User: The

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The160
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Posts by The

<prev • 59 results • page 1 of 6 • next >
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Answer: A: Help improve search paper skill.
... https://pubmed.ncbi.nlm.nih.gov/23875961/ ...
written 28 days ago by The160
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Answer: A: Extracting features or gene from PCA after calculating PCA for downstream analys
... https://stats.stackexchange.com/questions/115032/how-to-find-which-variables-are-most-correlated-with-the-first-principal-compone ...
written 3 months ago by The160
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Tutorials on linear models, mixed models, hierarchical models etc. for gene/protein expression
... Hello All, I'm looking for some tutorials on application of linear models , mixed models, hierarchical models etc. on gene or protein expression studies. Particularly how to use these statistical models to find out deferentially expressed genes and proteins. I'm looking for simple worked out exa ...
tutorial linear model written 5 months ago by The160 • updated 5 months ago by cokij551250
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How to plot a circular clustered heatmap with dendrogram
... Hello, I'm trying to plot a single circular clustered heatmap with dendrogram. The two column expression data is available from this [pastebin link][1] I was trying to play the the R package "[circlize][2]" , but couldn't make any progress so far. I wish to plot something similar, but only a sin ...
circular heatmap written 8 months ago by The160
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Dendrogram line width in heatmap.2
... Hi, Is there anyway to control the dendrogram line thickness in heatmap.2() function? This is how one can do that in pheatmap(). I'm looking for something similar in heatmap.2 [pheatmp dendrogram line width control ][1] [1]: https://stackoverflow.com/questions/50469883/change-line-width-of-de ...
R dendrogram lwd heatmap.2 heatmap written 10 months ago by The160
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Answer: A: Transform log2 fold changes in z-scores
... What I believe there is not sufficient 'scatter' in the plot. In your case the p-value is usually better(lower) with increase in absolute(fold change) almost monotonically . That might have to do something with the calculation of p-value in Rank Product analysis( do they still calculate it by ran ...
written 11 months ago by The160
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Answer: A: Extracting important gene with similar expression level from multiple samples
... How about selecting genes with least variance across samples? Otherwise some clustering will give you genes with similar expressions ...
written 11 months ago by The160
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Answer: A: Secondary Structure Alignment Method
... If I correctly remember , there was a paper in PNAS by George D Rose in late 90s which dealt with this. The goal was to find out structurally similar sequences based on predicted secondary structure. So far I remember they employed a simple scoring system (match/mismatch binary type): ![enter imag ...
written 11 months ago by The160
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Comment: C: How to "linearize" or "unfold" a PDB format structure to secondary structure?
... yes, as Michael wants to preserve the well defined secondary structure elements ...
written 11 months ago by The160
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Answer: A: How to "linearize" or "unfold" a PDB format structure to secondary structure?
... Can this help, with default values? I guess it outputs the model in PDB format as well "We set the default for the backbone dihedral angles to the extended conformation (ϕ = −120∘, ψ = 140∘, ω = 180∘)." [PeptideBuilder: A simple Python library to generate model peptides][1] [Github repository][2] ...
written 11 months ago by The160

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Popular Question 9 months ago, created a question with more than 1,000 views. For Distance between two gene sets
Popular Question 15 months ago, created a question with more than 1,000 views. For Distance between two gene sets
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Epic Question 2.5 years ago, created a question with more than 10,000 views. For R: Scaling the rows of a matrix
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Distance between two gene sets
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Great Question 3.7 years ago, created a question with more than 5,000 views. For R: Scaling the rows of a matrix
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Popular Question 4.9 years ago, created a question with more than 1,000 views. For Fisher'S Exact Test For Gene Rank Enrichment
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Using Perl Text::Wrap For Wrapping Text
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Scholar 5.4 years ago, created an answer that has been accepted. For A: Mapping multiple expression data on KEGG genes and metabolites

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