YuLab-SMU clusterProfiler issues

YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data

https://yulab-smu.top/biomedical-knowledge-mining-book/

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issues

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simplify Function Keeps Identical Gene Sets

#744 DarioS opened 1 day ago
0
Unable to Convert Pathway ID to Gene Set

#743 DarioS opened 1 day ago
0
enrichKEGG issue：the Description column and ID information are identical in 4.10.0

#742 onmyojiyys opened 3 days ago
0
Update groupGO.R

#741 ewail opened 1 week ago
0
how to install clusterProfiler 4.2.2 version?

#740 toddey opened 1 week ago
2
enricher not working properly

#739 Gambrian closed 2 weeks ago
4
I'm having trouble when I use simplify on the result of compareCluster

#738 HMU-lyz closed 2 weeks ago
4
smth wrong with enrichGO

#737 tsoshukming opened 3 weeks ago
1
gsePathway not found

#736 NicoHadas closed 3 weeks ago
1
Dotplot to show only selected pathways from compareCluster result

#735 asmariyaz23 closed 4 weeks ago
5
Meta-analysis Functionality is Not Available

#734 DarioS opened 1 month ago
0
Mitochondrial Genes and Annotations missing from EnrichGO

#733 Dragonmasterx87 opened 1 month ago
3
goplot encountered an error

#732 Long-zhe closed 1 month ago
4
How to run enrichment analysis of metabolites using clusterProfier

#731 Krithika-Bhuvan opened 1 month ago
1
how to compare different conditions

#730 Flu09 opened 1 month ago
0
enrichWP is not working for a few organisms

#729 prateekgv opened 1 month ago
3
gofilter function ERROR: object 'topNode' not found

#728 yulchen810 opened 1 month ago
1
Error: unable to open database file Traceback:

#727 jmzhang1911 opened 1 month ago
1
错误于fortify.compareClusterResult(object, showCategory = showCategory, : 找不到对象'gcsize

#725 Soft283 closed 1 month ago
1
enrichWP error

#724 LoetC closed 3 weeks ago
2
clusterProfiler: BgRatio N value does not equal set gene universe size

#723 fafaris39 opened 2 months ago
1
using compareCluster to compare gene sets from different species

#722 lanasushko opened 2 months ago
1
problem with gseGO()

#721 Flu09 opened 2 months ago
1
Question about GO terms in clusterProfiler

#720 shuaizh117 opened 3 months ago
3
RStudio is crashing when running compareCluster

#719 nfancy opened 3 months ago
1
goplot no longer works with clusterProfiler 4.12.3

#718 davetang closed 1 month ago
2
Can't install clusterProfiler 4.12.3 on R-4.4.0

#717 davetang opened 3 months ago
1
ridgePlot Axis Ticks Spacing is Sometimes Insufficient

#716 DarioS opened 3 months ago
1
GeneRatio in dotplot as number instead of fraction

#715 nina-hahn closed 3 months ago
9
dplyr and clusterprofile version 4.10.1

#714 lzy604 opened 3 months ago
1
ERROR in enrichGO,when seting ont = "ALL",Error in data.frame(..., check.names = FALSE) : 行名里有缺失值。

#713 XIANZHE-LI opened 3 months ago
1
KEGG analysis of metabolites

#712 Echo-ylq opened 3 months ago
2
Unable to install r package for clusterProfiler

#711 shaliniC23 opened 4 months ago
1
enrichKegg function, qvalueCutoff not working, getting as well non-significant results

#710 nina-hahn opened 4 months ago
4
gseKEGG function running indefinitely with a gene list of over 3000 genes

#709 Sophia409 opened 4 months ago
1
No gene can be mapped when using enrichKEGG

#708 Yanqiu-T opened 4 months ago
11
"I performed the gseGO function using clusterProfiler for all ontologies together, but I wasn't able to apply the simplify function to remove redundancy. I tried various options suggested online, but none worked. As a workaround, I ran gseGO for each ontology (BP, MF, CC) separately and then removed redundancy for each ontology using GOsim. Is it correct to combine the results from all ontologies into one file and then combining it with metadata from one ontology (e.g., the output of gseGO for BP) to create enrichment plots?" or what could be the easiest way to perfrom that

#707 Sidragull57 opened 4 months ago
13
"400 Bad Request" using enrichKEGG function from the clusterProfiler

#706 RouaPopescu opened 4 months ago
2
compareCluster GSEA + universal annotation = does not work

#705 philousap opened 4 months ago
1
size = qvalue does not work with ridgeplot function()

#704 CharlineJnnt closed 3 months ago
3
The GeneRatio denominator does not correspond to the number of input genes.

#703 CharlineJnnt opened 4 months ago
1
gseGO Produces Results Table with Zero Rows

#702 DarioS opened 4 months ago
2
User Manual Has Minimal Discussion of Universe Choices

#701 DarioS opened 4 months ago
0
[FeatureRequest] color category and gene labels differently in `cnetplot`

#700 wbvguo opened 4 months ago
0
Error with Enricher function

#699 ambikapokhrel opened 4 months ago
1
Retrieve the set of genes with assigned GO

#698 m-bogaerts opened 5 months ago
1
A strange non-given GO comment appears

#697 Chewxway opened 5 months ago
8
Upsetplot is cropped

#696 nina-hahn opened 5 months ago
4
Different behaviour of gseGO upon setting nPerm=1000

#695 olgabaranov closed 5 months ago
2
gseKEGG using KEGG database error (cannot open URL 'https://rest.kegg.jp/conv/ncbi=geneid/mmu': HTTP status was '400 Bad Request')

#694 ChoIYS98 opened 6 months ago
1