In the multi-messenger era, coordinating observations between astronomical facilities is mandatory to study transient phenomena (e.g. Gamma-ray bursts) and is achieved by sharing information with the scientific community through networks such as the Gamma-ray Coordinates Network. The facilities usually develop real-time scientific analysis pipelines to detect transient events, alert the astrophysical community, and speed up the reaction time of science alerts received from other observatories. We present in this work the RTApipe framework, designed to facilitate the development of real-time scientific analysis pipelines for present and future gamma-ray observatories. This framework provides pipeline architecture and automatisms, allowing the researchers to focus on the scientific aspects and integrate existing science tools developed with different technologies. The pipelines automatically execute all the configured analyses during the data acquisition. This framework can be interfaced with science alerts networks to perform follow-up analysis of transient events shared by other facilities. The analyses are performed in parallel and can be prioritised. The workload is highly scalable on a cluster of machines. The framework provides the required services using containerisation technology for easy deployment. We present the RTA pipelines developed for the AGILE space mission and the prototype of the SAG system for the ground-based future Cherenkov Telescope Array observatory confirming that the RTApipe framework can be used to successfully develop pipelines for the gamma-ray observatories, both space and ground-based.