biomedical-knowledge-mining-book
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YuLab-SMU
:books: Biomedical knowledge mining using GOSemSim and clusterProfiler
Hi! thanks for writing such a helpful book! I had a question about the code on compare cluster in chapter 14 especially 14.2 I have 2 dataframes with the following...
I am trying to run the exact same code of treeplot from https://rdrr.io/github/GuangchuangYu/enrichplot/man/treeplot.html But getting the following error > treeplot(ego2, showCategory = 10) ! # Invaild edge matrix for ....
Hi. I noticed the links to the treeplot() function documentation are broken in chapter 15. Here is the working link: https://rdrr.io/github/GuangchuangYu/enrichplot/man/treeplot.html Thank you for making this amazing resource!
The URL `http://bio-bigdata.hrbmu.edu.cn/CellMarker/download/Human_cell_markers.txt` in the example code of section 12.2 is refusing connections. There is a .xlsx file available at `http://bio-bigdata.hrbmu.edu.cn/CellMarker/CellMarker_download.html` but the headers have names with different formats.
I have a set of Entrez id. I preform it used enrichKEGG, and warnging as followed. --> No gene can be mapped.... --> Expected input gene ID: --> return NULL......
I was trying to build the tree plot, however, the function of pairwise_termsim cannot be recognized by R, others were all fine, is this happened before, how to solve this...
I am confused about what the the red and blue rectangles in a gseaplot2 graph are supposed to signify. Looking at the source code of gseaplot2 and gsInfo, it seems...
There seems to be multiple errors when I tried to generate a pdf using the provided Makefile. Many of the functions are not available like `get_wp_organisms()` even though clusterProfiler is...
Dear Yu, I'm Dr. Nhat Le, a biostatistician/bioinformatics from [OUCRU ](https://www.oucru.org/vi/) Vietnam. Could you please incorporate phenotype permutation into your GSEA function? I think since the input gene list can...
