Package: smartsnp 1.1.0

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).

Authors:Salvador Herrando-Perez [aut], Ray Tobler [ctb], Christian Huber [ctb, cre]

smartsnp_1.1.0.tar.gz
smartsnp_1.1.0.zip(r-4.5)smartsnp_1.1.0.zip(r-4.4)smartsnp_1.1.0.zip(r-4.3)
smartsnp_1.1.0.tgz(r-4.5-x86_64)smartsnp_1.1.0.tgz(r-4.5-arm64)smartsnp_1.1.0.tgz(r-4.4-x86_64)smartsnp_1.1.0.tgz(r-4.4-arm64)smartsnp_1.1.0.tgz(r-4.3-x86_64)smartsnp_1.1.0.tgz(r-4.3-arm64)
smartsnp_1.1.0.tar.gz(r-4.5-noble)smartsnp_1.1.0.tar.gz(r-4.4-noble)
smartsnp_1.1.0.tgz(r-4.4-emscripten)smartsnp_1.1.0.tgz(r-4.3-emscripten)
smartsnp.pdf |smartsnp.html✨
smartsnp/json (API)
NEWS

# Install 'smartsnp' in R:
install.packages('smartsnp', repos = c('https://christianhuber.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/christianhuber/smartsnp/issues

Pkgdown site:https://christianhuber.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

5.32 score 7 stars 6 scripts 285 downloads 5 exports 44 dependencies

Last updated 1 years agofrom:01e53da532. Checks:1 OK, 8 NOTE, 3 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 24 2025
R-4.5-win-x86_64NOTEMar 24 2025
R-4.5-mac-x86_64NOTEMar 24 2025
R-4.5-mac-aarch64NOTEMar 24 2025
R-4.5-linux-x86_64NOTEMar 24 2025
R-4.4-win-x86_64NOTEMar 24 2025
R-4.4-mac-x86_64NOTEMar 24 2025
R-4.4-mac-aarch64NOTEMar 24 2025
R-4.4-linux-x86_64NOTEMar 24 2025
R-4.3-win-x86_64WARNINGMar 24 2025
R-4.3-mac-x86_64WARNINGMar 24 2025
R-4.3-mac-aarch64WARNINGMar 24 2025

Exports:read_packedancestrymapsmart_mvasmart_pcasmart_permanovasmart_permdisp

Dependencies:bitbit64bootSVDcliclustercodetoolscpp11crayondata.tablefansiffforeachgluehmsiteratorslatticelifecyclemagrittrMASSMatrixmgcvnlmepermutepillarpkgconfigprettyunitsprogressR6RcppRcppArmadilloRcppEigenRcppParallelRfastrlangRSpectratibbletidyselecttzdbutf8vctrsveganvroomwithrzigg

Example PCA, PERMANOVA and PERMDISP analysis

Rendered frommallard_smartpca_analysis.Rmdusingknitr::rmarkdownon Mar 24 2025.

Last update: 2021-06-19
Started: 2021-06-07

Projecting ancient samples

Rendered fromaDNA_smartpca_analysis.Rmdusingknitr::rmarkdownon Mar 24 2025.

Last update: 2021-06-19
Started: 2021-06-12

Using VCF and PLINK formatted files with smartsnp

Rendered fromConverting_VCF_and_PLINK_formats.Rmdusingknitr::rmarkdownon Mar 24 2025.

Last update: 2021-06-23
Started: 2021-06-13