For example,how is magnetic field data from Venus Express, in Venus Solar Orbital(VSO) coordinates transformed into Mean Field Aligned Coordinates? What are the elements for the rotation matrix for Venus? How is this done using a software?
My experience (Cassini/Beagle2) is that space agencies and institutes tend to write their own codes for such frame transformations. A spacecraft manual (yes, there is a thick set of volumes accompanying each craft) will spell out the basis set of the spacecraft, how the payloads are oriented with respect to it, and the Principal Investigator's team will then themselves use that to orient their dataset to the spacecraft frame.
The mission ops people of the project will know the spacecraft attitude from star-trackers and the like, and the payload data can then be corrected to planeto-centric or heliocentric frames by the PI teams.
I would guess that a few hundred lines of FORTRAN are involved.
The NAIF Spice Toolkit (https://naif.jpl.nasa.gov/naif/toolkit.html) is the standard software used for those types of transformations. Spacecraft data typically include SPICE kernels that provide information on the coordinate system of the spacecraft that are used for these transformations.
The above three answers are not helpful to you, because they throw the ball over the wall.
If you can define the Venus Solar Orbital (VSO) coordinates and the Mean Field Aligned Coordinates with respect to the Venus (equatorial) centered inertial, VCI say, then the rotation matrix for the transform in the (Planetary or Heliocentric) Sun Centered Inertial (SCI) coordinate system is easy to construct.
I am an Astrodynamicist working with Earth centered satellites and debris in Earth Centered Inertial (ECI) coordinate system and its transformations to other spacecraft and planet coordinate systems all the times. However, I know only a little about Sun Centered Inertial (SEI) coordinate system, but their transformation should be similar. If you can define the VSO and any coordinate system you want, I can give you the few lines of code you need in a short time. Glad to help.