User: egeulgen

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egeulgen1000
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Istanbul
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https://github.com/ege...
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1 day, 18 hours ago
Joined:
4 years ago
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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 • 37 results • page 1 of 4 • next >
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Comment: C: pathfindR - Enrichment Analysis using Active Subnetworks
... hey, package ‘pathfindR.data’ is not available (for R version 3.6.2) You need to have R version 4 installed. ...
written 3 months ago by egeulgen1000
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Comment: C: pathfindR - Enrichment Analysis using Active Subnetworks
... hey, I think it's an issue with `pak`. `install.packages("pathfindR")` should work. You may try with devtools for the development version: install.packages("devtools") # if you have not installed "devtools" devtools::install_github("egeulgen/pathfindR") ...
written 4 months ago by egeulgen1000
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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 11 months ago by egeulgen1000
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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 12 months ago by egeulgen1000
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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 12 months ago by egeulgen1000
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Comment: C: Enrichment pathways comparison between conditions
... oh, also see https://www.biostars.org/p/66377/ ...
written 12 months ago by egeulgen1000
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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 12 months ago by egeulgen1000
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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 12 months ago by egeulgen1000
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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 13 months ago by egeulgen1000
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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 13 months ago by egeulgen1000

Latest awards to egeulgen

Prophet 3 months ago, created a post with more than 20 followers. For Enrichment Analysis, Clustering and Scoring with pathfindR
Appreciated 9 months 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 11 months ago, created a question with more than 5,000 views. For Enrichment Analysis, Clustering and Scoring with pathfindR
Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.
Supporter 12 months ago, voted at least 25 times.
Gold Standard 15 months ago, created a post with more than 25 bookmarks. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Popular Question 23 months ago, created a question with more than 1,000 views. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Popular Question 24 months ago, created a question with more than 1,000 views. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Librarian 2.0 years ago, created a post with more than 10 bookmarks. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Prophet 2.2 years ago, created a post with more than 20 followers. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Appreciated 2.3 years ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: enrichment of gene set with enrichR
Scholar 2.3 years ago, created an answer that has been accepted. For A: Plotting the expression values for two genes in a range of cells
Appreciated 2.3 years ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Appreciated 2.4 years ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: enrichment of gene set with enrichR
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: enrichment of gene set with enrichR

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