User: ivanarg2

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ivanarg260
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Posts by ivanarg2

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Comment: C: how to find metabolites
... You can then run regular gene set enrichment analysis, as below: fgsea(metabolites.gs, ranks, nperm = 1000) ## ranks is from your differential expression analysis, i.e., a t-statistic (logFC/logFC.sd) The resulting list of 'pathways' (really, metabolites), will tell you the enrichment of metab ...
written 2.3 years ago by ivanarg260
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Answer: A: how to find metabolites
... Based on this, with some modifications: > https://support.bioconductor.org/p/107927/ library(KEGGREST) library(org.Hs.eg.db) library(annotate) ## Get enzyme-gene annotations res1 = keggLink("enzyme", "hsa") tmpDF1 = data.frame(ec = res1, gene = names(res1)) ...
written 2.3 years ago by ivanarg260
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Answer: A: breast cancer transcriptome
... Use the Xena Browser, selected TCGA BRCA, select "Phenotype" and the "sample_type" will give you tumor and normal data. You can play with the heatmaps as well as download the data. https://xenabrowser.net/heatmap/ ...
written 2.3 years ago by ivanarg260
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Comment: C: how to find metabolites
... Check section 4.5.2 here: https://bioconductor.org/packages/release/bioc/vignettes/piano/inst/doc/piano-vignette.pdf and reference 6 therein. They describe making 'gene sets' where each gene set is a metabolite, and the genes within each set are the enzymes related to metabolism of that metabolite. ...
written 2.3 years ago by ivanarg260
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Differential expression - design matrix with multiple factors and paired samples
... I'm analyzing gene expression data from an experiment where I have (i) 6 different mice (A:D); (ii) 2 different time points ("pre" and "post" treatment); and (iii) 2 different response types ("responder" vs. "non-responder"). I'm trying to find genes with differential expression after treatment in t ...
limma rna-seq written 2.3 years ago by ivanarg260 • updated 2.3 years ago by Devon Ryan96k

Latest awards to ivanarg2

Popular Question 7 weeks ago, created a question with more than 1,000 views. For RNASeq user experience with Novogene?
Popular Question 15 months ago, created a question with more than 1,000 views. For RNASeq user experience with Novogene?
Scholar 2.3 years ago, created an answer that has been accepted. For A: how to find metabolites
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: how to find metabolites

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