User: Jacob Warner

gravatar for Jacob Warner
Jacob Warner580
Reputation:
580
Status:
Trusted
Location:
Website:
https://2-bitbio.com/
Twitter:
@ScientistJake
Last seen:
7 hours ago
Joined:
12 months ago
Email:
w***********@gmail.com

Posts by Jacob Warner

<prev • 91 results • page 1 of 10 • next >
0
votes
2
answers
100
views
2
answers
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 10 days ago by Jacob Warner580
1
vote
2
answers
130
views
2
answers
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 12 days ago by Jacob Warner580
0
votes
1
answer
410
views
1
answers
Comment: C: RShiny interactive volcano plots
... Cheers. Since it's an answer now I cleaned it up a bit for the Googles. ...
written 9 weeks ago by Jacob Warner580
1
vote
1
answer
244
views
1
answers
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 9 weeks ago by Jacob Warner580
0
votes
1
answer
244
views
1
answers
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 9 weeks ago by Jacob Warner580
2
votes
1
answer
244
views
1
answers
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 9 weeks ago by Jacob Warner580
0
votes
1
answer
199
views
1
answers
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 10 weeks ago by Jacob Warner580
2
votes
1
answer
410
views
1
answers
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 10 weeks ago by Jacob Warner580
0
votes
1
answer
233
views
1
answers
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 10 weeks ago by Jacob Warner580
1
vote
1
answer
233
views
1
answers
Answer: A: trimming RNA-seq reads with adapter sequence?index? using trimmomatic
... Hello, I would recommend first running [fastqc][1] to first and check the over-represented sequences. The adapter contamination (and any other artifacts) should show up there. Then you can run trimmomatic tweaking the settings below: java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq ...
written 10 weeks ago by Jacob Warner580

Latest awards to Jacob Warner

Supporter 26 days ago, voted at least 25 times.
Scholar 9 weeks ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 4 months ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 4 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
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: 3D PCA issue
Rising Star 8 months ago, created 50 posts within first three months of joining.
Scholar 9 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 775 users visited in the last hour