User: Agamy89

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Agamy890
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Posts by Agamy89

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How to compare gene clusters of non-model organisms using clusterProfiler package?
... Hi everyone, I am doing a transcriptomic analysis of a particular fungus according to pH change. I have determined DEG and enriched GO using topGO Package (as the genus I am working with is a non-model organism and I have to use my own GO annotation file). Next, I have done soft clustering in order ...
software error R next-gen rna-seq written 18 months ago by Agamy890 • updated 17 months ago by Biostar ♦♦ 20
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Comment: C: Visualization of Gene Ontology using bubble plot.
... Thank you for your suggestion. Actually, the form of visualization using clusterProfiler package is perfect in one of my cases; I performed several soft clustering and wanted to compare their GO in one graph instead of several graphs. However, I find difficulty to visualize my GO using clusterProfil ...
written 18 months ago by Agamy890
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Visualization of Gene Ontology using bubble plot.
... I would like to ask if anybody has an idea about visualizing the gene ontology on R using bubble plot as shown in Fig 3 of this report? https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/evu070 I am analyzing a data of transcriptomic analysis of a dimorphic fungus by comparing the expressi ...
R rna-seq sequencing written 19 months ago by Agamy890 • updated 14 days ago by patrick.kraetschmer10
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Comment: C: How to extract from original counts genes with > or equal 2 fold change and FDR
... Hi, At first, I'd like to thank you so much for your suggestion. As far as I know, **exactTest ()** need only two groups for making the comparison, but I still know in RNA-Seq analysis and R language handling. I have tried to perform the test for fold change as following **exactResults <- exactTe ...
written 20 months ago by Agamy890
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How to extract from original counts genes with > or equal 2 fold change and FDR <0.001?
... I am analyzing RNA-Seq data in a time course dependent manner (5-time points). I set up three replicates for each time point, so total samples are 15. I want to apply this data to fuzzy soft clustering analysis to figure out the cluster genes change according to the time points and explore the enric ...
R rna-seq written 20 months ago by Agamy890 • updated 20 months ago by Jake Warner730

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