clusterProfiler

clusterProfiler copied to clipboard

something wrong of setReadable

6

老师您好 在运行setReadable时遇到了报错现象 > 代码如下： GSEA_KEGG.R1 KEGG KEGG GSEA_KEGG GSEA_KEGG.R1

williambi1

parameter explaination of GSEA function

1

Hi, I was trying to run the GSEA function and got confused with its parameters `exponent`, which is documented as `weight of each step`. ``` GSEA( geneList, exponent = 1,...

wbvguo

Error in testForValidKeytype(x, keytype) : Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.

1

Hi: I have an unsolvable problem when running this code.  How can I solve it? Best XI Li

lifannn11

Hi! I am doing an analysis with clusterProfiler. I am wondering if it would make sense to let enrichKEGG count duplicate k numbers (KEGG numbers such as "K02760") for pathway...

diefuechsin

How to combine different compareCluster results?

1

i have compareCluster enrichKEGG and enrichGO results with same input. and i want to show 2 different results in one dotplot. how to merge multiple compareCluster results?

Kyeongmi-Lee

heatplot function; color scale is switched

1

``` library(DOSE) data(geneList) de 2] edo

zellerivo

How to split the results of compareCluster?

1

The geneList contains three groups. After running the following code `GSEA_GO

Ldec12

How to generate gseaplots from the result of compareCluster gseaGO or gseaKEGG functions?

2

We have ran the compareCluster gseaGO or gseaKEGG functions and there were three groups. Now we want to generate the gseaplot2 from the result, but after we ran the codes:...

JiahuaQu

On my attempt to increase the number of permutations in gseGO I am faced with an unexpected behaviour of the function: ``` > set.seed(1) > gse dim(gse) [1] 7 11...

olgabaranov

gseKEGG using KEGG database error (cannot open URL 'https://rest.kegg.jp/conv/ncbi=geneid/mmu': HTTP status was '400 Bad Request')

1

Regarding the KEGG annotation usage error, I have already followed up with #572 Seems like the error comes from not updating R or BiocManager or clusterprofiler.. I am currently using...

ChoIYS98