Pinned Repositories
CAENDR
cegwas2-nf
GWA mapping with C. elegans
CellProfiler
CellProfiler Image Analysis Tools
CeNDR
dry-guide
The Guide to Computing in the Andersen Lab
Genetic-Analysis
IBiS-Bootcamp
liftover-utils
Utilities for lifting over genome coordinates in C. elegans
pyPipeline
Andersen Lab Python-based pipeline for variant calling.
VCF-kit
VCF-kit: Assorted utilities for the variant call format
Andersen Lab's Repositories
AndersenLab/VCF-kit
VCF-kit: Assorted utilities for the variant call format
AndersenLab/dry-guide
The Guide to Computing in the Andersen Lab
AndersenLab/CAENDR
AndersenLab/andersenlab.github.io
Andersen Lab Website
AndersenLab/cellprofiler-nf
A nextflow pipeline to run CellProfiler pipelines on raw images and process output
AndersenLab/easyXpress
easyXpress is an R package for the analysis and visualization of high-throughput image-based nematode data
AndersenLab/NemaScan
GWA Mapping and Simulation with C. elegans, C. tropicalis, and C. briggsae
AndersenLab/post-gatk-nf
Subset isotype-only vcf, build tree etc. steps after variant calling and isotype assignment
AndersenLab/alignment-nf
A nextflow pipeline for genome sequences alignment
AndersenLab/annotation-nf
Annotate VCF with snpeff and bcsq
AndersenLab/impute-nf
AndersenLab/low_coverage_concordance
Code to analyze concordance of a sequenced strain to an isotype reference strain
AndersenLab/noaa-nf
AndersenLab/wi-gatk
The new GATK-based pipeline for wild isolate C. elegans strains
AndersenLab/Ce_geneAnno-sh
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.
AndersenLab/cv
Andersen Curriculum Vitae
AndersenLab/HDR_haplotypePlotter
R script that generates gene-level visualization of hyper-divergent haplotypes using G2G alignments
AndersenLab/pathogenDiscovery-sh
C. elegans pathogen discovery through taxonomic classification from unaligned wild strains reads
AndersenLab/variantanno-sh
Shells scripts to run tools (SIFT, VEP, ANNOVAR) to annotate variants in selfing Caenorhabditis WI VCFs
AndersenLab/2024_cyp35D1_TBZ_manuscript
All code, data, and plots from 2024 TBZ manuscript
AndersenLab/caenorhabditis_colors
Color codes for Caenorhabditis species and strains
AndersenLab/concordance-nf
AndersenLab/delly-nf
Nextflow workflow for calling INDELs with delly
AndersenLab/EHP_manuscript
This repository holds data, code, and plots for the Environmental Health Perspectives manuscript written with Dr. Scott Glaberman
AndersenLab/genomes-nf
scripts and tools for managing genomes
AndersenLab/isotype-nf
Nextflow pipeline for calling isotype groups
AndersenLab/miRNA_variant_filter-sh
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
AndersenLab/NAR_CaeNDR_manuscript
Code and data used in the Nucleic Acids Research manuscript describing CaeNDR
AndersenLab/nil-ril-nf
Nextflow pipeline for calling NILs and RILs
AndersenLab/trim-fq-nf