User: Jake Warner

gravatar for Jake Warner
Jake Warner670
Reputation:
670
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Trusted
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Website:
https://2-bitbio.com/
Twitter:
@ScientistJake
Last seen:
1 month, 1 week ago
Joined:
1 year, 8 months ago
Email:
w***********@gmail.com

Posts by Jake Warner

<prev • 98 results • page 1 of 10 • next >
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Answer: A: Is there any alternative for CD_Hit to remove redundancy from asemmbled trinity
... Getting 'unigenes' from Trinity assemblies is tricky business. I've found that [Corset][1] performs better than CD-Hit. Another idea is to BLAST all the transcripts and group them by reciprocal best blast hit. [1]: https://github.com/Oshlack/Corset/wiki ...
written 4 months ago by Jake Warner670
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Answer: A: local web BLAST server
... It doesn't email but I've found [sequence server][1] to be very useful as a local blast server. [I also wrote one][2] that runs on R-shiny to which you could easily add the mail tool from Sej Modha's comment. Just change the output to a txt and send that as the mail message. [1]: https://www ...
written 4 months ago by Jake Warner670
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Comment: C: WGCNA network with condition and normal samples
... Hi, You are correct, the genes which are regulated by the treatment will move as a group and show up as a module. But even if most of the genes move they wont move in the same *way* and you will detect multiple modules (I'm oversimplifying a bit here). A big factor is the number of samples overall ...
written 4 months ago by Jake Warner670
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Comment: C: Problem for understanding the number of modules in construction network based on
... Hi Modzari, This is more of an R problem and less of a WGCNA or RNAseq/array problem. What the code you pasted does, is import an annotation file which is a series of columns with gene name, probe name, genomic coordinates etc, and associate those annotations with the results of the correlation tes ...
written 4 months ago by Jake Warner670
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Answer: A: WGCNA network with condition and normal samples
... Hi, WGCNA is unsupervised in the network construction and phenotypic data is used for post hoc correlation tests. So in basic terms all the expression data is fed in at once and if a group of genes responds specifically to one treatment they should be detected as a module and correlate with the sa ...
written 4 months ago by Jake Warner670
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Answer: A: Problem for understanding the number of modules in construction network based on
... Hi, `blockwiseModules` stores the module assignments in `colors`. So to count the modules you can see how many levels are in the `colors` vector: my_network <- = blockwiseModules(datExpr, ...) module_assignments <- my_network$colors #count the modules nlevels(factor(m ...
written 5 months ago by Jake Warner670
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Answer: A: Clustering and extracting gene IDs with same expression profiles
... Hi, You could use your kMeans approach then score the individual genes by comparing them to the centroid. First get the centroids: # function to find centroid in cluster i clust.centroid = function(i, dat, clusters) { ind = (clusters == i) colMeans(dat[ind,]) } kClustc ...
written 8 months ago by Jake Warner670
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Comment: C: Sensitive (BLAST like) and fast alignment of millions of sequences against human
... [PLAST][1] does all the BLAST like programs (blastn, blastp,blastx etc) and in my testing is [Faster and more sensitive][2] than Diamond. [1]: https://plast.inria.fr [2]: http://www.2-bitbio.com/2017/07/blastx-is-too-slow-heres-some.html ...
written 9 months ago by Jake Warner670
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Answer: A: How do you extract data coordinates from PCA in R?
... From the comments it sounds like your autoplot is scaling the data. Using ggplot plots the proper PC1 and PC2 components should get the plot you want: library(ggplot2) scores = as.data.frame(pca.data$x) p <- ggplot(data = scores, aes(x = PC1, y = PC2)) + geom_point(size=2) ...
written 9 months ago by Jake Warner670
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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 11 months ago by Jake Warner670

Latest awards to Jake Warner

Scholar 4 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: 3D PCA issue
Supporter 10 months ago, voted at least 25 times.
Scholar 11 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 13 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 13 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 16 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: 3D PCA issue
Rising Star 17 months ago, created 50 posts within first three months of joining.
Scholar 18 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 20 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data

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