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michael love
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DESeq2 time course with two genotypes
deseq2
timecourse
michael love
multiple time points
5.4 years ago
cp1015
• 0
0
votes
4
replies
910
views
DESeq2 Design Formula
DESeq2
michael love
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
gkuffel
▴ 10
0
votes
1
reply
1.3k
views
DESeq2 PCA plotting
deseq2
michael love
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
sam.far.7
• 0
1
vote
11
replies
2.0k
views
Need help with DESeq2's contrast feature
deseq2
michael love
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
Ashu
▴ 10
2
votes
3
replies
1.8k
views
DESeq2 for time series using time as continuous and looking at effect of time on DE
deseq2
timecourse
multiple time points
mlr
michael love
updated 6.6 years ago by
Michael Love
43k • written 6.7 years ago by
ap874
• 0
5
votes
10
replies
13k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love
Salmon
tximport
tx2gene
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
pvd2107
▴ 30
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Answer: SingleR with multiple single cell references
by
Aaron Lun
★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies
by
ATpoint
★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
Answer: To count or not to count multi-overlapping reads?
by
Gordon Smyth
52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2?
by
ATpoint
★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
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Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
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