Moderator: EagleEye
EagleEye ♦ 6.5k
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- Website:
- https://decodebiology....
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- gridhrahakshi
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- Joined:
- 5 years, 2 months ago
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Investigating field of biology by applying logics of computer science, statistics and mathematics.
Posts by EagleEye
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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 6 days ago by
EagleEye ♦ 6.5k
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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 6 days ago by
EagleEye ♦ 6.5k
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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 4 weeks ago by
EagleEye ♦ 6.5k
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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 4 weeks ago by
EagleEye ♦ 6.5k
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... Sorry, I am not able to understand your suggestion. Can you please explain ? ...
written 4 weeks ago by
EagleEye ♦ 6.5k
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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
...
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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 8 weeks ago by
EagleEye ♦ 6.5k
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... If you have list of gene symbols, use this simple tool and has detailed instructions https://www.biostars.org/p/108669/ ...
written 9 weeks ago by
EagleEye ♦ 6.5k
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Answer:
A: GO enrichment tools
... Check out https://www.biostars.org/p/108669/ ...
written 10 weeks ago by
EagleEye ♦ 6.5k
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Answer:
A: Sample Mouse RNA-Seq Dataset
... Here you go,
**An RNASeq normal tissue atlas for mouse and rat**
**Deposit:** https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6081/
**Raw files:** https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6081/samples/ ...
written 3 months ago by
EagleEye ♦ 6.5k
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7 days ago,
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For A: Something better than GSEA?
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For A: How to check the type of identifier from ensembl?
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For A: How to interpret the result of GO analysis using Ontologizer ?
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For C: Survey: What colour theme do you use in your terminal?
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For New article on TCGA data & useful resource: Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers
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For New article on TCGA data & useful resource: Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers
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For New article on TCGA data & useful resource: Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers
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11 months ago,
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For A: How to interpret the result of GO analysis using Ontologizer ?
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15 months ago,
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15 months ago,
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For A: How to interpret the result of GO analysis using Ontologizer ?
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For A: How to check the type of identifier from ensembl?
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For A: How to check the type of identifier from ensembl?
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15 months ago,
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For A: How to interpret the result of GO analysis using Ontologizer ?
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