Batagelj, V.: Analysis of bibliographic networks. PhD course on networks, Uppsala University, November 18, 2016.
Download Pajek from Andrej's site. There is also a manual. You can also look at Pajek's mailing list.
For detailed introduction to network analysis with Pajek and description of Pajek's capabilities see the book ESNA 2. For analysis of large networks see the book Understanding ....
For transforming Web of Sciencs (WoS) data into a collection of Pajek networks you can use a program (in Python) WoS2Pajek.
Batagelj, V.: Towards temporal bibliographic networks. PEERE, Vilnius, March 7, 2017.