User: Gabriel

gravatar for Gabriel
Gabriel50
Reputation:
50
Status:
New User
Location:
Paris
Last seen:
3 days, 23 hours ago
Joined:
5 months, 2 weeks ago
Email:
g***********@gmail.com

Biomedical Engineering major

Posts by Gabriel

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Getting a list of up and down regulated genes in a pathway
... What? In the link you sent it says there are 50 proteins in the geneset ...
written 17 days ago by Gabriel50
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Answer: A: Getting a list of up and down regulated genes in a pathway
... Download the WIKIPATHWAYS gmt files, load them into R, then select the genes from said pathway, and find the differentially expressed genes from said gene vector ...
written 17 days ago by Gabriel50
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Finding the official list of genes from Geneontology(GO) gene sets
... Example gene set: GO:0000002 When I use different tools, I get different lists of genes! g:Profiler vs gageData and more. The thing is I have not yet been able to find an up to date list of genes for this gene set. I want to do it in R preferably, and just get a vector of all the genes from geneon ...
genesets annotation go rna-seq written 17 days ago by Gabriel50
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Comment: A: Network plot from expression data in R using igraph
... When I run the code > commSummary <- data.frame( + mst.communities$names, + mst.communities$membership, + mst.communities$modularity + ) I get this error: Error in data.frame(mst.communities$names, mst.communities$membership, : arguments imply differing number of rows: 290, 288 ...
written 8 weeks ago by Gabriel50
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Is there a way to visualize log fold changes for Reactome pathways in R?
... With KEGG, we can use the tool Bioconductor to plot our pathways with the logfold changes for our datasets, using R. Like this: ![Pathview visualization of fold changes][1] This can also be done with WikiPathways and Cytoscape, by downloading the images and uploading the fold changes into cytoscape ...
bioconductor reactome pathview rna-seq written 11 weeks ago by Gabriel50
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How to get wikipathways without disease and cancer ontologies?
... I am doing GSEA on RNA-seq data and I am using the file from here: http://data.wikipathways.org/current/gmt/ In this file, there are pathways such as "WP4217 Ebola Virus Pathway on Host" which I am not interested in. Where can I find the wikipathways without disease ontologies? ...
wikipathways gene ontology rna-seq gsea written 11 weeks ago by Gabriel50
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What is the best way to rank genes for GSEA?
... I am doing pathway and gene ontology analysis using Gene Set Enrichment Analysis(GSEA). For the tools, you need to provide a ranked gene list, however, various papers have provide different recommendations on how to do this. Is there a current consensus on what is the ideal way to do this? I've bee ...
gene ranking gsea go rna-seq written 3 months ago by Gabriel50 • updated 3 months ago by Pietro70
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Comment: C: What causes Linear relations on MAplots?
... Sorry didn't see it until now, done. ...
written 3 months ago by Gabriel50
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Comment: C: What causes Linear relations on MAplots?
... Thank you. Your answer checks out! I used the identify() function to extract one of the gene names from the lines, and then I checked the raw data. It seems one group had all columns as 0, and the control group had all columns from 50-90 for that specific gene. ...
written 4 months ago by Gabriel50
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What causes Linear relations on MAplots?
... Hello I am sort of a newbie in statistical science, so I hope this isn't a terrible question. I am doing an analysis on example data, and I do the MAplot on my normalized counts from my DESeq2 results. This is what I get: ![MA plot with a linear relationship][1] So we have a normal(i think) MAplot ...
maplot logfold change rna-seq written 4 months ago by Gabriel50

Latest awards to Gabriel

Scholar 17 days ago, created an answer that has been accepted. For A: Getting a list of up and down regulated genes in a pathway

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