R.SamBada: Processing Pipeline for 'SamBada' from Pre- To Post-Processing

Processing pipeline for 'SamBada' from pre- to post-processing. 'SamBada' is a landscape genomic software designed to run univariate or multivariate logistic regression between the presence of a genotype and one or several environmental variables. See Stucki (2017) <doi:10.1111/1755-0998.12629> and <https://github.com/Sylvie/sambada>. The package provides functions that can be classified into four categories: 1) Install 'SamBada' 2) Preprocessing (prepare genomic file into standards compatible with 'SamBada' and apply quality-control; retrieve environmental conditions at sampling location; prepare environmental file including removal of correlated variables and computation of population structure) 3) Processing (run 'SamBada' on multiple cores using 'Supervision') 4) Post-processing (calculate p-values and q-values, produce interactive Manhattan plots and query 'Ensembl' database, produce maps).

Version: 0.1.3
Imports: SNPRelate, gdsfmt
Suggests: Rcpp, utils, data.table, shiny, plotly, httr, biomaRt, ggplot2, sp, packcircles, raster, mapplots, spdep, rgdal, gdalUtils, rworldmap, doParallel, foreach, knitr, rmarkdown
Published: 2022-01-05
Author: Solange Duruz, Sylvie Stucki, Oliver Selmoni, Elia Vajana
Maintainer: Solange Duruz <solange.duruz at alumni.epfl.ch>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
Materials: NEWS
CRAN checks: R.SamBada results


Reference manual: R.SamBada.pdf
Vignettes: R.SamBada


Package source: R.SamBada_0.1.3.tar.gz
Windows binaries: r-devel: R.SamBada_0.1.3.zip, r-release: R.SamBada_0.1.3.zip, r-oldrel: R.SamBada_0.1.3.zip
macOS binaries: r-release (arm64): R.SamBada_0.1.3.tgz, r-oldrel (arm64): R.SamBada_0.1.3.tgz, r-release (x86_64): R.SamBada_0.1.3.tgz, r-oldrel (x86_64): R.SamBada_0.1.3.tgz
Old sources: R.SamBada archive


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