Negin Valizadegan

Why do enrichGo and enrichKEGG have qvaluecutoff but not gseGO and gseKEGG?

1

I am wondering why qvaluecutoff option is only set for the ORA and not the GSEA in this package. ### Prerequisites + [ ] Have you read [Feedback](https://guangchuangyu.github.io/clusterprofiler/#feedback) and follow...

Hello, I have a problem and that is because ClusterProfiler requires ordering fold change values from highest to lowest at the start, when creating the top pathways using enrichplot/cnetplot, only...

EnrichKegg still shows all pvalues even after specifying a specific pvalue cutoff

3

Although I use pvalueCutoff, the results still show pvalues larger than 0.1. Why is that? `kk2

Is this tool being maintained?

2

There doesn't seem to be responses to any recent issues or updates. Are you maintaining this tool?

comp_barplot seem to have issues with domain being unknown

1

Hello, I have an ASV where all levels are unknown as following: `Taxonomy Table: [1 taxa by 7 taxonomic ranks]: Domain Phylum Class Order Family Genus Species 55b5947908a70f952516e813b1ca9e71 "Unclassified" "Unclassified"...