Moderator: EagleEye

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EagleEye5.8k
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Sweden
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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 • 887 results • page 2 of 89 • next >
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Answer: A: Extract a chromosome from a WIG file
... Try IGV '[toTDF][1]' to convert your 'WIG' files into binary tiled data (TDF). This loads into IGV lot faster than 'WIG' files. [1]: https://software.broadinstitute.org/software/igv/igvtools_commandline ...
written 28 days ago by EagleEye5.8k
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Answer: A: how to find out which cellular pathways a gene belongs to?
... https://www.biostars.org/p/108669/ ...
written 4 weeks ago by EagleEye5.8k
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Answer: A: Is it possible to analyze differentially expressed genes without sample replicat
... If you like to use only logFC as cut-off (without replicates), have a look at [GFOLD][1]. [1]: https://bitbucket.org/feeldead/gfold/wiki/Home ...
written 4 weeks ago by EagleEye5.8k
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Answer: A: Is there any way to create graphics of the Go enrichment, if I already have my G
... Have a look at [ReviGO][1] in case you already have ranked GO terms. [1]: http://revigo.irb.hr/ ...
written 6 weeks ago by EagleEye5.8k
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Answer: A: Gene ontology analysis
... Hello, If you think presenting those pathways make sense for your study, you can relax the criteria. **Example:** 1) You can use p-value instead of FDR/Benjamini 2) Even then if you don't get, you can also go upto p-value < 0.1 (10%) 3) Otherwise, you might be using very stringent criteria d ...
written 7 weeks ago by EagleEye5.8k
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Comment: C: How do you convert featureCounts output into composition of mapped reads by RNA
... Consider this matrix as 'featurecounts.matrix' in the below example. Follow other steps I mentioned. ...
written 9 weeks ago by EagleEye5.8k
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Comment: C: Mapsplice 2 error
... Please report your recent command used and also the error log. ...
written 10 weeks ago by EagleEye5.8k
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Comment: C: GSEA analysis and pathway mapping
... https://www.biostars.org/p/108669/ ...
written 10 weeks ago by EagleEye5.8k
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Comment: C: How do you convert featureCounts output into composition of mapped reads by RNA
... You mean you got matrix like this, Geneid Ctrl Treated ENSG00000223972 0 0 ENSG00000227232 0 0 ENSG00000278267 0 0 ...
written 10 weeks ago by EagleEye5.8k
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Answer: A: How do you convert featureCounts output into composition of mapped reads by RNA
... If in case you used GTF file as reference annotation, 1) You can just convert the annotation into table format. Example: https://www.biostars.org/p/208102/#212022 2) Import you GTF converted table (`Geneid GeneSymbol Chromosome Start End Class Strand Length`) and your matrix from featurecounts (` ...
written 10 weeks ago by EagleEye5.8k

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Teacher 6 weeks 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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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 4 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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