User: rpolicastro
rpolicastro • 2.0k
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Posts by rpolicastro
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Answer:
A: CUT&RUN analysis pipeline
... You don't need to do anything too special. Trim adapters with your favorite software, align to genome using BWA-MEM or bowtie2, and call peaks using MACS2.
Most of the fancy stuff with CUT&RUN is when you have paired end data. With paired end data you get information on insert/fragment size, wh ...
written 2 days ago by
rpolicastro • 2.0k
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... I definitely agree on that point. Tidyverse isn't faster than base R or data.table for most things since it's designed more so for convenience. I definitely recommend people to get comfortable with base R before learning tidyverse. ...
written 3 days ago by
rpolicastro • 2.0k
1
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42
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... The figure legend lists the tests used. It says t-test was used for age. ...
written 3 days ago by
rpolicastro • 2.0k
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... You should post this as an answer, since it uses array reshaping it would be the fastest. ...
written 3 days ago by
rpolicastro • 2.0k
0
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3
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94
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3
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... I figured I would post a tidyverse solution since they asked for one, but indeed base R and data.table allows for much faster solutions. ...
written 3 days ago by
rpolicastro • 2.0k
3
votes
3
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94
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3
answers
... It will be a lot simpler to first make a group key table.
library("tidyverse")
groups <- tibble(
sample=colnames(normCounts),
group=rep(seq(1, ncol(normCounts)/3), each=3)
)
> groups
# A tibble: 9 x 2
sample group
1 Sample_1 1
...
written 3 days ago by
rpolicastro • 2.0k
0
votes
3
answers
94
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3
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... Are the triplicate groups sequential? As in, are Sample_1, Sample_2, and Sample_3 part of the first group? ...
written 3 days ago by
rpolicastro • 2.0k
0
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48
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... You can proceed as normal with single nuclei data. ...
written 3 days ago by
rpolicastro • 2.0k
0
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56
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Comment:
C: FDR values in clusterProfiler
... I don't think the tools you listed use the same statistical test. I believe DAVID uses a modified fishers exact test, PANTHER uses a binomial test, and clusterProfiler uses the hypergeometric test. This would result in different p-values for each tool, and of course different FDR corrected p-values. ...
written 4 days ago by
rpolicastro • 2.0k
0
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2
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89
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Comment:
C: Deseq2 Biological replicates
... By including 'individual' in your model, you are already including information about biological replicates. It looks like you just want a model such as `~ conditions + individual + family` that takes into account all of your predictors. ...
written 5 days ago by
rpolicastro • 2.0k
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