R/SGCCA

Author : Etienne CAMENEN

Key-words:

omics, RGCCA, multi-block

EDAM operation

analysis, correlation, visualisation

Contact

arthur.tenenhaus@l2s.centralesupelec.fr

Short description

Performs multi-variate analysis (PCA, CCA, PLS, R/SGCCA, etc.) and produces textual and graphical outputs (e.g. variables and individuals plots).

Description

A user-friendly multi-blocks analysis (Regularized Generalized Canonical Correlation Analysis, RGCCA) with all default settings predefined. The software produces figures to explore the analysis' results: individuals and variables projected on two components of the multi-block analysis, list of top variables and explained variance in the model.

More information about:

• RGCCA
• input / output formats

Usage instruction

Installation

conda create -n rgcca -c icm-iconics rgcca-launcher

Execution (with Russet data)

conda activate rgcca && \
cd ${CONDA_PREFIX} && \
wget https://raw.githubusercontent.com/BrainAndSpineInstitute/rgcca_Rpackage/master/inst/extdata/agriculture.tsv && \
Rscript R/launcher.R -d agriculture.tsv

More information about the command-line parameters here.