenlab.github.io

  Public
  Andersen Lab Website

  HTML

  •

  MIT License

  •33 forks in AndersenLab/andersenlab.github.io•22 stars in AndersenLab/andersenlab.github.io•00 issues in AndersenLab/andersenlab.github.io•22 pull requests in AndersenLab/andersenlab.github.io•Updated Nov 9, 2026Nov 9, 2026

• NemaSize

  Public
  Python

  •

  Apache License 2.0

  •00 forks in AndersenLab/NemaSize•00 stars in AndersenLab/NemaSize•00 issues in AndersenLab/NemaSize•00 pull requests in AndersenLab/NemaSize•Updated Nov 9, 2026Nov 9, 2026

• cv

  Public
  Andersen Curriculum Vitae

  11 fork in AndersenLab/cv•00 stars in AndersenLab/cv•00 issues in AndersenLab/cv•00 pull requests in AndersenLab/cv•Updated Nov 8, 2026Nov 8, 2026

• nemascan-nf

  Public
  An updated NemaScan nextflow workflow for version 26+

  Python

  •00 forks in AndersenLab/nemascan-nf•00 stars in AndersenLab/nemascan-nf•00 issues in AndersenLab/nemascan-nf•00 pull requests in AndersenLab/nemascan-nf•Updated Nov 5, 2026Nov 5, 2026

• VCF-kit

  Public
  VCF-kit: Assorted utilities for the variant call format

  pythonvcf

  pythonvcf

  Python

  •

  MIT License

  •2626 forks in AndersenLab/VCF-kit•136136 stars in AndersenLab/VCF-kit•1919 issues in AndersenLab/VCF-kit•00 pull requests in AndersenLab/VCF-kit•Updated Nov 2, 2026Nov 2, 2026

• NemaSize-nf

  Public
  Nextflow

  •

  Apache License 2.0

  •00 forks in AndersenLab/NemaSize-nf•00 stars in AndersenLab/NemaSize-nf•00 issues in AndersenLab/NemaSize-nf•00 pull requests in AndersenLab/NemaSize-nf•Updated Oct 20, 2026Oct 20, 2026

• Ce_geneAnno-sh

  Public
  This is a repository for storing all scripts related to genome assembly, gene annotation, SV calling, GFF/FA file manipulation, functional enrichment analysis, …

  Jupyter Notebook

  •00 forks in AndersenLab/Ce_geneAnno-sh•00 stars in AndersenLab/Ce_geneAnno-sh•00 issues in AndersenLab/Ce_geneAnno-sh•00 pull requests in AndersenLab/Ce_geneAnno-sh•Updated Oct 18, 2026Oct 18, 2026

• variantanno-sh

  Public
  Shells scripts to run tools (SIFT, VEP, ANNOVAR) to annotate variants in selfing Caenorhabditis WI VCFs

  Shell

  •00 forks in AndersenLab/variantanno-sh•00 stars in AndersenLab/variantanno-sh•00 issues in AndersenLab/variantanno-sh•00 pull requests in AndersenLab/variantanno-sh•Updated Oct 11, 2026Oct 11, 2026

• nil-ril-nf

  Public
  Nextflow pipeline for calling NILs and RILs

  nextflow

  nextflow

  Nextflow

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  MIT License

  •11 fork in AndersenLab/nil-ril-nf•00 stars in AndersenLab/nil-ril-nf•00 issues in AndersenLab/nil-ril-nf•00 pull requests in AndersenLab/nil-ril-nf•Updated Sep 28, 2026Sep 28, 2026

• geneAnno-nf

  Public
  Nextflow pipeline that predicts gene models in nematode genomes using BRAKER.

  Nextflow

  •00 forks in AndersenLab/geneAnno-nf•00 stars in AndersenLab/geneAnno-nf•00 issues in AndersenLab/geneAnno-nf•00 pull requests in AndersenLab/geneAnno-nf•Updated Sep 22, 2026Sep 22, 2026

• assembly-nf

  Public
  Nextflow pipeline for hifiasm de novo assembly and HiFi long-read sequencing quality control.

  Nextflow

  •00 forks in AndersenLab/assembly-nf•00 stars in AndersenLab/assembly-nf•00 issues in AndersenLab/assembly-nf•00 pull requests in AndersenLab/assembly-nf•Updated Sep 21, 2026Sep 21, 2026

• cbriggsae_anthelmintic_drc

  Public
  Data, scripts, and figures for the C. briggsae anthelmintic dose response (DRC) paper

  R

  •00 forks in AndersenLab/cbriggsae_anthelmintic_drc•11 star in AndersenLab/cbriggsae_anthelmintic_drc•00 issues in AndersenLab/cbriggsae_anthelmintic_drc•00 pull requests in AndersenLab/cbriggsae_anthelmintic_drc•Updated Sep 7, 2026Sep 7, 2026

• hdr-nf

  Public
  A reproducible nextflow to call HDRs in selfing nematodes.

