Moderator: EagleEye

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EagleEye6.2k
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https://decodebiology....
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Investigating field of biology by applying logics of computer science, statistics and mathematics.

Posts by EagleEye

<prev • 914 results • page 1 of 92 • next >
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Comment: C: can lnc-RNA target coding RNA?
... You must investigate all the transcript isoforms individually using triplexator. ...
written 10 days ago by EagleEye6.2k
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Comment: C: can lnc-RNA target coding RNA?
... What do you mean by "all transcript sequences" ? Are you referring to different isoforms ? ...
written 10 days ago by EagleEye6.2k
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Answer: A: DE and enrichment analysis pipeline
... Have a look at [VIPER][1] (I have not used it personally but it looks interesting). [1]: https://bitbucket.org/cfce/viper/overview ...
written 14 days ago by EagleEye6.2k
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Comment: C: How to separate lncRNA and mRNA from RNA-Seq data for differential expression?
... Please explain how you performed the analysis? Alignment -> quantification (which annotation) -> Differential expression (which tool) ? And what kind of file you have now (paste sample output)? When you provide more information, you get more specific response. ...
written 21 days ago by EagleEye6.2k
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Comment: C: can lnc-RNA target coding RNA?
... Sorry for late response, I forgot to reply. Yes, compete sequence from MEG3 was used for the prediction. You can get DNA FASTA sequence of any lncRNA from GENCODE, "Fasta files" section from this [link][1]. Also UCSC and ENSEMBL can be an option to extract DNA FASTA sequences. [1]: https://www. ...
written 27 days ago by EagleEye6.2k
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Comment: C: how to install Juicer hi-c
... Ideally it should not be a problem but try this, Edit the script '/home/app/Desktop/apps/Juicer/CPU/juicer.sh' juiceDir="/opt/juicer" change to juiceDir="/home/app/Desktop/apps/Juicer/" ...
written 4 weeks ago by EagleEye6.2k
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Answer: A: how to install Juicer hi-c
... Hi, I followed these steps to use hg38 restriction sites in juicer, **Step 1) Use 'findRestrictionSites.pl' from [HiCUP][1] pipeline.** **Edit** my $chr_file = "/proj/uppstore2018034/santhilal/bin/juicer/Homo_sapiens.GRCh38.dna.chromosome.$chromosome".".fa.gz"; system("wget ftp:// ...
written 4 weeks ago by EagleEye6.2k
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Comment: C: gene ontology analysis based on transcript biotype
... I would recommend you to perform DE analysis separately (since protein coding expression might create biasness due to its abundance). **Some database examples:** **LncRNA Ontology** http://www.bio-bigdata.com/lncrnaontology/ **LncRNA2Function** mlg.hit.edu.cn/lncrna2function/ (not working, may ...
written 4 weeks ago by EagleEye6.2k
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Answer: A: gene ontology analysis based on transcript biotype
... Most of the gene ontology database or repositories or tools only cover protein_coding biotypes. I would recommend you to separate the protein coding genes from your analysis and perform gene enrichment analysis only for those. Though there are some specialized database annotate gene ontology or func ...
written 4 weeks ago by EagleEye6.2k
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Hi, please check with p-values in both case or use the same criteria (p-value or FDR etc.,). I do not know how DAVID processes the annotation and handle the database. Also check how many number of genes each tool could match for individual terms. You can also verify GeneSCF results with some other t ...
written 5 weeks ago by EagleEye6.2k

Latest awards to EagleEye

Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: Survey: What colour theme do you use in your terminal?
Appreciated 3 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Good Answer 3 months 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?
Scholar 3 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 5 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 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?
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 ?
Appreciated 7 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?
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 8 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?
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Survey: What colour theme do you use in your terminal?
Scholar 8 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 8 months ago, created an answer with at least 3 up-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: How to check the type of identifier from ensembl?

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