Linganisha mbinu

	Uchanganuzi wa Mtandao wa RNA-seq wa Kiini Kimoja	Uchanganuzi wa Uboreshaji wa Njia
Nyanja	Bioinformatiki	Bioinformatiki
Familia	Process / pipeline	Process / pipeline
Mwaka wa asili	2015–2017 (rapid development alongside scRNA-seq methods; SCENIC 2017)	2003–2005
Mwanzilishi	Aibar et al. (SCENIC, gene regulatory networks); Jin et al. (CellChat, cell-cell communication networks)	Mootha et al. (2003); systematised by Subramanian et al. (2005)
Aina	Computational bioinformatics pipeline	Statistical functional annotation method
Chanzo asilia	Aibar, S., González-Blas, C. B., Moerman, T., Huynh-Thu, V. A., Imrichova, H., Hulselmans, G., ... & Aerts, S. (2017). SCENIC: single-cell regulatory network inference and clustering. Nature Methods, 14(11), 1083–1086.	Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., & Mesirov, J. P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545–15550.
Majina mbadala	scRNA-seq network analysis, single-cell gene regulatory network inference, scGRN analysis, single-cell co-expression network analysis	PEA, overrepresentation analysis, ORA, functional enrichment analysis
Zinazohusiana	6	6
Muhtasari	Network-based single-cell RNA-seq analysis extends standard scRNA-seq workflows by constructing and interrogating molecular interaction networks — gene regulatory networks, co-expression networks, or cell-cell communication graphs — from single-cell transcriptomic data. Rather than treating each gene independently, this approach captures the coordinated activity of gene circuits and intercellular signalling pathways within and between cell populations, enabling a systems-level view of transcriptional regulation at single-cell resolution.	Pathway enrichment analysis (PEA) is a statistical approach that takes a list of genes or proteins of interest — typically derived from a differential expression or proteomics experiment — and identifies which pre-defined biological pathways or functional gene sets are represented more often than expected by chance. By mapping individual molecular changes onto curated pathway knowledge bases such as KEGG, Gene Ontology, or Reactome, PEA translates long gene lists into interpretable biological processes, making it a central tool in the post-analysis of high-throughput omics experiments.