castgen
castgen: R package with methods for estimating the number of individuals to sample from a population in order to capture a predefined percentage of diversity
Science Score: 26.0%
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Repository
castgen: R package with methods for estimating the number of individuals to sample from a population in order to capture a predefined percentage of diversity
Basic Info
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- Stars: 1
- Watchers: 1
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- Releases: 1
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Metadata Files
README.md
castgen
This package and included functions were developed for the American chestnut landscape genomics manuscript. The aim was to develop a method for estimating the number of individuals to sample from a population in order to capture a predefined percentage of diversity within a breeding population.
Getting Started
A VCF file with GT information or a genotype matrix can be used as input
Installation
```{R}
castgen is available from CRAN and can be installed using the following command:
install.packages("castgen")
```
Output data
The output will provide the following information:
```
Number of individuals to sample = 22.0
95% Confidence Intervals = (16.378127142052662, 27.621872857947338)
Iterations performed = 5 ```
Citation
If you use this package, please cite:
A.M. Sandercock, J.W. Westbrook, Q. Zhang, & J.A. Holliday, A genome-guided strategy for climate resilience in American chestnut restoration populations, Proc. Natl. Acad. Sci. U.S.A. 121 (30) e2403505121, https://doi.org/10.1073/pnas.2403505121 (2024).
Notes
The capturediversity functions were converted from a Python function <https://github.com/alex-sandercock/Capturegenomic_diversity>. These R versions of the function are much (much) faster to run and have the option to run in parallel depending on cores available.
Owner
- Name: Alexander Sandercock
- Login: alex-sandercock
- Kind: user
- Twitter: sandercock_alex
- Repositories: 1
- Profile: https://github.com/alex-sandercock
PhD Student in Genetics, Bioinformatics, and Computational Biology @virginia_tech | ICTAS Doctoral Scholar
GitHub Events
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- Release event: 1
- Push event: 16
- Pull request event: 3
- Create event: 2
Last Year
- Release event: 1
- Push event: 16
- Pull request event: 3
- Create event: 2
Packages
- Total packages: 1
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Total downloads:
- cran 195 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 1
- Total maintainers: 1
cran.r-project.org: castgen
Estimate Sample Size for Population Genomic Studies
- Homepage: https://github.com/alex-sandercock/castgen
- Documentation: http://cran.r-project.org/web/packages/castgen/castgen.pdf
- License: Apache License (≥ 2)
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Latest release: 1.0.2
published 11 months ago
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Maintainers (1)
Dependencies
- Rdpack >= 0.7 imports
- doParallel >= 1.0.17 imports
- dplyr >= 1.1.2 imports
- foreach >= 1.5.2 imports
- vcfR >= 1.15.0 imports