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Recent Replies
Comment: including samples for which group is unknown to help adjust for another variable
by
pilargmarch
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80
So, if I understand correctly, you're suggesting that I identify which principal components can separate the tested patients well into thei…
Comment: ggsave() bug in ggplot2?
by
Trivas
★
1.1k
Is it possible this is because you're saving it as a .jpg? Do you still get this error if you save as a .png?
Answer: what is the difference between FindVariableFeatures and FindAllMarkers?
by
rpolicastro
12k
There isn't an expectation for the lists to match up completely. You could for instance have a gene with low absolute variance across the d…
Comment: My kernel is killing the pairtools dedup script, how to prevent that?
by
NikhilP
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20
The problem is this script takes around 3hrs to process and after that the kernel kills it. When i first ran this command that time i check…
Answer: Understanding Used Assembly: Why aren't authors specific about patch version?
by
Jeremy Leipzig
21k
> "The fact that patch-version does matter for looking up variants at an exact position"
This in incorrect. A freeze is a freeze. No one a…
Comment: Impute haplotypes (ImputePipelinePlugin) execution error - PHG
by
jrodrigu
•
0
First, thanks for the quick replay. So, answering your questions.
(1) PHG version 1.4
(2) There are 37 nodes and 9 of reference ranges. How…
Comment: The inchworm process failed. Trinity running error.
by
GenoMax
129k
This likely is the issue.
> You'll need to either reduce the size of your data set or run Trinity
> on a server with more memory available…
Answer: including samples for which group is unknown to help adjust for another variable
by
Vincent Laufer
★
2.9k
In addition to the stratified analysis above, which you might consider framing as a LRT through DESeq2, another approach is to conduct a pr…
Comment: including samples for which group is unknown to help adjust for another variable
by
Vincent Laufer
★
2.9k
one gets that message from time to time in reasonably powered datasets.
ill write out a second approach right quick
Comment: including samples for which group is unknown to help adjust for another variable
by
pilargmarch
▴
80
Thank you for your response! I didn't think of doing the stratified analysis because of the small sample sizes, but it is worth trying. Com…
Comment: ggsave() bug in ggplot2?
by
Medeea
•
0
sorry, I was actually thinking that maybe you meant this
$ file Figure1.jpg
Figure1.jpg: JPEG image data, baseline, precision 8, 2500x150…
Comment: Single Cell Rna Seq Using BD Rhapsody
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GenoMax
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Good to know. I was unaware that `kb` can understand BD data. I was under the impression that one needed to use BD software for the initial…
Answer: Data is not displaying in DATABASE......error is not showing in IDE
by
Dr William Klubinski
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30
It seems error might be due to a problem with the way u construct SQL query. the $sql variable isn't being assigned a value in some scenari…
Comment: how to run FacetsSuite wrapper scripts on command line
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GenoMax
129k
Unfortunately the vignette is not very clear. It appears that you need to compile a program called `snp-pileup` and have it available in th…
Answer: how to sort a fasta file
by
Dr William Klubinski
▴
30
Using Python:
This code reads your FASTA file, stores the entries in a dictionary and writes them back to a new FASTA file in a sorted o…
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