Software requirements for 2019 mixOmics workshops

We list below some installation requirements to ensure the mixOmics workshop will run smoothly for everyone. Please update / install prior to the workshop to avoid a WIFI backload.

Software installation and updates. 

0 – Mac OS users only: install X Quartz first https://www.xquartz.org/

1 – To obtain the latest update of mixOmics, you will need to pull from our gitHub page via the devtools and the install_github libraries. Install the libraries ‘devtools’ in R, then load and install mixOmics from gitHub:

install.packages("devtools")
# then load
library(devtools)
install_github("mixOmicsTeam/mixOmics")

The mixOmics package should directly import the following packages: igraph, rgl, ellipse, corpcor, RColorBrewer, plyr, parallel, dplyr, tidyr, reshape2, methods , matrixStats , rARPACK, gridExtra .

2 – Check after install that the following does not throw any error (see step 0) and that the welcome message confirms you have installed version 6.7.1:

>library(mixOmics) 
Loaded mixOmics 6.7.1

We also advise to use the software RStudio

The other option in step 1 is to install directly from Bioconductor (but you may not have the latest version, as bioconductor updates only every 6 months):

if (!requireNamespace("BiocManager", quietly = TRUE))     install.packages("BiocManager") BiocManager::install("mixOmics", version = "3.8")

If R makes any complain, you may have to install the latest R version here: https://cran.r-project.org/

Wifi might be available on site, but it is preferable that you make those installations before the workshop to avoid delays for the analyses.

Any question regarding the requirements and software installation: email us at mixomics[at]math.univ-toulouse.fr

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