User: EagleEye

gravatar for EagleEye
EagleEye5.3k
Reputation:
5,330
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Location:
Sweden
Website:
https://www.researchga...
Twitter:
gridhrahakshi
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Last seen:
46 minutes ago
Joined:
3 years, 10 months ago
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Investigating field of biology by applying logics of computer science, statistics and mathematics.

Posts by EagleEye

<prev • 834 results • page 1 of 84 • next >
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Answer: A: Venue to publish a bioinformatics tool
... Here are few journals to consider, - BMC Bioinformatics - PLOS Computational Biology - GigaScience - Nucleic Acids Research - Genome Biology (Software) ...
written 3 hours ago by EagleEye5.3k
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Answer: A: Pathway enrichment analysis of gene set
... With [GeneSCF][1] batch run, you can try all those database with single run. Selecting the database depends on your experiment or study or interest. KEGG always gives you broad perspective of pathway terms (metabolism, gene regulation, cellular processes, disease and signaling pathways). In Gene ...
written 3 days ago by EagleEye5.3k
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Comment: C: DGE analysis using stranded and unstranded RNA-seq libraries.
... Hi, My point was, there are evidence for both positive and negative correlation with good publications. So there is no general rule that sense and antisense are globally anti-correlated or positively correlated. There are many factors contributing to that (some times it is species dependent too). ...
written 5 days ago by EagleEye5.3k
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Comment: C: DGE analysis using stranded and unstranded RNA-seq libraries.
... Hi, I do not think these statements are true "since antisense transcripts usually have opposite expression dynamics than their sense counterparts" and "in a condition, if a gene is overexpressed, there is a good chance that its antisense will be underexpressed". If you are talking about natural anti ...
written 6 days ago by EagleEye5.3k
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Comment: C: duplicate 'row.names' are not allowed
... Because your rownames (First row) are same and you asked R to read the file by considering first row as rownames (row.names=1). Because of indexing issue R cannot take same name for multiple rows. In your case it looks like your fourth column seems to be non-repetitive. You can consider using row.n ...
written 10 days ago by EagleEye5.3k
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Comment: C: duplicate 'row.names' are not allowed
... Report the R function you used to read your file. Also provide exact error message. ...
written 10 days ago by EagleEye5.3k
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Hi **KEGG**: http://rest.kegg.jp/list/organism **Gene Ontology**: http://www.geneontology.org/gene-associations/go_annotation_metadata.all.json **Reactome & NCG**: Human only You can also find this information on [GeneSCF documentation][1] under heading '**3. Preparing database**'. Also the ...
written 10 days ago by EagleEye5.3k
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Answer: A: Filtering of lncRNAs and mRNAs for Differential expression analysis from RNA-seq
... This post will give you some idea, https://www.biostars.org/p/207680/#207685 I would recommend you to perform DE analysis separately (since protein coding expression might create biasness due to its abundance). ...
written 11 days ago by EagleEye5.3k
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Answer: C: deepTools plot profile problem
... What happens If you provide this parameter just with SPACE in double quotes for plotProfile, --regionsLabel " " ...
written 11 days ago by EagleEye5.3k
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Comment: C: extract isoform sequences of splicing variants?
... From where did you get this name "r.4357_4358ins4358-2785_4358-2719" ? source !!! ...
written 12 days ago by EagleEye5.3k

Latest awards to EagleEye

Teacher 5 days ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Appreciated 9 days ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Commentator 10 days ago, created a comment with at least 3 up-votes. For C: Survey: What colour theme do you use in your terminal?
Scholar 11 days ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Scholar 17 days ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Appreciated 6 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Appreciated 7 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Appreciated 9 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Epic Question 10 months ago, created a question with more than 10,000 views. For Gene Set Clustering based on Functional annotation (GeneSCF)
Scholar 10 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Scholar 11 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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