User: egeulgen

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egeulgen880
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Istanbul
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Posts by egeulgen

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Enrichment pathways comparison between conditions
... oh, also see https://www.biostars.org/p/66377/ ...
written 15 hours ago by egeulgen880
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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 15 hours ago by egeulgen880
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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 15 hours ago by egeulgen880
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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 27 days ago by egeulgen880
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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 29 days ago by egeulgen880
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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 4 weeks ago by egeulgen880
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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 12 weeks ago by egeulgen880
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BWA - [fread] Input/output error
... [UPDATE] So sorry to update this so late, this turned out to be an error due to a hardware issue and was fixed when the hard disk was replaced. Hello all, I'm trying to align paired-end read files to the reference genome using the following command (bwa version: 0.7.17-r1188): `bwa mem $ref_genom ...
software error alignment bwa written 7 months ago by egeulgen880
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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... thank you. glad you like the tutorial. Performing the analysis with p-values would be wrong, I would suggest instead to change the p value threshold (i.e. to change the argument `p_val_threshold `) to a higher value (e.g. 0.1). ...
written 10 months ago by egeulgen880
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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... In some cases (especially if the number of input genes is low), pathfindR may not find any active subnetworks and therefore no enriched pathways. The message stating "Could not find any interactions for XX (XX%) genes in the PIN." is more relevant for genes not mapping onto the PIN. ...
written 11 months ago by egeulgen880

Latest awards to egeulgen

Supporter 15 hours ago, voted at least 25 times.
Gold Standard 12 weeks ago, created a post with more than 25 bookmarks. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Popular Question 10 months ago, created a question with more than 1,000 views. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Popular Question 11 months ago, created a question with more than 1,000 views. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Librarian 12 months ago, created a post with more than 10 bookmarks. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Prophet 15 months ago, created a post with more than 20 followers. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Appreciated 15 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: enrichment of gene set with enrichR
Scholar 16 months ago, created an answer that has been accepted. For A: Plotting the expression values for two genes in a range of cells
Appreciated 16 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Appreciated 17 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: enrichment of gene set with enrichR
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: enrichment of gene set with enrichR

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