R.SamBada (0.1.2)

0 users

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) 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.

2 previous versions



  (0 votes)


  (0 votes)

Log in to vote.


No one has written a review of R.SamBada yet. Want to be the first? Write one now.

Related packages:(20 best matches, based on common tags.)

Search for R.SamBada on google, google scholar, r-help, r-devel.

Visit R.SamBada on R Graphical Manual.