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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gseGO Produces Results Table with Zero Rows

#702 DarioS opened 3 days ago
2
User Manual Has Minimal Discussion of Universe Choices

#701 DarioS opened 3 days ago
0
FeatureRequest: color category and gene labels differently in `cnetplot`

#700 wbvguo opened 1 week ago
0
Error with Enricher function

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

#698 m-bogaerts opened 2 weeks ago
1
A strange non-given GO comment appears

#697 Chewxway opened 3 weeks ago
8
Upsetplot is cropped

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

#695 olgabaranov closed 3 weeks 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 1 month ago
1
Perform gseaplot2 using seurat DEG output.

#693 synatkeamsk opened 1 month ago
0
How do I change the width of each coloum in the heatmap in the treeplot?

#692 CyrusWang57 opened 1 month ago
0
compareCluster - Error in check_gene_id - but work perfectly with standar procedure (not using compareCluster)

#691 philousap opened 2 months ago
1
All p-values are equal to 1

#690 aminakur opened 2 months ago
1
enrichKEGG "No gene can be mapped"

#689 dengzf2021 opened 2 months ago
2
How to convert geneID from the enrichKEGG output from entrez to gene symbol?

#688 thisisamirv closed 2 months ago
2
OrgDb for maize

#687 enriquepola1996 opened 2 months ago
1
ont = "BP" in enricher () function

#686 enriquepola1996 opened 2 months ago
1
gson 格式在最新版 enrichKEGG中出错

#685 Shuixin-Li opened 2 months ago
4
Error in testForValidKeytype(x, keytype) : Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.

#684 lifannn11 opened 2 months ago
1
something wrong of setReadable

#683 williambi1 opened 2 months ago
6
bitr报错

#682 wangtanzhang612 closed 2 months ago
1
Count duplicate K Numbers (KEGG) for enrichKEGG?

#681 diefuechsin opened 2 months ago
0
feature request: add message suggesting to cite fgsea package when it's used for GSEA analysis

#680 assaron closed 2 months ago
3
How to combine different compareCluster results?

#678 Kyeongmi-Lee opened 3 months ago
1
How to split the results of compareCluster?

#677 Ldec12 opened 3 months ago
1
heatplot function; color scale is switched

#676 zellerivo opened 3 months ago
1
compareCluster's enrichGO difference in results when stating ont = "ALL" vs NULL

#675 jestlin15 closed 3 months ago
1
change in name of wikipathway file and enrichWP function do not work anymore

#674 boutrys closed 3 months ago
2
How to generate gseaplots from the result of compareCluster gseaGO or gseaKEGG functions?

#673 JiahuaQu opened 3 months ago
2
Entire species designation is included in KEGG Pathway name

#670 npokorzynski closed 4 months ago
4
problem in run compareCluster

#669 gongxin8888 opened 4 months ago
4
[feature request] Support metabolite enrichment analysis

#668 Landau1994 closed 2 months ago
2
How to color code cnetplot nodes from enrichrResult data

#667 hlnicholls opened 4 months ago
4
Trouble with gseKEGG on mac sonoma 14.2

#666 annecar opened 4 months ago
1
Not able to install clusterProfiler on Colab

#665 pmhchang opened 5 months ago
3
fix: :bug: fix some mistake in KEGG category

#664 ryuzheng closed 4 months ago
1
Dotplot() cannot change color

#663 GuanKX99 closed 4 months ago
2
Update kegg_category.rda

#662 ryuzheng closed 5 months ago
0
Unable to load clusterProfiler (4.11.0.00) - object ‘ls2df’ not exported by 'namespace:yulab.utils'`

#661 zoezhao1030 closed 5 months ago
0
Cannot library(clusterProfiler)

#660 HLinChen closed 5 months ago
2
GSEA long time no response

#659 Xingsongli opened 5 months ago
21
Emmaplot with the top activated and supressed from dotplot?

#658 Leandromvelez opened 5 months ago
4
When there's only one term ID in the dataframe passed as TERM2GENE in enricher

#657 mansi-aggarwal-2504 opened 5 months ago
0
update CITATION

#656 Clearmind777 closed 5 months ago
0
clusterProfiler custom annotated list

#655 mansi-aggarwal-2504 closed 5 months ago
2
compareCluster does not give a warning/message that numeric universe is ignored for fun = "enrichGO"

#654 IwanParf opened 6 months ago
0
How to use compareCluster for GSEA on the Msigdb database?

#653 Ldec12 opened 6 months ago
4
gseKEGG()函数运行时出错

#652 ZhanshenWu opened 6 months ago
6
compareCluster Function Support for gsonList Objects in clusterProfile?

#650 Chris-lang478 opened 6 months ago
0
Error in download.file(url, quiet = quiet, method = "libcurl"), libcurl cannot be change

#648 Junyan1996 opened 7 months ago
2