fafax093-design/scRNA-neonatal-microglia-analyses-2025: v1.0.0 – Initial code release

Initial public release of the analysis code supporting the study: Neonatal inflammation disrupts a temporally restricted neurodevelopment-associated microglial program in the mouse brain This release contains the analysis code for: primary single-cell RNA-sequencing data processing and quality control; integration, clustering, marker identification, and microglial-state annotation; visualization and Gene Ontology enrichment; UCell pathway scoring; Monocle 3 trajectory and pseudotime analysis; scFEA metabolic-flux post-processing; pseudobulk transcription-factor activity analysis; cross-dataset label transfer and integration with an external developmental microglia dataset. Transcriptome sequencing data are available under: BioProject ID: PRJNA1329933 Large sequencing files and processed Seurat objects are not included in this repository.