User: EagleEye

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EagleEye4.9k
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Investigating field of biology by applying logics of computer science, statistics and mathematics.

Posts by EagleEye

<prev • 805 results • page 1 of 81 • next >
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... HI, I have a list of 54000 gene-ids I want to annotate all the genes. Is there any other R package or command-line software that I can use? **Answer:** Make this as separate post/question on Biostars. You will get quick help. ...
written 5 hours ago by EagleEye4.9k
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Hi, In GeneSCF you can only use Gene Symbols ([Example][1]) or Entrez GeneIDs ([Example][2]) as input. And the reason for the error you mentioned is because your input gene list does not match with the database consists of only Gene symbols and Entrez IDs ([Check reported issue][3]). It is also cl ...
written 5 hours ago by EagleEye4.9k
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Hi, COMMAND-: ./prepare_database -db=GO -org=goa_human ERROR-: rm: cannot remove '/home/ibab/software/geneSCF-master-source-v1.1-p2/class/lib/db/gene_info_limit.gz': No such file or directory **Answer:** Do not worry about this error. When it is not found, GeneSCF can download the database. ERROR ...
written 6 hours ago by EagleEye4.9k
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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 3 days ago by EagleEye4.9k
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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 3 days ago by EagleEye4.9k
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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 8 days ago by EagleEye4.9k
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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 12 days ago by EagleEye4.9k
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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 15 days ago by EagleEye4.9k
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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 18 days ago by EagleEye4.9k
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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 25 days ago by EagleEye4.9k

Latest awards to EagleEye

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

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