The book is a tutorial for gene information query, gene/protein/probe identifier conversion, gene enrichment analysis, and publication-level plotting.
If you are new to R, do not worry, this book will set enough example codes to help you. After reading this book, you could plot figures based on your data.
- Part 1 (Search Information) introduces how to search gene metadata and PubMed papers.
- Part 2 (ID Conversion) describes ID conversion among symbol & alias, NCBI Entrez, Ensembl, Uniprot and microarray probe.
- Part 3 (Enrichment Analysis) describes the gene sets and two widely used functional enrichment methods: over-representation analysis (ORA) and functional class scoring (FCS).
- Part 4 (Plotting) includes 13 ORA plots, 5 FCS-GSEA plots, 2 Venn plots, and 1 Volcano plot.