KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes.

KEGG(Kyoto Encyclopedia of Genes and Genomes)由日本京都大学生物信息学中心的Kanehisa实验室于1995年建立，是一个整合了基因组、化学和系统功能信息的数据库。KEGG把从已经完整测序的基因组中得到的基因目录与更高级别的细胞、物种和生态系统水平的系统功能关联起来。

转录组鉴定了差异表达基因后，通常会进行GO或KEGG富集分析，识别这些差异基因的功能或参与调控的通路，来说明关键基因表达上调/或下调后可能会导致哪功能或通路被激活/或抑制，进而与表型进行联系。 目前能够进行GO、KEGG富集分析的工具有很多，不同的工具之间在算法、数据库上存在不同，因此结果也可能大相径庭。 本篇就以R包clusterProfiler的方法为例（该包基于 超几何分布 的原理），展示如何基于给定的差异基因列表进行GO、KEGG富集分析。 使 …

This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics.

A package that provides a client interface to the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. Only for academic use by academic users belonging to academic institutions (see ). Note that KEGGREST is based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.

Nov 8, 2020 · KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes.

KEGGgraph is a R/Biocoductor package to parse KEGG PATHWAYS in graph objects. Install KEGGgraph using BiocManager, the R package that manages Bioconductor packages. BiocManager:: install("KEGGgraph") Please see the vignettes as well as help files for examples. Questions, suggestions, comments?

A set of functions to analyse and plot the KEGG information using tidygraph, ggraph and ggplot2. The detailed documentation is here using bookdown.

We demonstrate the capabilities of the KEGGgraph package, an interface between KEGG pathways and graph model in R as well as a collection of tools for these graphs. Superior to preceding approaches, KEGGgraph maintains the pathway topology and allows further anal-ysis or dissection of pathway graphs. It parses the regularly updated KGML (KEGG XML)

Jan 9, 2023 · 分别介绍了如何使用DAVID在线分析工具对基因进行GO/KEGG功能富集分析、使用R ggplot包对获得的基因GO/KEGG功能富集结果进行可视化、使用R clusterProfiler包和R AnnotationHub包对基因进行GO/KEGG功能富集分析、OrgDb包制作以及结果可视化等。故，我重新整理了一波，并补充 ...