smartsnp: Fast Multivariate Analyses of Big Genomic Data
Fast computation of multivariate analyses of small (10s to 100s markers) to big (1000s to 100000s) genotype data. Runs Principal Component Analysis allowing for centering, z-score standardization and scaling for genetic drift, projection of ancient samples to modern genetic space and multivariate tests for differences in group location (Permutation-Based Multivariate Analysis of Variance) and dispersion (Permutation-Based Multivariate Analysis of Dispersion).
| Version: | 1.2.0 |
| Depends: | R (≥ 3.6.0) |
| Imports: | bootSVD, data.table, foreach, Rfast, RSpectra, vegan, vroom, Rcpp |
| LinkingTo: | Rcpp, RcppArmadillo |
| Suggests: | markdown, knitr, rmarkdown |
| Published: | 2025-06-09 |
| DOI: | 10.32614/CRAN.package.smartsnp |
| Author: | Salvador Herrando-Perez
 [aut],
Ray Tobler [ctb],
Christian Huber
[ctb, cre] |
| Maintainer: | Christian Huber <christian.domitian.huber at gmail.com> |
| BugReports: | https://github.com/ChristianHuber/smartsnp/issues |
| License: | MIT + file LICENSE |
| URL: | https://christianhuber.github.io/smartsnp/ |
| NeedsCompilation: | yes |
| Language: | en-GB |
| Materials: | README, NEWS |
| CRAN checks: | smartsnp results |
Documentation:
| Reference manual: | smartsnp.html , smartsnp.pdf |
| Vignettes: |
Using VCF and PLINK formatted files with smartsnp (source) Projecting ancient samples (source) Example PCA, PERMANOVA and PERMDISP analysis (source) |
Downloads:
| Package source: | smartsnp_1.2.0.tar.gz |
| Windows binaries: | r-devel: smartsnp_1.2.0.zip, r-release: smartsnp_1.2.0.zip, r-oldrel: smartsnp_1.1.0.zip |
| macOS binaries: | r-release (arm64): smartsnp_1.2.0.tgz, r-oldrel (arm64): smartsnp_1.2.0.tgz, r-release (x86_64): smartsnp_1.2.0.tgz, r-oldrel (x86_64): smartsnp_1.2.0.tgz |
| Old sources: | smartsnp archive |
Linking:
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