User: vinayjrao
vinayjrao • 110
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Posts by vinayjrao
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... That's an extremely handy option. Thanks again :) ...
written 4 months ago by
vinayjrao • 110
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... Thanks. This works too. I could use the `.{2}` when I have larger repeats of any nucleotide/amino acid. Although, I would like to know why it `[\1G]` and not `[ATG]`? ...
written 4 months ago by
vinayjrao • 110
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... Thanks a lot. It's perfect. ...
written 4 months ago by
vinayjrao • 110
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... Hello,
I've been trying to write a code to find a consensus motif in a given sequence, and for this purpose, I was only able to reach till finding a substring in a string. I want to be able to allot multiple nucleotides/amino acids at each position, and also enter N/X representing any of the nucleo ...
written 4 months ago by
vinayjrao • 110
• updated
4 months ago by
Carlo Yague • 4.3k
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... I'm sorry for the incomplete information, I used the GSEA tool published by Broad Institute. The organism was human, and I was specifically looking into the HR Defect signature as described by Peng et al. The aim is study the enrichment of the geneset after tumor induction.
I used the h.all referen ...
written 4 months ago by
vinayjrao • 110
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... It's actually only 10 genes represented in the barcode plot, but yes they belong to 10 different genesets.
I'm sorry for the incomplete information, I used the GSEA tool published by Broad Institute. The organism was human, and I was specifically looking into the HR Defect signature as described by ...
written 4 months ago by
vinayjrao • 110
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... Hello,
I am performing GSEA to study the enrichment of a particular geneset upon tumor induction. I have run the analysis using default parameters and the barcode plot generated only shows 10 significant genes enriched out of 215.
I want to know if it could imply biological significance, or have I ...
written 4 months ago by
vinayjrao • 110
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... Ankit,
If you want to study the effects of the mutation at the protein level, you could translate and perform a BLAST. If sequences aren't reported, those would be novel variants. ...
written 5 months ago by
vinayjrao • 110
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... Ankit,
At what level do you want to understand the effect of the mutations? If it's at the protein level, you could simply translate your sequences and perform a BLAST. In cases where you get a high query cover and identity would carry mutations in regions other than the splice sites. In case of sp ...
written 5 months ago by
vinayjrao • 110
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... If you have a set of canonical splice variants of each gene, then you could separate out only the non-canonical variants and look for the mutations. Once you find the mutations, you could check if the variant and its effects have been reported. ...
written 5 months ago by
vinayjrao • 110
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