Package: R.SamBada
Type: Package
Title: Processing Pipeline for 'SamBada' from Pre- To Post-Processing
Version: 0.1.3
Date: 2021-12-23
Author: Solange Duruz, Sylvie Stucki, Oliver Selmoni, Elia Vajana
Maintainer: Solange Duruz <solange.duruz@alumni.epfl.ch>
Description: 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).
License: GPL (>= 2)
Imports: SNPRelate, gdsfmt
LinkingTo:
RoxygenNote: 7.1.2
Suggests: Rcpp, utils, data.table, shiny, plotly, httr, biomaRt,
        ggplot2, sp, packcircles, raster, mapplots, spdep, rgdal,
        gdalUtils, rworldmap, doParallel, foreach, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-01-04 17:41:25 UTC; cri
Repository: CRAN
Date/Publication: 2022-01-05 00:00:05 UTC
Built: R 4.0.5; ; 2022-01-25 00:06:28 UTC; unix
