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Michael Love
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3
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DESeq2 time course with two genotypes
deseq2
timecourse
michael love
multiple time points
4.6 years ago
cp1015
• 0
0
votes
4
replies
728
views
DESeq2 Design Formula
DESeq2
michael love
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
gkuffel
▴ 10
0
votes
1
reply
1.0k
views
DESeq2 PCA plotting
deseq2
michael love
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
sam.far.7
• 0
1
vote
11
replies
1.5k
views
Need help with DESeq2's contrast feature
deseq2
michael love
updated 5.7 years ago by
Michael Love
41k • written 5.7 years ago by
Ashu
▴ 10
2
votes
3
replies
1.5k
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 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
ap874
• 0
5
votes
10
replies
11k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love
Salmon
tximport
tx2gene
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
pvd2107
▴ 30
6 results • Page
1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…
Answer: Handling multiple differential expression comparisons
by
Michael Love
41k
It's typical that results are presented with each group having its own FDR control. So presenting each comparison with the adjusted p-va…
Comment: Too many significant genes when integrating gtex and tcga
by
ATpoint
★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
Answer: fgsea significant result
by
ATpoint
★ 4.1k
Set a fixed seed before running this. Note that a FDR of 0.25 in fgsea is wildly and overly lenient. See https://support.bioconductor.o…
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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