R.SamBada (0.1.1)

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

http://cran.r-project.org/web/packages/R.SamBada

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) and . 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).

Maintainer: Solange Duruz
Author(s): Solange Duruz, Sylvie Stucki, Oliver Selmoni, Elia Vajana

License: GPL (>= 2)

Uses: gdsfmt, SNPRelate, ggplot2, sp, spdep, rgdal, data.table, Rcpp, foreach, rworldmap, raster, doParallel, knitr, httr, mapplots, shiny, gdalUtils, rmarkdown, packcircles, plotly

Released 2 months ago.


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