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R.SamBada
View on CRAN: Click
here
Download and install R.SamBada package within the R console
Install from CRAN:
install.packages("R.SamBada")
Install from Github:
library("remotes")
install_github("cran/R.SamBada")
Install by package version:
library("remotes")
install_version("R.SamBada", "0.1.3")
Attach the package and use:
library("R.SamBada")
Maintained by
Solange Duruz
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-04-12
Latest Update: 2023-06-01
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 doi10.11111755-0998.12629 and httpsgithub.comSylviesambada.The package provides functions that can be classified into four categories1 Install SamBada2 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 structure3 Processing run SamBada on multiple cores using Supervision4 Post-processing calculate p-values and q-values produce interactive Manhattan plots and query Ensembl database produce maps.
How to cite:
Solange Duruz (2019). R.SamBada: Processing Pipeline for "SamBada" from Pre- To Post-Processing. R package version 0.1.3, https://cran.r-project.org/web/packages/R.SamBada. Accessed 21 Dec. 2024.
Previous versions and publish date:
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imports, suggests or enhances
Functions, R codes and Examples using
the R.SamBada R package
Some associated functions: R.SamBada-package . createEnv . downloadSambada . plotManhattan . plotMap . plotResultInteractive . prepareEnv . prepareGeno . prepareOutput . sambadaParallel . setLocation .
Some associated R codes: Postprocessing.R . Preprocessing.R . RSamBada.R . Run_sambada.R . Full R.SamBada package functions and examples
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