“…Here, we briefly describe methods regarding how to perform transcriptome analyses and a mini-collection of publicly available transcriptome data. Although detailed protocols, workflows, parameters, and versions for each tool need to be modified depending on the aims of experiments ( Hao et al, 2023 , Hong and Jeong, 2023 , Jang et al, 2022 , Ju et al, 2023 , Park et al, 2023 ), our guideline will be valuable for biologists who are not bioinformaticians to analyze their own and publicly available RNA-seq data. Users will need to refer to other papers for assessing microarray, scRNA sequencing data ( Ryu et al, 2023 , Hwang, 2023 , Kim, 2023 , Kim and Lee, 2023 ), and hardware requirements for transcriptome analysis, which we did not include in this guideline.…”