@inbook{2d7526f8f1f84bc2ab08c7e6fe826ba1,
title = "Become Competent in Generating RNA-Seq Heat Maps in One Day for Novices Without Prior R Experience",
abstract = "Heat map visualization of RNA-seq data is a commonplace task. However, most laboratories rely on bioinformaticians who are not always available. Biological scientists are afraid to prepare heat maps independently because R is a programming platform. Here, using RNA-seq data for 16 differentially expressed genes in WNT pathway between embryonic stem cells and fibroblasts, I share a tutorial for novices without any prior R experience to master the skills, in one day, required for preparation of heat maps using the pheatmap package. Procedures described include installation of R, RStudio, and the pheatmap package, as well as hands-on practices for some basic R commands, conversion of RNA-seq data frame to a numeric matrix suitable for generation of heat maps, and defining arguments for the pheatmap function to make a desired heat map. More than 20 template scripts are provided to generate heat maps and to control the dimensions and appearances of the heat maps.",
keywords = "Heat maps, Human embryonic stem cells, pheatmap, RNA-seq, RStudio, Tutorial, WNT pathways",
author = "Kejin Hu",
note = "Funding Information: The author{\textquoteright}s work is supported by NIH (1R01GM127411-01A1) and the American Heart Association (17GRNT33670780). The author appreciates the testing of this tutorial by Drs. Ricardo Cevallos and Jobaida Akther, both of whom were at the level of fresh postdoctoral scientists in biology and medical sciences without any prior experience in R and preparation of heat maps at the time of testing. This tutorial was also tested by the group members of Dr. Ren-he Xu at Macau University including Roma Borkar, Dejin Zheng, Ye Yi, Siyi Fu, Borong Huang, Sen Ye, Guihui Qin, Haibo Peng, Changkun Yang, Daryl Yichi Zhang, and Philip Naderev Lagniton. Publisher Copyright: {\textcopyright} 2021, Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2021",
doi = "10.1007/978-1-0716-1084-8_17",
language = "English",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "269--303",
booktitle = "Methods in Molecular Biology",
}