User: pat.longjump

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Posts by pat.longjump

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Comment: C: Question: Can I visualize individual genes of pathways when running goanna or ke
... The > v <- topGO(go, n=100) was actually in run in the next line not as displayed here ...
written 9 months ago by pat.longjump0 • updated 9 months ago by genomax68k
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Can I visualize individual genes of pathways when running goanna or kegga?
... Hi, I was running kegga and goana as follows: > kegga.de=kegga(lrt, species="Mm") > go <- goana(lrt, species= 'Mm') > v <- topGO(go, n=100) For both, the output is a list of pathways that show a number of upregulated, downregulated, or unchanged genes. See below: ![ ...
R rna-seq written 9 months ago by pat.longjump0 • updated 9 months ago by genomax68k
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(Closed) Can I visualize individual genes of pathways when running goanna or kegga?
... Hi, I was running goanna and kegga in R: kegga.de=kegga(lrt, species="Mm") go <- goana(lrt, species= 'Mm') topGO(go, n=50) For both the output is a list of pathways that show a number of uregulated, downregulated, or unchanged genes. See below: [goana result][1] [1]: https://dr ...
R rna-seq written 9 months ago by pat.longjump0 • updated 9 months ago by Istvan Albert ♦♦ 80k
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Comment: C: What is the best method ChIPseq differential binding analysis?
... Thank you very much! I appreciate your input! ...
written 16 months ago by pat.longjump0
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What is the best method ChIPseq differential binding analysis?
... Hi all, I want to quantitatively compare ChIP-seq data! Experimental condition: - same background cell line but samples differ (WT, KO1) - same antibody was used to pull down transcription factor (not histone) - identical library preparation and sequencing parameters My goal is to perform a diffe ...
chip-seq written 16 months ago by pat.longjump0 • updated 16 months ago by Rory Stark510
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GSEA Heatmap Expression Scale
... Hi all, I ran GSEA through the Broad Institut's desktop application. I want to show a scale for the heat maps that shows fpkm expression. Does the GSEA software provide me this or will I need to create one manually? If yes, how would I approach this? Here is an example of what I would want: ![GSEA ...
gene rna-seq gsea heatmap written 21 months ago by pat.longjump0
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Comment: C: Add gene names for significant genes in volcano plot (CummeRbund)
... Just the basic command > csVolcano(genes(object = cuff_data), x = 'Sample1', y = 'Sample2', alpha=0.05, showSignificant=TRUE) ...
written 24 months ago by pat.longjump0
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Add gene names for significant genes in volcano plot (CummeRbund)
... Hi all, I generated a volcano plot with CummeRbund. Now I want to label the significant genes with the gene names. How can this be done? Thanks! ...
R cummerbund rna-seq written 24 months ago by pat.longjump0
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How to highlight single gene in volcano plot?
... Hi all, I am in the process of creating a volcano plot from my cuffdiff data. I am using cummeRbund. I want to highlight a single gene of interest in the plot, with a different color. How may I approach this? Thank you in advance for the help! ...
R cummerbund rna-seq written 24 months ago by pat.longjump0 • updated 24 months ago by theobroma221.1k
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Cuffquant and Cuffnorm: merged.gtf or genes.gtf
... Hi all, I was wondering if it is best to use **merged.gtf** (from cuffmerge) or **genes.gtf** as annotation files for cuffquant and cuffnorm? It would be nice to hear the rational for choosing one over the other. Thank you! ...
tuxedo rna-seq sequencing written 2.3 years ago by pat.longjump0

Latest awards to pat.longjump

Popular Question 8 months ago, created a question with more than 1,000 views. For Add gene names for significant genes in volcano plot (CummeRbund)
Popular Question 8 months ago, created a question with more than 1,000 views. For What is the best method ChIPseq differential binding analysis?
Popular Question 8 months ago, created a question with more than 1,000 views. For How to determine the breast cancer subtype based on mRNA data?
Popular Question 8 months ago, created a question with more than 1,000 views. For How to determine the breast cancer subtype based on mRNA data?
Popular Question 16 months ago, created a question with more than 1,000 views. For GSEA heatmap for all genes?

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