User: Corentin

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Corentin50
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Posts by Corentin

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Comment: C: Help! How to plot RNASeq data in PCA
... As an alternative to PCA you can also try MDS plots : https://www.rdocumentation.org/packages/edgeR/versions/3.14.0/topics/plotMDS.DGEList but it should give similar results ...
written 5 days ago by Corentin50
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Answer: A: expression to networking
... If you have access to the enzyme annotations for your genes, you can use the KEGG API which can link enzymes to kegg pathways (http://www.kegg.jp/kegg/rest/keggapi.html). You can use R (or your favorite language) to access the API. The file to link enzymes and pathways is available here : http://re ...
written 5 weeks ago by Corentin50
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Answer: A: CNV detection techniques, algorithms, applications ...
... Hi, There are already a few tools out there for CNV detection: [https://omictools.com/cnv-detection2-category][1] . They are often specialised in Exome sequence data. You can take a look at how they work. Their implementation is described in the associated paper (when there is one). I know that ...
written 5 months ago by Corentin50
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Comment: C: RSEM: identical expression for different cufflinks transcripts
... Thank you for your answer, I had a look with IGV and these transcripts are indeed overlapping isoforms (they are almost the same). ...
written 5 months ago by Corentin50
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RSEM: identical expression for different cufflinks transcripts
... Hi, I ran the tuxedo pipeline on rna seq data. And I used RSEM/limma for the differential expression analysis. I noticed something peculiar in the counts matrix from RSEM, some transcripts have exactly the same expression level for all the samples: "TCONS_00086761" 46.23 46.23 61.4 ...
cufflinks rna-seq expression written 5 months ago by Corentin50

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Scholar 5 weeks ago, created an answer that has been accepted. For A: expression to networking
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: expression to networking

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