Moderator: EagleEye

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EagleEye6.6k
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https://decodebiology....
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gridhrahakshi
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Investigating field of biology by applying logics of computer science, statistics and mathematics.

Posts by EagleEye

<prev • 945 results • page 1 of 95 • next >
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Answer: A: Whats best practice for Gene set enrichment analysis?
... Have a look at this simple tool which works with most updated database, https://www.biostars.org/p/108669/ ...
written 4 weeks ago by EagleEye6.6k
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Comment: C: Tools To Find Gene Ontology Term Enrichment
... 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 EagleEye6.6k
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Comment: C: GO terms associated to a list of genes
... 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 EagleEye6.6k
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Comment: C: Analyzing LogRPKM Counts Data for finding DEGs(Differential Expressed Genes)
... 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 EagleEye6.6k
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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 EagleEye6.6k
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Comment: C: ComplexHeatmap break values appear different in the plots
... `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 EagleEye6.6k
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Comment: C: ComplexHeatmap break values appear different in the plots
... 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 EagleEye6.6k
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Comment: C: ComplexHeatmap break values appear different in the plots
... Sorry, I am not able to understand your suggestion. Can you please explain ? ...
written 6 months ago by EagleEye6.6k
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ComplexHeatmap break values appear different in the plots
... 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 ...
complexheatmap written 6 months ago by EagleEye6.6k • updated 6 months ago by ATpoint31k
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Comment: C: Duplicated genes symbol from supplementary information paper
... 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 EagleEye6.6k

Latest awards to EagleEye

Scholar 3 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Appreciated 10 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Scholar 10 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Scholar 11 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Survey: What colour theme do you use in your terminal?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Survey: What colour theme do you use in your terminal?
Appreciated 16 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Appreciated 16 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Scholar 16 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Scholar 21 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Scholar 21 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?

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