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 – Install the mixOmics package from Bioconductor You may need to install the latest R version and the latest BiocManager package installed following these instructions (if you use R versions <=3.5.0) refer to the instructions at the end of the link). Install mixOmics using the following code:
## install BiocManager if not installed if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
## install mixOmics
BiocManager::install('mixOmics')
The mixOmics package should directly import the following packages: igraph, rgl, ellipse, corpcor, RColorBrewer, plyr, parallel, dplyr, tidyr, reshape2, methods , matrixStats , rARPACK, gridExtra .
1 alternative – To obtain the latest update of mixOmics(as Bioconductor updates every 6 months our package) 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")
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 > 6.10. If this is not the case, try step 1 alternative (installation from gitHub):
>library(mixOmics)
Loaded mixOmics 6.10.x
We also advise using the software RStudio
If R makes any complain, you may have to install the latest R version here: https://cran.r-project.org/
Wifi will 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