Citations

Please cite the original TCC paper when referring to DEGES-based normalization:

  • Sun J, Nishiyama T, Shimizu K, Kadota K. TCC: an R package for comparing tag count data with robust normalization strategies. BMC Bioinformatics. 14:219, 2013. 10.1186/1471-2105-14-219

In addition, cite the method papers for the normalization and DEG screening functions used in the DEGES workflow.

  • If norm_tmm() is used, cite the TMM normalization paper: Robinson MD, Oshlack A. A scaling normalization method for DEG analysis of RNA-seq data. Genome Biology. 11:R25, 2010. 10.1186/gb-2010-11-3-r25

  • If test_edger() or other edgeR-based functions are used, cite edgeR: Chen Y, Chen L, Lun ATL, Baldoni PL, Smyth GK. 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, 2025. 10.1093/nar/gkaf018

  • If norm_rle(), test_deseq2(), or other DESeq2-based functions are used, cite DESeq2: Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 15:550, 2014. 10.1186/s13059-014-0550-8