User: Jacob Warner

gravatar for Jacob Warner
Jacob Warner590
Reputation:
590
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Trusted
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Website:
https://2-bitbio.com/
Twitter:
@ScientistJake
Last seen:
2 months, 1 week ago
Joined:
1 year, 3 months ago
Email:
w***********@gmail.com

Posts by Jacob Warner

<prev • 92 results • page 1 of 10 • next >
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Answer: A: Clustering and extracting gene IDs with same expression profiles
... Hi, You could use your kMeans approach then score the individual genes by comparing them to the centroid. First get the centroids: # function to find centroid in cluster i clust.centroid = function(i, dat, clusters) { ind = (clusters == i) colMeans(dat[ind,]) } kClustc ...
written 11 weeks ago by Jacob Warner590
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Comment: C: Sensitive (BLAST like) and fast alignment of millions of sequences against human
... [PLAST][1] does all the BLAST like programs (blastn, blastp,blastx etc) and in my testing is [Faster and more sensitive][2] than Diamond. [1]: https://plast.inria.fr [2]: http://www.2-bitbio.com/2017/07/blastx-is-too-slow-heres-some.html ...
written 3 months ago by Jacob Warner590
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Answer: A: How do you extract data coordinates from PCA in R?
... From the comments it sounds like your autoplot is scaling the data. Using ggplot plots the proper PC1 and PC2 components should get the plot you want: library(ggplot2) scores = as.data.frame(pca.data$x) p <- ggplot(data = scores, aes(x = PC1, y = PC2)) + geom_point(size=2) ...
written 3 months ago by Jacob Warner590
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Comment: C: RShiny interactive volcano plots
... Cheers. Since it's an answer now I cleaned it up a bit for the Googles. ...
written 5 months ago by Jacob Warner590
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Comment: C: RNA-seq Co-expression network construction from the output of DESeq2
... Yes I filter lowly expressed features. The developers of WGCNA recommend as well: > Probesets or genes may be filtered by mean expression or variance (or > their robust analogs such as median and median absolute deviation, > MAD) since low-expressed or non-varying genes usually represent ...
written 5 months ago by Jacob Warner590
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Comment: C: RNA-seq Co-expression network construction from the output of DESeq2
... No problem, try it a few ways. I found little difference between log2(x+1), rlog and varianceStabilizingTransformation when it came to the most highly connected genes. ...
written 5 months ago by Jacob Warner590
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Answer: A: RNA-seq Co-expression network construction from the output of DESeq2
... Hi! [Point 4 in the WGCNA FAQ][1] addresses this: > We then recommend a variance-stabilizing transformation. For example, > package DESeq2 implements the function > varianceStabilizingTransformation which we have found useful, but one > could also start with normalized counts (or RPKM ...
written 5 months ago by Jacob Warner590
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Comment: C: How do you find similar gene expression pattern to your GOI?
... Maybe you could cluster the data, then find which cluster your GOI is in. The other cluster members should have a similar profiles. A more complex way is to generate clusters using your input genes as initialization centroids. Although maybe somebody could give some insight because I have no exp ...
written 5 months ago by Jacob Warner590
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Answer: C: RShiny interactive volcano plots
... Assuming the rest of the app works you can use the `selectInput()` to change the data. It looks like the DE test is loaded at the `read.table` call? If that's true you can do: ui <- ## your code before ... selectInput(inputId= 'DEtest', label='Pick a timepoint!', choices = c("3" ...
written 5 months ago by Jacob Warner590
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Comment: C: trimming RNA-seq reads with adapter sequence?index? using trimmomatic
... I'm pretty sure the standard TruSeq3 adapter file will work, but to be sure you can look up your adapters [here][1] (page 18) and add them to a fasta file. I would include the universal and index adapter. [1]: https://support.illumina.com/content/dam/illumina-support/documents/documentation/che ...
written 5 months ago by Jacob Warner590

Latest awards to Jacob Warner

Supporter 4 months ago, voted at least 25 times.
Scholar 5 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 7 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 8 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 10 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: 3D PCA issue
Rising Star 11 months ago, created 50 posts within first three months of joining.
Scholar 13 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 14 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data

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