User: Gabriel

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Gabriel60
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Paris
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Biomedical Engineering major

Posts by Gabriel

<prev • 13 results • page 1 of 2 • next >
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Is there a package for ORA where I can supply my own gmt files?
... I am looking to do standardized Gene Ontology analysis based on a cutoff and Overrepresentation Analysis(ORA, not GSEA). For this, I've been using gprofiler, etc. But I need to do this in a standardized way where I can supply my own versioned .gmt files. In topGO, you have to use "their" GO files, ...
geneset bioconductor go ora gmt files written 14 days ago by Gabriel60
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Comment: C: Future prospects: NGS vs Gene editing(using CRISPR CAS9, AAVs and similar method
... I think I have an immunity against wetlab, because it bores me to do the tedious labor. I was hoping Gene editing had more theory and bioinformatics in it(predicting Cas9 offset targets, designing the primers and PCR for gene editing tests) just like RNA-seq. But If it's more hours in the wetlab tha ...
written 4 months ago by Gabriel60
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Forum: Future prospects: NGS vs Gene editing (using CRISPR CAS9, AAVs and similar methods)
... What is going to be the better of the two employment wise in the coming decades? I know Both are incredibly strong and growing, but that NGS is more recent, whereas Gene Editing has more medical applications and thus draws big money from big pharma. Which one is a wiser bet for a future career pla ...
crispr-cas9 forum ngs written 4 months ago by Gabriel60 • updated 4 months ago by ATpoint30k
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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 7 months ago by Gabriel60
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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 7 months ago by Gabriel60
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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 7 months ago by Gabriel60 • updated 6 months ago by Biostar ♦♦ 20
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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 9 months ago by Gabriel60
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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 10 months ago by Gabriel60
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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 10 months ago by Gabriel60
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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 10 months ago by Gabriel60 • updated 10 months ago by Pietro100

Latest awards to Gabriel

Popular Question 12 weeks ago, created a question with more than 1,000 views. For What is the best way to rank genes for GSEA?
Scholar 7 months 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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