ROOT is a very powerful modular scientific software framework for data analysis created by CERN. Albeit it is based on C++, one can use PyROOT by integrating C++ and Python libraries (one of the most easiest powerful language). PyROOT can also be used through root notebook (Jupyter). I have used both ROOT and PyROOT for data analysis in my project at NISER.
GEANT4 is a toolkit for the simulation of the passage of particles through matter developed by CERN. It has a wide range of applications from high energy, nuclear, particle, detector physics to medical science, space science. I have used GEANT4 to simulate detector in my project at NISER.
MATLAB is a very popular software known for its wide range of application. For various numerical computation, I use MATLAB.
Mathematica is another popular versatile software for numerical computation, data analysis etc.