Thanks for sharing the useful resources, it was really helpful.

Libraries in R:

multinet: https://cran.r-project.org/web/packages/multinet/multinet.pdf

MUNA: https://github.com/Issamfalih/MUNA/

muxViz: http://muxviz.net/

Libraries in Python:

Pymnet: http://www.mkivela.com/pymnet/

Py3plex : https://github.com/SkBlaz/py3plex

networkX (specially if you can reduce your multilayer network into a MultiGraph, or a MultiDiGraph): http://networkx.github.io/

Mully: An R Package to Create, Modify and Visualize Multilayered Graphs

You can find at : https://www.mdpi.com/2073-4425/9/11/519/pdf

Kamal Berahmand

https://stackoverflow.com/questions/47338678/what-is-the-most-efficient-library-to-work-with-multilayer-networks-in-python-or

http://www.mkivela.com/pymnet/

https://www.researchgate.net/post/Do_you_know_what_tools_can_be_used_to_deal_with_multi-layer_network_mutiplex_network_in_social_networks_or_complex_networks