We present, here, advanced DFT-NEGF techniques that we have implemented in our ATOmistic MOdelling Solver, ATOMOS, to explore transport in novel materials and devices and in particular in van-der-Waals heterojunction transistors. We describe our methodologies using plane-wave DFT, followed by a Wannierization step, and linear combination of atomic orbital DFT, that leads to an orthogonal and non-orthogonal NEGF model, respectively. We then describe in detail our non-orthogonal NEGF implementation including the Sancho-Rubio and electron-phonon scattering within a non-orthogonal framework. We also present our methodology to extract electron-phonon coupling from first principle and include them in our transport simulations. Finally, we apply our methods towards the exploration of novel 2D materials and devices. This includes 2D material selection and the Dynamically-Doped FET for ultimately scaled MOSFETS, the exploration of vdW TFETs, in particular the HfS2/WSe2 TFET that could achieve high on-current levels, and the study of Schottky-barrier height and transport through a metal-semiconducting WTe2/WS2 VDW junction transistor.