User: egeulgen

gravatar for egeulgen
egeulgen990
Reputation:
990
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Location:
Istanbul
Website:
https://github.com/ege...
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Last seen:
7 hours ago
Joined:
3 years, 5 months ago
Email:
e*******@gmail.com

I'm one of the developers for the R package pathfindR, a tool for active-subnetwork-oriented enrichment analysis. My special intests are interaction-network-based analyses of complex diseases, especially cancer. I also try to develop solutions for personalized analysis of NGS data for oncological cases.

Posts by egeulgen

<prev • 35 results • page 1 of 4 • next >
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Comment: C: UpSet R plot using text files
... maybe check out [UpSetR][1]? [1]: https://github.com/hms-dbmi/UpSetR ...
written 4 months ago by egeulgen990
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Comment: C: correlations between principal components and known variables
... Internally `plotPCA()` uses `princomp()`, see the [source code][1]. You can use `loadings()` to get what you want. Please read the documentations via `?princomp`, `?loadings`, `?plotPCA` etc. to understand what these functions do, what their arguments do and what they return. Documentation exists f ...
written 5 months ago by egeulgen990
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Answer: A: correlations between principal components and known variables
... Assuming you are using `princomp()`, the PC scores are stored in `pca_res$scores` so you can use these (e.g. `pca_res$scores[, 1]` for PC1) and investigate any correlation (simple correlation may not do the trick though, see the answer here: [https://stats.stackexchange.com/questions/115032][1]). I ...
written 5 months ago by egeulgen990
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Comment: C: Enrichment pathways comparison between conditions
... oh, also see https://www.biostars.org/p/66377/ ...
written 5 months ago by egeulgen990
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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... > only used to provide a direction of the expression change That is correct. The change values are only used for visualization purposes (indicating up/down change). ...
written 5 months ago by egeulgen990
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Answer: A: Enrichment pathways comparison between conditions
... Initially, I thought you could try a *multivariate* hypergeometric distribution based test, implemented as [MultiHypergeometric][1] in the CRAN package extraDistr. After searching a while, however, [this article][2] also looks very promising: > ... developed a theoretical framework for computin ...
written 5 months ago by egeulgen990
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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... Hey. Great to hear you liked the package. The logFC values are optional and are only used during KEGG pathway diagram visualization via pathview, which scales the values between -1 and 1. So the base should not matter. The active subnetwork search only utilizes the gene symbols and associated p valu ...
written 6 months ago by egeulgen990
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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... hello again. Thank you for pointing that out! After the initial tutorial post, we made some changes on how the active subnetworks are filtered (that is more stringent). That's why the example above didn't work. I've updated the above example and made sure it works, should be fine now :) ...
written 6 months ago by egeulgen990
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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... Hello, Glad you found the tutorial useful. The function did not raise an error but rather gives a warning that no enriched gene sets were identified. I cannot tell, given only the above warnings, what might be the issue but I think the custom gene set you use for the analysis might be the problem. I ...
written 6 months ago by egeulgen990
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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... Hey Fil, Glad you like the tutorial. I can't immediately think of any reason why the HTML outputs are empty but do open up an issue on [our GitHub page][1] if this persists. For determining the 36 genes without interactions in the PIN, you may use the following: input_df <- RA_input # you ...
written 8 months ago by egeulgen990

Latest awards to egeulgen

Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Plotting the expression values for two genes in a range of cells
Great Question 4 months ago, created a question with more than 5,000 views. For Enrichment Analysis, Clustering and Scoring with pathfindR
Autobiographer 4 months ago, has more than 80 characters in the information field of the user's profile.
Supporter 5 months ago, voted at least 25 times.
Gold Standard 8 months ago, created a post with more than 25 bookmarks. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Popular Question 16 months ago, created a question with more than 1,000 views. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Popular Question 17 months ago, created a question with more than 1,000 views. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Librarian 17 months ago, created a post with more than 10 bookmarks. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Prophet 20 months ago, created a post with more than 20 followers. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Appreciated 21 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: enrichment of gene set with enrichR
Scholar 21 months ago, created an answer that has been accepted. For A: Plotting the expression values for two genes in a range of cells
Appreciated 21 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Appreciated 22 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: enrichment of gene set with enrichR
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: enrichment of gene set with enrichR

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