-
Hey everyone,
I am a beginner in bioinformatics, and I am currently working on the annotation results from eggNOG-mapper (emapper-2.1.9) to conduct an enrichment analysis with the information from t…
-
org.gitools.datasources.idmapper.MappingException: java.io.IOException: Server returned HTTP response code: 400 for URL: http://rest.kegg.jp/link/genes/path:eco00730
org.gitools.datasources.modules.i…
-
Hi,
I'm having an issue with the "selectedPathways" argument in the oncoplot function, when using my own user-defined pathways. I either get the error below (with code):
```
oncoplot(maf = wgs.m…
-
Hello,
I am encountering an error when using the enrichKEGG function from the clusterProfiler package with my own created library for Klebisella pneumoniae subsp. pneumoniae HS11286 (taxid: 1125630).…
-
-
Hello,
I am encountering an issue while using the gseKEGG function from the clusterProfiler package for GSEA enrichment analysis. I have provided a gene list containing just over 3000 genes, but the …
-
Hello,
I've been using pathview for some time now but do have a question. Are you able to map KEGG drugs onto KEGG pathways using pathview?
Best,
Jordan
-
Hi again!
I have two questions about converting KOs to KEGG pathways.
Regardless if I am analyzing KOs or KEGG pathways, I am using the "pred_metagenome_unstrat.tsv" as my input (please let me k…
-
Hi,
Thank you for this useful package. I was wondering, whether there are plans to also include KEGG pathway maps in SGBNview. I know that those are covered by Pathview but with SGBNview it looks l…
-
I am trying to run ggpicrust2, and am having an issue. Below is the script I'm running:
# Load necessary data: abundance data and metadata
KO_abundance_file