User: egeulgen

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egeulgen450
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Posts by egeulgen

<prev • 18 results • page 1 of 2 • next >
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Comment: C: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
... The expression matrix for the pathway scores is the same matrix as the one you use for differential expression analysis. Columns are samples, rows are genes and the values are expression values. ...
written 9 weeks ago by egeulgen450
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Comment: C: Plotting the expression values for two genes in a range of cells
... you have to have a column called `Cell` filled with the row names, i.e. `"cell1, cell2, ..."` should be in a column named `Cell` ...
written 3 months ago by egeulgen450
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Answer: A: Plotting the expression values for two genes in a range of cells
... You can plot such a "lollipop plot" using ggplot2: cell_data <- read.csv("~/Downloads/data.csv") library(reshape2) library(ggplot2) cell_data_molten <- melt(cell_data) cell_data$Total <- cell_data$Gene.A + cell_data$Gene.B for_levels <- cell_data$C ...
written 3 months ago by egeulgen450
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Comment: C: Gene expression meta analysis
... see this [related question][1] [1]: https://www.biostars.org/p/207056/ ...
written 3 months ago by egeulgen450
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Comment: C: Building a biologically meaningful design matrix for limma/voom in a large RNASe
... Since the mutations are mutually-exclusive I'd create a vector `Muts`, in which the mutation status is specified for each subject, i.e.: Muts <- c("Mut1", "Mut1", "Mut2", .... , "Control", ...) I would create a design matrix as below: Mutations <- factor(Muts, levels = c("Mut1", "Mu ...
written 3 months ago by egeulgen450
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Tutorial: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... In this tutorial, I'll try to provide a brief overview of the capabilities of our pathway analysis R package [pathfindR][1]. The tool is in [CRAN][2] and its vignette can be found [here][3]. We also have a detailed [wiki][4]. This tool is designed to improve pathway enrichment analysis by firstly i ...
pathway R tutorial active subnetwork enrichment written 3 months ago by egeulgen450
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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 4 months ago by egeulgen450
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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 4 months ago by egeulgen450
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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 months ago by egeulgen450
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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 months ago by egeulgen450

Latest awards to egeulgen

Librarian 8 days ago, created a post with more than 10 bookmarks. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Prophet 11 weeks ago, created a post with more than 20 followers. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Appreciated 3 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: enrichment of gene set with enrichR
Scholar 3 months ago, created an answer that has been accepted. For A: Plotting the expression values for two genes in a range of cells
Appreciated 3 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Appreciated 5 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: enrichment of gene set with enrichR
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: enrichment of gene set with enrichR

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