User: b.d237

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b.d237140
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National University of Ireland, Galway
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de novo viral miRNA discovery

Posts by b.d237

<prev • 31 results • page 1 of 4 • next >
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Answer: A: Appropriate gene IDs for enrichment analysis (with clusterProfiler)
... Follow the detailed workflow here : https://github.com/twbattaglia/RNAseq-workflow : # Add ENTREZ ID results$entrez <- mapIds(x = org.Mm.eg.db, keys = row.names(results), column = "ENTREZID", keytype = "SYMBOL", ...
written 7 days ago by b.d237140
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Comment: C: Multiple plots outputs using for loop in R
... Many thanks Prakash!! ...
written 28 days ago by b.d237140
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Comment: C: Multiple 'plotEnrichments' using loop in R
... Hi Ram, Yes I am using R studio. To test that theory I placed outfile="/Users/b/Desktop/Hallmarks_plots.pdf" pdf(file=outfile) ..FOR LOOP.. dev.off() To try and capture all plots in 1 pdf. The resulting pdf cannot be opened (is damaged). ...
written 28 days ago by b.d237140
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Multiple plots outputs using for loop in R
... Hi, I have been using the package [fgsea][1], and I would like to use a for loop in R to output multiple Enrichment plots. So far I can generate a plot of the desired pathway using: plotEnrichment(pathway = pathways.hallmark[["HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION"]], gseaPar ...
fgsea R loop written 28 days ago by b.d237140 • updated 28 days ago by Prakash1.4k
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Comment: C: Gene Set Enrichment Analysis after DESeq2
... Try row.names = TRUE. Also, you want to use col.names = FALSE, as GSEA complains when 'Gene' and 'metric' are in the rnk. file. ...
written 5 weeks ago by b.d237140
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Comment: C: Gene Set Enrichment Analysis after DESeq2
... **`.....`** filtered <- na.omit(y) write.table(filtered ,file="DE_genes.rnk",quote=F,sep="\t",row.names=F) ...
written 5 weeks ago by b.d237140
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Comment: C: DESEQ2 Design formula testing cell type across condition
... Yeah I think I had gone too far, design = ~ condition + celltype + condition:celltype Is not what I was after. Leaving out condition:celltype allowed me to control for the effects of condition. My phrasing was unclear -- instead of 'across condition', I should have said controlling for condit ...
written 10 weeks ago by b.d237140
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DESEQ2 Design formula testing cell type across condition
... Hi, I am attempting to compare the following samples in DESEQ2 that follow and experimental design of: condition celltype Ctrl A Ctrl B Ctrl C Ctrl D CYTO A CYTO B CYTO C CYTO D (Replica ...
deseq2 design rna-seq written 11 weeks ago by b.d237140 • updated 10 weeks ago by Biostar ♦♦ 20
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Comment: C: GATK Panel Of Normals (PoN)
... The error output tells you what the problem is. -v is not a recognized option. You probably want to use -V instead of -vcfs Uppercase, not lower case. ...
written 3 months ago by b.d237140
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Answer: A: prediction of viral miRNAs by Vmir analyzer...
... Contacted the developer Adam Grundhoff, its available here: [VMir Analyzer][1] [1]: http://virus-genomics.org/software/vmir/vmir.html ...
written 4 months ago by b.d237140

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