User: egeulgen

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egeulgen190
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190
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Istanbul
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https://github.com/ege...
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3 days, 9 hours ago
Joined:
1 year, 8 months ago
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Posts by egeulgen

<prev • 12 results • page 1 of 2 • next >
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Answer: A: haplotypecaller can not run in single bam file
... try omitting the -ERC GVCF argument or provide the sample name to sample_name argument if it's a multi-sample BAM file ...
written 5 days ago by egeulgen190
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Answer: A: Determine whether it is MSI (micro satellite instability) or not
... I don't have any experience with MSIsensor. In our lab, we use MSIseq, which offers a decision tree model classifier. You can train a decision tree model or use the default one. It then classifies the tumor as "MSI-H" or "non-MSI-H". Maybe this might help; from [MSIseq's article][1]: "Tumors in whi ...
written 7 days ago by egeulgen190
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Comment: C: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
... We’re looking into your issue on Github. We will try to include a visualization of the enrichment results in the next version (considering a bubble chart but feel free to share any ideas of what you had in mind). ...
written 5 weeks ago by egeulgen190
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Comment: C: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
... Thank you for the feedback! To answer them: 1. We did not think it would make any difference 2. We will try to include an example for `pathmap` in the next version 3. The pathways are already visualized and can be viewed through the HTML reports. Would you expand on how we could provide more vis ...
written 5 weeks ago by egeulgen190
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Comment: C: Visualization of protein similarity matrix
... maybe try calculating the manhattan distances and then MDS? ...
written 3 months ago by egeulgen190
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Comment: C: Differential Expression fro GEO Data
... before all do `dir.create("data")` ...
written 3 months ago by egeulgen190
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Comment: C: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
... You can see an example application in the vignette (`browseVignettes("pathfindr_vignette")`). We also have a [wiki][1]. [1]: https://github.com/egeulgen/pathfindR/wiki ...
written 3 months ago by egeulgen190
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Comment: C: enrichment of gene set with enrichR
... try `enriched <- enrichr(my_genes[, 1], dbs)` ...
written 3 months ago by egeulgen190
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Comment: C: enrichment of gene set with enrichR
... 1. Save the excel file as a csv file on excel (e.g. as "my_file.csv") 2. In R, read them into a vector with `my_genes <- read.csv("my_file.csv")` 3. Run `enriched <- enrichr(my_genes, dbs)` ...
written 3 months ago by egeulgen190
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Answer: A: enrichment of gene set with enrichR
... Put your genes in a vector: `my_vec <- c("Gene1", "Gene2", ..., "Gene8000")`. Then you can run `enriched <- enrichr(my_vec, dbs) ` ...
written 3 months ago by egeulgen190

Latest awards to egeulgen

Appreciated 5 weeks ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: enrichment of gene set with enrichR
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: enrichment of gene set with enrichR

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