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The vast demand for diverse applications raises new networking challenges, which have encouraged the development of a new paradigm of Internet of Things (IoT), e.g., LoRa. LoRa is a proprietary spread spectrum modulation technique that provides a solution for long-range and ultra-low power-consumption transmission. Due to promising prospects of LoRa, significant effort has been made on this compelling technology since its emergence. In this article, we provide a comprehensive survey of LoRa from a systematic perspective: LoRa analysis, communication, security, and its enabled applications. First, we summarize works focusing on analyzing the performance of LoRa networks. Then, we review studies enhancing the performance of LoRa networks in communication. Afterward, we analyze the security vulnerabilities and countermeasures. Finally, we survey the various LoRa-enabled applications. We also present comparisons of existing methods, together with insightful observations and inspiring future research directions.