ABSTRACT Atmospheric characterization of exoplanets from the ground is an actively growing field of research. In this context, we have created the ATMOSPHERIX consortium: a research project aimed at characterizing exoplanets atmospheres using ground-based high-resolution spectroscopy. This paper presents the publicly available data analysis pipeline and demonstrates the robustness of the recovered planetary parameters from synthetic data. Simulating planetary transits using synthetic transmission spectra of a hot Jupiter that were injected into real SPIRou observations of the non-transiting system Gl 15 A, we show that our pipeline is successful at recovering the planetary signal and input atmospheric parameters. We also introduce a deep learning algorithm to optimize data reduction which proves to be a reliable, alternative tool to the commonly used principal component analysis. We estimate the level of uncertainties and possible biases when retrieving parameters such as temperature and composition and hence the level of confidence in the case of retrieval from real data. Finally, we apply our pipeline onto two real transits of HD 189733 b observed with SPIRou and obtain similar results than in the literature. In summary, we have developed a publicly available and robust pipeline for the forthcoming studies of the targets to be observed in the framework of the ATMOSPHERIX consortium, which can easily be adapted to other high resolution instruments than SPIRou (e.g. VLT-CRIRES, MAROON-X, ELT-ANDES).