  R

  •00 forks in AndersenLab/hdr-nf•00 stars in AndersenLab/hdr-nf•00 issues in AndersenLab/hdr-nf•00 pull requests in AndersenLab/hdr-nf•Updated Aug 14, 2026Aug 14, 2026

• wi-gatk

  Public
  The new GATK-based pipeline for wild isolate C. elegans strains

  Nextflow

  •33 forks in AndersenLab/wi-gatk•11 star in AndersenLab/wi-gatk•66 issues in AndersenLab/wi-gatk•00 pull requests in AndersenLab/wi-gatk•Updated Aug 11, 2026Aug 11, 2026

• CB_PopGen_HDR_MS

  Public
  scripts, figures, and tables for C. briggsae PopGen and HDR manuscript

  R

  •00 forks in AndersenLab/CB_PopGen_HDR_MS•00 stars in AndersenLab/CB_PopGen_HDR_MS•00 issues in AndersenLab/CB_PopGen_HDR_MS•00 pull requests in AndersenLab/CB_PopGen_HDR_MS•Updated Aug 10, 2026Aug 10, 2026

• CAENDR

  Public
  HTML

  •

  MIT License

  •33 forks in AndersenLab/CAENDR•44 stars in AndersenLab/CAENDR•00 issues in AndersenLab/CAENDR•99 pull requests in AndersenLab/CAENDR•Updated Aug 10, 2026Aug 10, 2026

• isotype-nf

  Public
  Nextflow pipeline for calling isotype groups

  Python

  •

  MIT License

  •11 fork in AndersenLab/isotype-nf•00 stars in AndersenLab/isotype-nf•00 issues in AndersenLab/isotype-nf•00 pull requests in AndersenLab/isotype-nf•Updated Aug 5, 2026Aug 5, 2026

• fq-processing-nf

  Public
  A nextflow pipeline for taking raw sequenced reads (fastqs) and performing trimming, species check, alignment, and genotype checking

  Nextflow

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  MIT License

  •00 forks in AndersenLab/fq-processing-nf•00 stars in AndersenLab/fq-processing-nf•00 issues in AndersenLab/fq-processing-nf•00 pull requests in AndersenLab/fq-processing-nf•Updated Jul 24, 2026Jul 24, 2026

• gene_rename_workflow

  Public
  Combine OrthoFinder and Reciprocal Best Blast Hits to annotate gene names across Caenorhabditis species

  R

  •00 forks in AndersenLab/gene_rename_workflow•00 stars in AndersenLab/gene_rename_workflow•00 issues in AndersenLab/gene_rename_workflow•00 pull requests in AndersenLab/gene_rename_workflow•Updated Jul 22, 2026Jul 22, 2026

• nemascan-sims-nf

  Public
  Nextflow workflow for running GWA simulations

  R

  •00 forks in AndersenLab/nemascan-sims-nf•00 stars in AndersenLab/nemascan-sims-nf•1010 issues in AndersenLab/nemascan-sims-nf•00 pull requests in AndersenLab/nemascan-sims-nf•Updated Jul 21, 2026Jul 21, 2026

• Ct_pop_gen_project

  Public
  R

  •00 forks in AndersenLab/Ct_pop_gen_project•00 stars in AndersenLab/Ct_pop_gen_project•00 issues in AndersenLab/Ct_pop_gen_project•00 pull requests in AndersenLab/Ct_pop_gen_project•Updated Jul 17, 2026Jul 17, 2026

• easyXpress

  Public
  easyXpress is an R package for the analysis and visualization of high-throughput image-based nematode data

  HTML

  •

  MIT License

  •22 forks in AndersenLab/easyXpress•33 stars in AndersenLab/easyXpress•1111 issues in AndersenLab/easyXpress•00 pull requests in AndersenLab/easyXpress•Updated Jul 10, 2026Jul 10, 2026

• gtcheck-nf

  Public
  Nextflow workflow for checking sample variants against known variants to verify identity

  Nextflow

  •

  MIT License

  •00 forks in AndersenLab/gtcheck-nf•00 stars in AndersenLab/gtcheck-nf•00 issues in AndersenLab/gtcheck-nf•00 pull requests in AndersenLab/gtcheck-nf•Updated Jul 2, 2026Jul 2, 2026

• CGC2_genome_MS

  Public
  Scripts, data, figures, and tables for the T2T Caenorhabditis briggsae reference genome manuscript.

  R

  •00 forks in AndersenLab/CGC2_genome_MS•00 stars in AndersenLab/CGC2_genome_MS•00 issues in AndersenLab/CGC2_genome_MS•00 pull requests in AndersenLab/CGC2_genome_MS•Updated Jun 8, 2026Jun 8, 2026

• NemaScan

  Public
  GWA Mapping and Simulation with C. elegans, C. tropicalis, and C. briggsae

  R

  •22 forks in AndersenLab/NemaScan•44 stars in AndersenLab/NemaScan•1111 issues in AndersenLab/NemaScan•00 pull requests in AndersenLab/NemaScan•Updated Jun 2, 2026Jun 2, 2026

• ce_cb_ct_betatubulin

  Public
  R

  •00 forks in AndersenLab/ce_cb_ct_betatubulin•00 stars in AndersenLab/ce_cb_ct_betatubulin•00 issues in AndersenLab/ce_cb_ct_betatubulin•00 pull requests in AndersenLab/ce_cb_ct_betatubulin•Updated May 29, 2026May 29, 2026