User: EagleEye

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EagleEye5.0k
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https://www.researchga...
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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 • 812 results • page 2 of 82 • next >
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Comment: C: Network analysis software
... Sorry I forgot to attach this link in above reply, https://david.ncifcrf.gov/content.jsp?file=update.html ...
written 9 weeks ago by EagleEye5.0k
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Comment: C: Network analysis software
... Hi pablo61991, Please let me know where did you find that information (about update in end of 2017)? - All I can see is recent update on DAVID 6.8 is Oct 2016 (https://david.ncifcrf.gov/content.jsp?file=release.html) and if I look at individual knowledge-base it looks like KEGG version is from De ...
written 9 weeks ago by EagleEye5.0k
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Comment: C: Rpkm (R Code)
... Any number of samples will work. Just make sure you are including lengths in the last column. ...
written 10 weeks ago by EagleEye5.0k
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Comment: C: Rpkm (R Code)
... you need a column in the end with lengths for corresponding RNA. That's all you need as input to above code. ...
written 10 weeks ago by EagleEye5.0k
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Comment: C: GO Annotations from geneontology.org
... Hi, in 'gene ontology' which closest organism are you looking for ? You can use [organism code][1] (**3. Preparing database**) in GeneSCF to retrieve the terms and genes specific to an organism of interest. [1]: http://genescf.kandurilab.org/documentation.php ...
written 11 weeks ago by EagleEye5.0k
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Answer: A: GO Annotations from geneontology.org
... You can try [GeneSCF][1], Example: https://www.biostars.org/p/231384/#231579 [1]: https://www.biostars.org/p/108669/ ...
written 11 weeks ago by EagleEye5.0k
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Answer: A: List of all GO terms
... GeneSCF will be simple to extract all the terms and corresponding genes as plain text (table format). https://www.biostars.org/p/231384/#231579 ...
written 12 weeks ago by EagleEye5.0k
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Comment: C: GO analysis: DAVID vs GREAT vs GOrilla
... Try GeneSCF mentioned [above][1]. Apart from enrichment analysis, It can download all the genes associated with individual terms as table/plain text (using ‘prepare_database’ module). [1]: https://www.biostars.org/p/177998/#233616 ...
written 3 months ago by EagleEye5.0k
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Answer: A: Rpkm (R Code)
... P<-read.table("input_table.txt",sep="\t",header=T) len <- ncol(p) rownames(p) <- p[,1] for(i in 2:ncol(p)-1) { d <-p[,i] l <- p[,len] #accessing the length column cS <- sum(as.numeric(p[,i])) #Total mapped reads pe ...
written 3 months ago by EagleEye5.0k
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Comment: C: stringtie cannot recognize Gencode GTF
... Are you sure about the path used for Gencode/GTF annotation is specified correctly ? ...
written 3 months ago by EagleEye5.0k

Latest awards to EagleEye

Teacher 6 days ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Appreciated 4 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Appreciated 5 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Appreciated 7 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Epic Question 8 months ago, created a question with more than 10,000 views. For Gene Set Clustering based on Functional annotation (GeneSCF)
Scholar 8 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Scholar 9 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to look up GO terms in BioMart using GI ID or Accession ID
Scholar 9 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Scholar 9 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 9 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?
Appreciated 10 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?

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