Questions tagged [clusterprofiler]
The clusterprofiler tag has no usage guidance.
9
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How to fix "No gene can be mapped, Expected input gene ID, return NULL..." error in clusterProfiler?
I am trying EnrichKEGG on a few gene samples of genes to check it works before inputting the full genome:
This is my data input as test.csv
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- 21
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Pathway Enrichment Analysis for one specific pathway?
I have a gene set containing a set of 1500 genes in which I did differential gene expression using limma voom pipeline. After this step I wanted to analyze a specific set of pathways the metabolism ...
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Interpretation of clusterProfiler results
I am using clusterProfiler for differential gene expression using this code:
https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html
I have a question about the third line of code:
<...
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How to analyse Orthofinder results
I read this paper (Colletotrichum shisoi sp. nov., an anthracnose pathogen of Perilla frutescens in Japan: molecular phylogenetic, morphological and genomic evidence). We ran Orthofinder and also ...
- 275
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How to identify specific motif for chip-seq data
For chip-seq data, I had analyzed the samples until motif discovery using both cluster profiler and Homer for each histone mark. I was wondering what is the efficient method to determine if each GO ...
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How to detail the specific GO terms
How can I get more specific GO terms when using clusterProfiler? I got my Dotplot by:
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- 441
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1
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344
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What does the setSize ordering mean?
I am running gseGO function from clusterProfiler and getting an output where terms are ordered by the ...
- 2,538
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1
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clusterProfiler, groupGO: meaning of GeneRatio
I am running groupGO function from clusterProfiler:
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groupGO parameters explanation (ont and level)
I need to use groupGO in clusterProfiler to find functional profile of a list of genes, and I am having trouble finding out what ...
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