Moderator: EagleEye
EagleEye ♦ 6.6k
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- https://decodebiology....
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Investigating field of biology by applying logics of computer science, statistics and mathematics.
Posts by EagleEye
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... Have a look at this simple tool which works with most updated database, https://www.biostars.org/p/108669/
...
written 4 weeks ago by
EagleEye ♦ 6.6k
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... Dear tarashanst,
It looks good. But the point of GO enrichment tools is to reduce the workload from the user's side. If the user has to prepare their own GO term dictionary, what exactly LightGOEA does? Looks like it only matches the user-provided gene list with the user-provided GO terms with asso ...
written 4 weeks ago by
EagleEye ♦ 6.6k
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... This tool will give you the terms for all your genes in the list. Additionally it will also provide enrichment analysis.
https://www.biostars.org/p/108669/ ...
written 3 months ago by
EagleEye ♦ 6.6k
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... Since they did not deposit RAW counts, you better reanalyze the FASTQ deposited files if you want to get good results. I had a look at the dataset, it was very interesting. But I have a small question since this is RNA-seq study, I would expect the samples to be collected before a certain time point ...
written 5 months ago by
EagleEye ♦ 6.6k
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Comment:
C: i need to find a database
... in general a web site that gives me the articles that have been released about a locus of the genome?
If you are looking for details about a particular gene locus and its related publications, try GeneCards.
**Example**: https://www.genecards.org/cgi-bin/carddisp.pl?gene=MYCN&keywords=MYCN
...
written 5 months ago by
EagleEye ♦ 6.6k
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... `Heatmap` function doesn't recognize the break values I mentioned using `min` and `max`.
> ht <- Heatmap( xm, col = colorRamp2(c(min(xm), 0, max(xm)), c("#6E6E6E", "white", "#31B404")), show_row_names = F, km = 2, column_names_gp = gpar(fontsize = 7), name="Tumors" )
> ht@matr ...
written 6 months ago by
EagleEye ♦ 6.6k
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... Dear ATpoint, thanks a lot for your suggestion. My problem is exactly opposite to the issue mentioned in the link you provided. I am not using default breaks, providing the breaks using `min` and `max` function. Above heatmap I provided is having symmetric legend scale, but my data does not have `mi ...
written 6 months ago by
EagleEye ♦ 6.6k
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... Sorry, I am not able to understand your suggestion. Can you please explain ? ...
written 6 months ago by
EagleEye ♦ 6.6k
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... Hi,
I am using `ComplexHeatmap` package for plotting. One strange thing I noticed is that, heatmap does not take maximum and minimum break values as specified using `max` and `min` functions from `R`.
**Code/commands used:**
> min(xm)
[1] -5.460918
> max(xm)
[1] 9.361317
...
0
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... How are the chromosomal locations of those repetitive gene symbols (same or different location) ?
And for your statement "I was wondering what is the best way to proceed", it is impossible to answer unless you explain what you like to do with those genes. ...
written 7 months ago by
EagleEye ♦ 6.6k
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