References

Chen Y, Chen L, Lun ATL, et al (2025) edgeR v4: Powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets. Nucleic acids research 53:gkaf018. https://doi.org/10.1093/nar/gkaf018

Kadota K, Nishiyama T, Shimizu K (2012) A normalization strategy for comparing tag count data. Algorithms for molecular biology : AMB 7:5. https://doi.org/10.1186/1748-7188-7-5

Li W, Lan P (2015) Genome-wide analysis of overlapping genes regulated by iron deficiency and phosphate starvation reveals new interactions in arabidopsis roots. BMC research notes 8:555. https://doi.org/10.1186/s13104-015-1524-y

Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biology 15:550. https://doi.org/10.1186/s13059-014-0550-8

Rodrigues FA, Fuganti-Pagliarini R, Marcolino-Gomes J, et al (2015) Daytime soybean transcriptome fluctuations during water deficit stress. BMC genomics 16:505. https://doi.org/10.1186/s12864-015-1731-x

Sakai H, Mizuno H, Kawahara Y, et al (2011) Retrogenes in rice (oryza sativa l. Ssp. Japonica) exhibit correlated expression with their source genes. Genome biology and evolution 3:1357—1368. https://doi.org/10.1093/gbe/evr111

Sun J, Nishiyama T, Shimizu K, Kadota K (2013) TCC: An r package for comparing tag count data with robust normalization strategies. BMC bioinformatics 14:219. https://doi.org/10.1186/1471-2105-14-219