clusterProfiler

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P.adjust values in dotplot do not match GO analysis values

7

Hello! Hope all is well. I am using both the `enrichGO` and `gseGO` functions. The analyses are going well, but I am uncovering a phenomenon I quite honestly don't understand....

lillianhorin

Unable to use compareCluster function with GSEA for three sets of genelists

1

Hi, I am using the latest version of ClusterProfiler (4.0.5) and R version is 4.1.1. I am trying to use clusterCompare function on three gene sets. str(InputList) List of 3...

aishwarya-gondane

fail to use read.gaf

1

In the namespace, I surprisely find clusterProfiler provide "read.gaf" to parse the .gaf profile but in my clusterProfile 4.4.2 and GOSemSim v2.22.0 I can't find this function. I wonder if...

wangzy20

Fail to reproduce `enrichKEGG` example

5

Hi, I fail to reproduce any plots related to KEGG, For example this snippet from the [documentation](http://yulab-smu.top/biomedical-knowledge-mining-book/clusterprofiler-kegg.html#clusterprofiler-kegg-pathway-ora) page, ``` data(geneList, package="DOSE") gene 2] kk No gene can be mapped.... -->...

hiraksarkar

ko2name run error

1

Hi, When I try to run the following command, I don't get the metabolic pathway for the ko2name comment, they are all NA My is data is bacterial metagenomics, how...

zhaohanshuang

KEGG related analysis report error again

3

> library(clusterProfiler) > packageVersion("clusterProfiler") [1] ‘4.8.1’ > sessionInfo() R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale: [1] LC_COLLATE=Chinese (Simplified)_China.utf8...

BaymaxzzZY

怎样使用自己构建的go和kegg的背景数据集分析

2

我们做的是非模式生物，由于我的物种没有很好的注释信息，所以我只能利用blast比对将自己的物种的基因和swissprot数据库进行比对，然后构建了go的背景库，利用 kobas比对到小鼠上构建了一个kegg的背景库，但是当我运行gsea的时候总是会出现问题，附件是我的代码 sorted_gene_expression_data

yangxinzhi

kegg parameter change

9

correction to download kegg.db

kkleinoros

could not find function "gseGO"

1

### Prerequisites + [ ] Have you read [Feedback](https://guangchuangyu.github.io/clusterprofiler/#feedback) and followed the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)? * [x ] make sure you are using the latest release version * [x ] read the...

nitinmahajan20

Does enrichGO support “ENSEMBL” format?

3

Hello, I am a beginner of bioinformatics and am using enrichGO to analyze up-regulated genes in tomato. My genes are in ensemble format (e.g. Solyc01g005730.3), but when I run >...

TianGong9