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DESeq2
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0
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40
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Adding gene names to DESeq result
DESeq2
updated 21 hours ago by
Basti
▴ 540 • written 23 hours ago by
Chelsea
• 0
0
votes
1
reply
67
views
struggling to create a heatmap
DESeq2
heatmaps
updated 2 days ago by
ATpoint
★ 2.1k • written 3 days ago by
m-bihie
▴ 10
0
votes
1
reply
75
views
collapseReplicates error after tximeta
fishpond
tximeta
DESeq2
updated 3 days ago by
Michael Love
39k • written 4 days ago by
Rihards Saksis
• 0
0
votes
2
replies
79
views
Which genes are outliers in DESeq2?
DESeq2
RNAseq
outlier
updated 3 days ago by
ATpoint
★ 2.1k • written 3 days ago by
James
• 0
2
votes
2
replies
77
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2
SpikeIn
Normalization
DifferentialExpression
updated 3 days ago by
ATpoint
★ 2.1k • written 3 days ago by
kalavattam
▴ 10
3
votes
1
reply
56
views
log2 of normalized counts for further analyzes
DESeq2
log2
normalized
counts
updated 3 days ago by
James W. MacDonald
62k • written 3 days ago by
Laia
▴ 10
0
votes
2
replies
76
views
DESeq2 parameter infernce
DESeq2
7 days ago • updated 5 days ago
BioEpi
• 0
0
votes
1
reply
64
views
DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2
LRT
continuous
coeficients
updated 6 days ago by
Michael Love
39k • written 7 days ago by
Laia
▴ 10
0
votes
1
reply
74
views
DESeq2 with sample effect, unequal sample sizes
DESeq2
updated 6 days ago by
Michael Love
39k • written 7 days ago by
rf
• 0
1
vote
3
replies
466
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq
LRT
DESeq2
lfcShrink
updated 16 hours ago by
ayabalbaa1990
• 0 • written 12 months ago by
Emma
• 0
5
votes
8
replies
794
views
Combat and dds Object
DESeq2
combat
updated 3 days ago by
ATpoint
★ 2.1k • written 18 months ago by
Bine
▴ 20
11 results • Page
1 of 1
Recent ...
Replies
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
by
Jonathan Göke
▴ 40
Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
by
Gordon Smyth
47k
Choosing which samples to normalize together is not dependent on library size but rather on (1) whether the tissue samples are comparable a…
Comment: Atena package - error (new user)
by
lalanis1
• 0
Thanks a lot, Calvo. Will run my files with revised version soon! Best regards, Lalani
Comment: Nested paired design with covariates in limma
by
Gordon Smyth
47k
Please post a new question with enough detail to answer your question. If you want bespoke advance, then you need to post the details of yo…
Comment: Question about GWASTools gdsSubset
by
Stephanie M. Gogarten
▴ 840
You could see if an attribute has been set on the genotype node indicating the order: ``` > library(gdsfmt) > gdsfile <- system.file("extda…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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James W. MacDonald
62k
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Michael Love
39k
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Gordon Smyth
47k
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Bogdan
▴ 660
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Martin Morgan
25k
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