Repositories list

• CGC2_genome_MS

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 25, 2026Apr 25, 2026

• CB_PopGen_HDR_MS

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

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• Ce_pangenome_MS

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

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• nemascan-sims-nf

  Public
  Nextflow workflow for running GWA simulations

  SourcePawn

  •00 forks•00 stars•88 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• annotation-nf

  Public
  Annotate VCF with snpeff and bcsq

  Perl

  •33 forks•22 stars•44 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• geneAnno-nf

  Public
  This is a nextflow process that predicts gene models in Caenorhabditis de novo assembled genomes using BRAKER3. The input to this process is a TSV/TXT that cont…

  Nextflow

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• ce_cb_ct_betatubulin

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• Ct_pop_gen_project

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 18, 2026Apr 18, 2026

• andersenlab.github.io

  Public
  Andersen Lab Website

  HTML

  •

  MIT License

  •33 forks•22 stars•00 issues•22 pull requests•Updated Apr 18, 2026Apr 18, 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•00 stars•00 issues•00 pull requests•Updated Apr 12, 2026Apr 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•00 stars•00 issues•00 pull requests•Updated Apr 9, 2026Apr 9, 2026

• HDR_haplotypePlotter

  Public
  R script that generates gene-level visualization of hyper-divergent haplotypes using G2G alignments

  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• assembly-nf

  Public
  Nextflow pipeline for hifiasm de novo assembly and sequencing quality control

  Nextflow

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 17, 2026Mar 17, 2026

• cv

  Public
  Andersen Curriculum Vitae

  11 fork•00 stars•00 issues•00 pull requests•Updated Mar 15, 2026Mar 15, 2026

• vertTrans_microbe_discovery

  Public
  C. elegans pathogen discovery through taxonomic classification from unaligned wild strains reads

  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 11, 2026Mar 11, 2026

• caenorhabditis_colors

  Public
  Color codes for Caenorhabditis species and strains

  00 forks•00 stars•00 issues•00 pull requests•Updated Mar 8, 2026Mar 8, 2026

• NemaScan

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

  R

  •33 forks•44 stars•1111 issues•00 pull requests•Updated Mar 2, 2026Mar 2, 2026

• trim-fq-nf

  Public
  Nextflow

  •

  MIT License

  •11 fork•00 stars•22 issues•00 pull requests•Updated Feb 11, 2026Feb 11, 2026

• migrate-sims-to-db-nf

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 10, 2026Feb 10, 2026

• wi-gatk

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

  Nextflow

  •33 forks•11 star•66 issues•00 pull requests•Updated Feb 5, 2026Feb 5, 2026

• PLG-1_project

  Public
  Jess's rotation project

  11 fork•00 stars•00 issues•00 pull requests•Updated Jan 15, 2026Jan 15, 2026

• ToxinGWAS_Manuscript

  Public
  Repository for Manuscript

  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Jan 13, 2026Jan 13, 2026

• post-gatk-nf

  Public
  Subset isotype-only vcf, build tree etc. steps after variant calling and isotype assignment

  Nextflow

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jan 8, 2026Jan 8, 2026

• 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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 18, 2025Nov 18, 2025

• variantanno-sh

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

  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 13, 2025Oct 13, 2025

• CAENDR

  Public
  HTML

  •

  MIT License

  •33 forks•44 stars•00 issues•99 pull requests•Updated Oct 8, 2025Oct 8, 2025

• calc_heritability

  Public
  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Sep 30, 2025Sep 30, 2025

• nil-ril-nf

  Public
  Nextflow pipeline for calling NILs and RILs

  nextflow

  nextflow

  Nextflow

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 28, 2025Jul 28, 2025

• isotype-nf

  Public
  Nextflow pipeline for calling isotype groups

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 18, 2025Jul 18, 2025