User: lucatucciarone

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Posts by lucatucciarone

<prev • 52 results • page 1 of 6 • next >
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Comment: C: Dotplot of selected GO terms with z-score via ggplot2
... Solved: pcm$term <- fct_rev(pcm$term) this solved the problem! ...
written 11 weeks ago by lucatucciarone50
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Comment: C: Dotplot of selected GO terms with z-score via ggplot2
... Thank you very much for all the suggestions, in the end I was able to have what I wanted. Now I have another problem: the order of my go terms in within the groups is the other way around! For example: Real order: GO1 Group1 GO2 Group1 GO3 Group1 GO1 Group2 GO2 Group2 GO3 ...
written 11 weeks ago by lucatucciarone50
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Comment: C: Dotplot of selected GO terms with z-score via ggplot2
... I actually think the problem is in the melt step, because I have 2 variables and not 1, for this reason I guess I should do something like in this post (https://stackoverflow.com/questions/1544907/melt-to-two-variable-columns). My long dataset should be something like this: GO_ID PADJ value ...
written 12 weeks ago by lucatucciarone50
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Comment: C: Dotplot of selected GO terms with z-score via ggplot2
... Thank you very much for the tutorial. I am trying to follow it but I am stuck at the plot step because what ggplot expects is basically this format: Identifier Variable1 Variable2_Cond1 Variable2_Cond2 Variable3_Cond3 Which in tutorial words would be: Sample Time OTU1 OTU2 OTU3 My prob ...
written 12 weeks ago by lucatucciarone50
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Dotplot of selected GO terms with z-score via ggplot2
... Hello everyone, By using the online tool David (https://david.ncifcrf.gov) for GO enrichment analysis and the R package **GOplot** (https://wencke.github.io) I was able to associate a z-score to my gene ontology results. I run the analysis for 3 different conditions (Cond1, Cond2, Cond3) and sele ...
ggplot2 david rna-seq go written 12 weeks ago by lucatucciarone50
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Comment: C: Link pathways to Gene Onthologies from RNA-seq differential expressed genes
... Marvelous, and after I have an identifier how can I link it to a certain Biological Process? ...
written 10 months ago by lucatucciarone50
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Comment: C: Link pathways to Gene Onthologies from RNA-seq differential expressed genes
... Unfortunately not, it's from the IPA knowledgeabase. I wanna say I'm not married to IPA, I can definitely switch to another tool if it would allow me to do what I'd like to : ) ...
written 10 months ago by lucatucciarone50
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Comment: C: Link pathways to Gene Onthologies from RNA-seq differential expressed genes
... Hello Jared! Thanks for helping me again : ) I got my pathways from IPA. Unfortunately though, IPA doesn't give me a clear idea of what biological process a specific pathway is activating or inhibiting. What I'd like to do is: 1) Performing Pathway analysis using the differentially expressed ge ...
written 10 months ago by lucatucciarone50
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Link pathways to Gene Onthologies from RNA-seq differential expressed genes
... Hello everybody! I was thinking whether existed a way to link a pathway to a GO-term (Biological process). For example, let's say I have MTOR signalling activated, I know from the literature that is linked with cell growth. Is there a way to compute all those relationships? Thanks! ...
rna-seq written 10 months ago by lucatucciarone50
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Comment: C: Visualize overlap differentially expressed genes of multiple comparisons.
... This seems more doable. Would you mind uploading a sample picture to see how it turn out? ...
written 10 months ago by lucatucciarone50

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Popular Question 4 months ago, created a question with more than 1,000 views. For Best tool for Motif enrichment of TFs
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