dsuz_popgen_gea
Population genomic and GEA analyses on Drosophila suzukii
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
-
✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
-
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (7.6%) to scientific vocabulary
Repository
Population genomic and GEA analyses on Drosophila suzukii
Basic Info
- Host: GitHub
- Owner: Sfeng666
- License: mit
- Language: Python
- Default Branch: main
- Size: 7.88 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
DsuzpopgenGEA: population genomics and GEA analyses on Drosophila suzukii
Code for major analyses performed in population genomic analyses and genome-environment association (GEA) analyses on Drosophila suzukii.
Related publication:
Analyses list
- Identify autosomal and X-linked contigs
- Annotate genomic features
- Calculate sequence divergence between two species
- Estimate genome-wide and synonymous nucleotide diversity, and illustrate window diversity across chromosome arms
- Estimate genome-wide and synonymous FST
- Estimate genome-wide and synonymous DXY
- Perform PCA on allele frequencies
- Build population tree and infer admixture from allele frequency
- Perform genome-environment association (GEA) analysis
- Identify environment-associated genes
- Perform GO enrichment of the top environment-associated genes
Environment setup
To set up the environment for above analyses, you could use conda:
conda env create -n environemnt_name --file environemnt_name.yml
Environment needed for each analysis is indicated in documentation of each analysis. Environmental package lists (environemnt_name.yml) for cross-platform install could be found under this directory.
If you have not installed conda, run the following command: ```
download miniconda
curl -sL \
"https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" > \
"Miniconda3.sh"
install miniconda
bash Miniconda3.sh ```
Owner
- Name: Siyuan Feng
- Login: Sfeng666
- Kind: user
- Location: Madison, WI
- Company: University of Wisconsin-Madison
- Website: https://scholar.google.com/citations?user=REHFXSsAAAAJ&hl=en
- Repositories: 2
- Profile: https://github.com/Sfeng666
Evolutionary biologist working on population genomics & comparative transcriptomics
Citation (CITATION)
To reference poolWGS2SNP in publications, please cite:
@article {Feng2023.07.03.547576,
author = {Siyuan Feng and Samuel P. DeGrey and Christelle Gu{\'e}dot and Sean D. Schoville and John E. Pool},
title = {Genomic Diversity Illuminates the Environmental Adaptation of Drosophila suzukii},
elocation-id = {2023.07.03.547576},
year = {2023},
doi = {10.1101/2023.07.03.547576},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2023/07/03/2023.07.03.547576},
eprint = {https://www.biorxiv.org/content/early/2023/07/03/2023.07.03.547576.full.pdf},
journal = {bioRxiv}
}
GitHub Events
Total
- Push event: 2
Last Year
- Push event: 2