The full documentation on https://yulab-smu.top/biomedical-knowledge-mining-book/ ?

[jielab]

Dear Prof. Yu:

Thanks for your nice software.

For your new paper "clusterProfiler 4.0: A universal enrichment tool for interpreting omics data" published this year, is the full documentation on https://yulab-smu.top/biomedical-knowledge-mining-book/ ? However, I could not find the following code on this URL, which was in your paper:

1. library(clusterProfiler)
2. g <- bitr(genes, 'ENTREZID', 'SYMBOL', 'org.Hs.eg.db')
3. ## downloaded from https://maayanlab.cloud/Enrichr/geneSetLibrary?mode=text&
4. libraryName=ENCODE_and_ChEA_Consensus_TFs_from_ChIP-X
5. encode <- read.gmt("ENCODE_and_ChEA_Consensus_TFs_from_ChIP-X.txt")

I ask this question, just want to make sure that I am reading the full and most up-to-date documentation.

Also, I got error messages shown as below, when I try to follow the code written on Chapter 15.

Can you please let me know how to address this?

Best regards, Jie

[GuangchuangYu]

yes, it is the full documentation.

However, the code in our manuscript is not necessarily in this document.

The full source code for the manuscript is hosted in https://github.com/YuLab-SMU/supplemental-clusterProfiler-v4.

---

issues in the screenshot:

1. you may using out-of-date version.
2. you need to install the pkg via BiocManager::install("org.Hs.eg.db").