User: priyankaraina10

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Posts by priyankaraina10

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Comment: C: Transcription factor targets for Human and Mouse genes
... Thank you for getting back ...
written 18 days ago by priyankaraina1010
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Transcription factor targets for Human and Mouse genes
... Dear All, I want to get transcription factor targets for my list of genes (For Human and Mouse) I have found ENCODE Transcription Factor Targets database (The link is given below). But I am looking for some other databases also if available. I will really appreciate if anyone can suggest any other ...
gene genome transcription factors written 19 days ago by priyankaraina1010 • updated 19 days ago by ATpoint18k
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(Closed) Error in as.vector(x) : no method for coercing this S4 class to a vector
... I tried to run the following code in R studio. Everything worked fine, except at the last step [write.table(mdat, "recount_mdat.csv")] when I tried to export the 'mdat', I got the following error: Error in as.vector(x) : no method for coercing this S4 class to a vector My code library(' ...
metadata r-studio rna-seq written 4 months ago by priyankaraina1010 • updated 4 months ago by benformatics890
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RNA-seq gene/transcript read counts database for Mouse
... Hi Is there any RNAseq gene/transcript read count database for the mouse? I already know about ARCHS4, looking for some other source. Thank you ...
data mining read count rna-seq written 4 months ago by priyankaraina1010
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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 6 months ago by priyankaraina1010 • updated 6 months ago by Kevin Blighe44k
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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 6 months ago by priyankaraina1010 • updated 6 months ago by kristoffer.vittingseerup1.9k
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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 6 months ago by priyankaraina1010 • updated 6 months ago by finswimmer11k
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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 6 months 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 6 months 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 6 months ago by priyankaraina1010 • updated 6 months ago by finswimmer11k

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Popular Question 11 weeks ago, created a question with more than 1,000 views. For Error in as.vector(x) : no method for coercing this S4 class to a vector

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