You might want to look into GNU Octave, it's like an open source version of Matlab which is often used for managing high dimensional data.
https://wikipedia.org/wiki/GNU_Octave
A couple other approach depending on the data and use are using relational database, storing the data in a database normalized form, then using a declarative style language like SQL to combine or exclude data in operations. And if it's mostly physics spacetime coordinates xyz+t tensor frameworks and libraries are built on top of most popular general purpose programming languages (python, c, java, etc) for that purpose.