Repositories list

• 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

• Ce-eri-67

  Public
  R

  •0•0•0•0•Updated Jun 3, 2024Jun 3, 2024