Andersen Lab

Johns Hopkins University

United States of America

Pinned Repositories

CAENDR
Language:HTML4 5 33
cegwas2-nf
GWA mapping with C. elegans
Language:R8 9 106
CellProfiler
CellProfiler Image Analysis Tools
Language:Shell3 8 20
CeNDR
Language:HTML5 9 846
dry-guide
The Guide to Computing in the Andersen Lab
4 11 27
Genetic-Analysis
8 12 02
IBiS-Bootcamp
Language:Shell40 10 02
liftover-utils
Utilities for lifting over genome coordinates in C. elegans
Language:Perl6 11 42
pyPipeline
Andersen Lab Python-based pipeline for variant calling.
Language:Python6 15 01
VCF-kit
VCF-kit: Assorted utilities for the variant call format
Language:Python122 18 4625

Andersen Lab's Repositories

AndersenLab/VCF-kit
VCF-kit: Assorted utilities for the variant call format
Language:Python122 18 4625
AndersenLab/cegwas2-nf
GWA mapping with C. elegans
Language:R8 9 106
AndersenLab/CAENDR
Language:HTML4 5 33
AndersenLab/dry-guide
The Guide to Computing in the Andersen Lab
4 11 27
AndersenLab/andersenlab.github.io
Andersen Lab Website
Language:HTML2 14 33
AndersenLab/easyXpress
easyXpress is an R package for the analysis and visualization of high-throughput image-based nematode data
Language:HTML2 7 222
AndersenLab/NemaScan
GWA Mapping and Simulation with C. elegans, C. tropicalis, and C. briggsae
Language:R2 6 154
AndersenLab/post-gatk-nf
Subset isotype-only vcf, build tree etc. steps after variant calling and isotype assignment
Language:Nextflow2 6 11
AndersenLab/sv-nf
A nextflow pipeline to call structural variants using short or long read data
Language:Nextflow2 6 3
AndersenLab/alignment-nf
A nextflow pipeline for genome sequences alignment
Language:Nextflow1 6 13
AndersenLab/annotation-nf
Annotate VCF with snpeff and bcsq
Language:Nextflow1 6 61
AndersenLab/bam-toolbox
A bam toolbox
Language:Python1 10 01
AndersenLab/cellprofiler-nf
A nextflow pipeline to run CellProfiler pipelines on raw images and process output
Language:Nextflow1 6 62
AndersenLab/impute-nf
Language:Nextflow1 8 0
AndersenLab/low_coverage_concordance
Code to analyze concordance of a sequenced strain to an isotype reference strain
Language:Shell1 3 0
AndersenLab/noaa-nf
Language:R11
AndersenLab/wi-gatk
The new GATK-based pipeline for wild isolate C. elegans strains
Language:Nextflow1 7 193
AndersenLab/Ce-eri-67
Language:R0 3 00
AndersenLab/bzml_manuscript
Language:R2 0
AndersenLab/concordance-nf
Language:R10 22
AndersenLab/Ct_pop_gen_project
Language:R
AndersenLab/cv
Andersen Curriculum Vitae
10 01
AndersenLab/delly-nf
Nextflow workflow for calling INDELs with delly
Language:Nextflow
AndersenLab/EHP_manuscript
This repository holds data, code, and plots for the Environmental Health Perspectives manuscript written with Dr. Scott Glaberman
Language:R5 0
AndersenLab/genomes-nf
scripts and tools for managing genomes
Language:Nextflow2 02
AndersenLab/LIN12_notch_MS
Intermediate files and scripts used for analyses and plots for the LIN-12/Notch signaling MS in collaboration with Helen Chamberlin
Language:R5 0
AndersenLab/NAR_CaeNDR_manuscript
Code and data used in the Nucleic Acids Research manuscript describing CaeNDR
Language:R5 0
AndersenLab/nil-ril-nf
Nextflow pipeline for calling NILs and RILs
Language:Nextflow11 02
AndersenLab/trim-fq-nf
Language:Nextflow11 101
AndersenLab/variantanno-sh
Shells scripts to run tools (SIFT, VEP, ANNOVAR) to annotate variants in selfing Caenorhabditis WI VCFs