software.Rmd

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title: "Software"
---

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### CaseOnly
- **Github repo**: https://github.com/RuiDongDR/CaseOnly
- **Description**: Simulates data for the case-only and case-control designs for the detection of interactions, calculates analytical bias of interaction term and evaluates the type I error and power for the case-only design
- **Reference**: **Dong R**, Wang GT, DeWan AT, Leal SM (2025) The case-only design is a powerful approach to detect interactions but should be used with caution. *BMC Genomics*, 26, 222. [PMID: 40050722](https://pubmed.ncbi.nlm.nih.gov/40050722/); [PMC11884093](https://pmc.ncbi.nlm.nih.gov/articles/PMC11884093/)

### Human-Origin-1kGP
- **Github repo**: https://github.com/YaulabTsinghua/Human-Origin-1kGP
- **Database**: http://yaulab.math.tsinghua.edu.cn/2022_1000genomesprojectdata/ 
- **Description**: Reconstructs the whole genomes of individuals from 1000 Genomes Project and the corresponding natural vectors and divided natural vectors
- **Reference**: **Dong R**, Pei S, Guan M, Yau SC, Yin C, He RL, Yau SST (2022) Full chromosomal relationships between populations and the origin of humans. *Frontiers in Genetics*, 12: 828805. [PMID: 35186019](https://pubmed.ncbi.nlm.nih.gov/35186019/); [PMC8847220](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8847220/)

### VirusDB
- **Database**: http://yaulab.math.tsinghua.edu.cn/VirusDB/
- **Description**: Computes natural vectors for user-submitted genome sequences and returns information on five predicted neighbors based on the Natural Vector algorithm.
- **Reference**: **Dong R**, Zheng H, Tian K, Yau SC, Mao W, Yu W, Yin C, Yu C, He RL, Yang J, Yau SST (2017) Virus database and online inquiry system based on natural vectors. Evolutionary Bioinformatics 13:1-7. [PMID: 29308007](https://pubmed.ncbi.nlm.nih.gov/29308007/); [PMC5751915](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5751915/)