User: sandeep.amberkar18

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Posts by sandeep.amberkar18

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Comment: C: Different filters for wheat in biomaRt package and website
... Thanks a lot Emily, I'll try it out! ...
written 6 weeks ago by sandeep.amberkar1810
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Different filters for wheat in biomaRt package and website
... Hello, I'm looking to download the Wheat TILLING & SNP data from Ensembl from the biomaRt package in Bioconductor. However, I've noticed that the filters available in biomart website are more than what you have in the Bioconductor package. For e.g. plantsDatabase <- useMart(biomart = 'p ...
ensembl biomart getbm written 7 weeks ago by sandeep.amberkar1810 • updated 7 weeks ago by Mike Smith1.1k
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Answer: A: How to choose the threshold of co-expression for gene expression networks
... Broadly what is it that you wish to achieve? There is no explanation for choosing a cutoff, be it of correlation or p-value. However for Spearman correlation there have been widely accepted ranges 1. Low correlation = 0.2 ~ 0.4 2. Med correlation = 0.4 ~ 0.6 3. High correlation = 0.7 ~ 0.9 Per ...
written 12 months ago by sandeep.amberkar1810
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Answer: A: Ensembl id to GeneSymbol with biomart
... More often there are many to many relationships between Ensembl ids and HGNC symbols, which is why it is very tedious to obtain exact gene symbols. It is better to use the mapIds function in org.Hs.eg.db to have those relations. I wrote a nifty function to identify these 1:1 mappings. It returns a l ...
written 19 months ago by sandeep.amberkar1810

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