Advancements in single-cell RNA sequencing (scRNA-seq) technologies have revolutionized our understanding of cellular heterogeneity and gene expression patterns within complex tissues. In this study, we present a comprehensive pipeline for analyzing scRNA-seq data obtained from the brainstem, focusing on the identification and characterization of distinct inspiratory neurons and subclusters of astrocytic cell types. Furthermore, we investigate the impact of inflammation on the neonatal inspiratory centers of the brainstem. The brainstem plays a crucial role in regulating essential physiological processes, including respiration. However, the specific cellular composition and functional diversity of inspiratory neurons within this region remain poorly understood. By employing scRNA-seq, we aim to dissect the intricate cellular landscape and molecular signatures of inspiratory neurons in the brainstem. Our pipeline incorporates pre-processing steps for quality control, normalization, and feature selection, followed by clustering algorithms to identify discrete cell populations. One of the primary objectives of this study is to distinguish between two key types of inspiratory neurons, namely Type-1 and Type-2 neurons. Through the integration of scRNA-seq data with known marker genes and gene ontology enrichment analysis, we aim to elucidate the unique transcriptional profiles and functional characteristics associated with each neuron subtype. This distinction will provide valuable insights into the underlying mechanisms governing the inspiratory process and facilitate a deeper understanding of respiratory disorders. In addition to inspiratory neurons, astrocytes, the most abundant glial cells in the brain, play a vital role in maintaining neuronal homeostasis and responding to various stimuli. We extend our analysis to identify and subcluster different astrocytic cell types present in the brainstem using scRNA-seq data. By utilizing unsupervised clustering algorithms and known astrocyte-specific markers, we aim to delineate subpopulations with distinct molecular signatures, allowing for a more refined characterization of astrocyte diversity and function within the brainstem. Furthermore, we investigate the effects of inflammation on the neonatal inspiratory centers of the brainstem. Inflammation has been implicated in numerous neurological disorders and can significantly impact neuronal function. By comparing scRNA-seq profiles of brainstem cells under inflammatory conditions to those of healthy controls, we aim to identify differentially expressed genes, signaling pathways, and cell populations that are affected by inflammation. This analysis will provide critical insights into the molecular mechanisms underlying the inflammatory response in the brainstem and its potential implications for respiratory function in neonates. By unraveling the impact of perinatal inflammatory stress on brainstem respiratory networks and ventilatory reflexes, our findings have the potential to inform the development of novel therapeutic strategies to enhance respiratory health in infants. Moreover, understanding the long-term consequences of perinatal inflammation on respiratory function will aid in mitigating the detrimental effects and improving the overall respiratory outcomes in individuals affected by such conditions.