User: Ready2Rapture

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Posts by Ready2Rapture

<prev • 7 results • page 1 of 1 • next >
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Comment: C: deepTools/Galaxy Optimize K-Means Clusters - Elbow Plot
... This worked well, thank you Devon. ...
written 3 months ago by Ready2Rapture20
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deepTools/Galaxy Optimize K-Means Clusters - Elbow Plot
... Hello, I'm trying to optimize my deeptools computeMatrix output for k-means clustering, but cannot properly generate an elbow plot. I've tried loading the matrix as [described in this post][1] and then attempting to plot wss in R via: m = read.delim("computeMatrixOperations.mat.gz", skip=1, h ...
deeptools galaxy chip-seq sequencing written 3 months ago by Ready2Rapture20 • updated 3 months ago by Mensur Dlakic4.2k
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Comment: C: bulk-RNAseq Endogenous retrovirus (ERV) Analysis for mouse
... This is basically it. I wanted to see if there were any alternatives to gEVE. Thanks! ...
written 5 months ago by Ready2Rapture20
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bulk-RNAseq Endogenous retrovirus (ERV) Analysis for mouse
... Hi all, I'm looking to analyze mouse ERVs from bulk-RNAseq but have mostly found data resources and pipelines for human ([ERVmap][1], [HERVd][2]). I've also found a mouse [ERE database][3] that appears to no longer be supported. The only reasonable resource I've found for mouse ERVs is [gEVE][4] ...
genome rna-seq written 5 months ago by Ready2Rapture20 • updated 5 months ago by Amar640
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Comment: C: Geometric Mean of Two Genes in Expression Matrix
... Thank you Akhil, this makes sense. The the paper they uses Transcripts per Million (TPM) count from RNA-seq in calculating the score. The data I'm looking at is a normalized Affy microarray experiment, but I can get the relative signal intensity as well. I am skeptical, however, of using this mea ...
written 2.4 years ago by Ready2Rapture20
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Geometric Mean of Two Genes in Expression Matrix
... Hello, This is probably a very simple question. I am currently working on an expression matrix to replicate a "cytolytic score" in R.[1] The cytolytic score is defined as "geometric mean of GZMA and PRF1". My goal is to then investigate the Pearson's correlation of this score with other genes of ...
R rna microarray rna-seq written 2.4 years ago by Ready2Rapture20 • updated 2.4 years ago by Ahill1.8k
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Maestro (Schrodinger Software), Protein Data Bank,
... Hi all, I am new to Maestro and have not done structural biology in quite a bit. I am examining protein structures and trying to find ways to determine properties of proteins I look at from PBD (protein data bank).  Please let me know if this topic is not covered in this forum and if there is a bet ...
structural bioinformatics pdb maestro written 4.2 years ago by Ready2Rapture20 • updated 4.0 years ago by Biostar ♦♦ 20

Latest awards to Ready2Rapture

Popular Question 2.3 years ago, created a question with more than 1,000 views. For Maestro (Schrodinger Software), Protein Data Bank,
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Geometric Mean of Two Genes in Expression Matrix

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