Linganisha mbinu

	Utafiti wa Uhusiano wa Epigenome-kote kwa Msingi wa Mfululizo wa Wakati	Uchambuzi wa Utekelezaji Tofauti wa RNA-seq
Nyanja	Bioinformatiki	Bioinformatiki
Familia	Process / pipeline	Process / pipeline
Mwaka wa asili	2010s	2008–2010 (RNA-seq DE methodology established)
Mwanzilishi	Extended from EWAS (Rakyan et al., 2011); longitudinal designs formalised by multiple groups ~2010s	Multiple groups; foundational methods from Anders & Huber (DESeq, 2010), Robinson, McCarthy & Smyth (edgeR, 2010)
Aina	Longitudinal epigenomic association pipeline	Quantitative genomics pipeline
Chanzo asilia	Pidsley, R., Zotenko, E., Peters, T. J., Lawrence, M. G., Risbridger, G. P., Molloy, P., ... & Clark, S. J. (2016). Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. Genome Biology, 17(1), 208.	Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550.
Majina mbadala	time-series EWAS, longitudinal EWAS, repeated-measures EWAS, dynamic methylation association study	RNA-seq DE analysis, transcriptomic differential expression, bulk RNA-seq DE, DEA
Zinazohusiana	3	6
Muhtasari	A time-series epigenome-wide association study (time-series EWAS) extends the classic cross-sectional EWAS design to longitudinal settings, measuring DNA methylation across the entire epigenome at multiple time points within the same subjects. The goal is to identify CpG sites whose methylation levels change systematically over time, or to characterise how epigenetic associations with an exposure or phenotype evolve across developmental stages, treatment periods, or disease trajectories.	RNA-seq differential expression (DE) analysis identifies genes whose transcript abundance differs significantly between two or more biological conditions — for example, treated versus control, or diseased versus healthy tissue. Starting from raw sequencing reads, the pipeline moves through alignment, count-based normalization, statistical modeling of count dispersion, hypothesis testing, and multiple-testing correction to produce a ranked list of differentially expressed genes accompanied by fold-change estimates and adjusted p-values.