clusterProfiler
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YuLab-SMU
:bar_chart: A universal enrichment tool for interpreting omics data
Dear Yu: I am surprised to find that some pathway, eg carbon metabolism ko01200, can not be plotted with fold change data. It just give a n empty default pathway....
I have noticed that cnetplots made with a compareCluster result will not colour the genes even when supplied with a sorted gene vector object as in 3.1 input [here](http://yulab-smu.top/clusterProfiler-book/chapter3.html) I've...
Hello, First of all, thank you so much for making such an amazing and helpful tool. I haven't been able to figure out how to do this based on existing...
enricher和GSEA可以搞一下。 `gson_GO`函数已经有了，，GO的分析就可以衔接。 这里`gson_GO`我不支持`ALL`，因为三个ONTOLOGY是独立的。我后面想要通过GSONList对象来支持。 然后输出对象可以是enrichResultList（默认）或者是enrichResult（简化版本，result data frame里多一个gsname的column）这样子两种的。这样子是通用的。可以比如KEGG、GO、wikiPathway一次过地跑富集。
dotplot show 'Aesthetics must be valid data columns . Problematic aesthetic(s): x = ~group...' error
Dear Dr. After I passing a formula to compareCluster func and get the compareCluster result object(formula_res), I use dotplot function to visualize my result , it get errors as follow:...
Hello! I've been trying to merge multiple gseaResult objects such as those from KEGG, Reactome and Wikipathways to generate one ridgeplot only, for an article I've done: ``` reactomegsea
A reproducible example. ``` data(geneList, package="DOSE") mydf
Cheers, I have differentially expressed genes for three conditions (3, 6 and 10 DAS). I do the cluster comparison using "enrichGO". For the Upregulated comparison it works very well, but...
### Describe your issue  is there any way to give scoreType='pos' in clusterProfiler,,? ### Ask in the right place * [ ] for bugs or feature requests, post here...
Hi, when I use ```enrichGO``` to perform GO enrichment analysis, I had a bug: ```Error in get("GO2ONT", envir = GO_DATA) : object 'GO2ONT' not found``` and this bug I think...
