User: pat.longjump
pat.longjump • 0
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Posts by pat.longjump
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... The
> v <- topGO(go, n=100)
was actually in run in the next line not as displayed here ...
written 16 months ago by
pat.longjump • 0
• updated
16 months ago by
genomax ♦ 76k
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... 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:
![ ...
written 16 months ago by
pat.longjump • 0
• updated
16 months ago by
genomax ♦ 76k
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420
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... 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 ...
written 16 months ago by
pat.longjump • 0
• updated
16 months ago by
Istvan Albert ♦♦ 82k
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... Thank you very much! I appreciate your input! ...
written 23 months ago by
pat.longjump • 0
5
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1
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2.4k
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6 follow
1
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... 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 ...
written 23 months ago by
pat.longjump • 0
• updated
23 months ago by
Rory Stark • 550
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... 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 ...
written 2.4 years ago by
pat.longjump • 0
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... Just the basic command
> csVolcano(genes(object = cuff_data), x = 'Sample1', y = 'Sample2', alpha=0.05, showSignificant=TRUE) ...
written 2.6 years ago by
pat.longjump • 0
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... 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! ...
written 2.6 years ago by
pat.longjump • 0
1
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1.3k
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1
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... 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!
...
written 2.6 years ago by
pat.longjump • 0
• updated
2.6 years ago by
theobroma22 • 1.1k
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... 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!
...
written 2.9 years ago by
pat.longjump • 0
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For Add gene names for significant genes in volcano plot (CummeRbund)
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15 months ago,
created a question with more than 1,000 views.
For What is the best method ChIPseq differential binding analysis?
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23 months ago,
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For GSEA heatmap for all genes?
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