User: priyankaraina10

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Posts by priyankaraina10

<prev • 9 results • page 1 of 1 • next >
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WGCNA threshold values
... Hi Everyone, I am using WGCNA for generating modules for my non-coding RNAseq data I doing a separate analysis for 13 different tissues. My question is what soft threshold value will be ideal and if I am using different threshold value for different tissues will it affect my overall analysis. My ...
rnaseq wgcna threshold clustering written 2 days ago by priyankaraina1010 • updated 2 days ago by Kevin Blighe33k
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5 follow
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Is Kallisto good for identifying non-coding RNA in a RNAseq data?
... Hi I generated a co-expression map using Kallisto for aligning reads. However, after completing my analysis, when I checked the gene_biotype for the gene list, I only found 3% non-coding RNA. I repeated the analysis with another data from (Skymap), I got similar results. My question is this normal ...
bioinformatics kallisto rna-seq allignment written 8 days ago by priyankaraina1010 • updated 8 days ago by kristoffer.vittingseerup1.0k
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Answer: A: Splitting each row of a correlation matrix into individual files
... awk '{print >> $1".txt"}' matrix.txt That will print each line into a file whose name is the 1st field of that line plus a (completely optional) .txt extension. If you don't want the gene name in the file, use: awk '{n=$1; $1="";print >> n".txt"}' matrix.txt And, if your first ...
written 13 days ago by priyankaraina1010 • updated 13 days ago by finswimmer7.9k
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Comment: C: Splitting each row of a correlation matrix into individual files
... IGHD2-15 IGHD3-22 IGHD3-16 IGHD3-10 IGHD2-15 1 0.696084 0.799736 0.818788 IGHD3-22 0.696084 1 0.691419 0.67505 IGHD3-16 0.799736 0.691419 1 0.810656 IGHD3-10 0.818788 0.67505 0.810656 1 ...
written 13 days ago by priyankaraina1010
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Comment: C: Splitting each row of a correlation matrix into individual files
... The pasted table format is not correct. it is a matrix ...
written 13 days ago by priyankaraina1010
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Splitting each row of a correlation matrix into individual files
... I have a correlation matrix of 22000 genes and for some analysis, I need to split each row of the matrix into a new file. Which means I need to create 22000 individual files. I don't want to use the split command (because I want to get the output file as the gene_name.txt) Input file (for 6 genes ...
gene unix split commands written 13 days ago by priyankaraina1010 • updated 13 days ago by finswimmer7.9k
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Comment: C: Correlation mutual rank calculation
... Thank you for getting back. Much appreciated. ...
written 27 days ago by priyankaraina1010
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Comment: C: Correlation mutual rank calculation
... Thank you for your suggestions. I am aware of the difference between R and R studio. My question was whether I can use a big file of 24GB in R studio (Desktop) Apologies for not being clear. Best Regards ...
written 27 days ago by priyankaraina1010
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Correlation mutual rank calculation
... Hi I have a correlation matrix for 34704 genes (size: 24GB). Is it possible to calculate the mutual rank of this file in R studio? # correlation rank matrix R <- t(apply(1-C, 1, rank)) # mutual rank matrix M <- sqrt(R * t(R)) ...
gene R correlation matrix written 28 days ago by priyankaraina1010 • updated 28 days ago by Jean-Karim Heriche17k

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