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SpikeIn
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0
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384
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Spike-in normalization method in ATACseq
sperm
Drosophila_melanogaster
ATACSeq
Normalization
SpikeIn
updated 8 weeks ago by
ATpoint
★ 4.6k • written 9 weeks ago by
Katerina
• 0
0
votes
2
replies
369
views
Analysis of transcription inhibition with DESeq2
SpikeIn
DESeq2
Normalization
written 4 months ago by
ADopico
• 0
0
votes
1
reply
518
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn
RUVSeq
DESeq2
RUV
updated 5 months ago by
Michael Love
43k • written 6 months ago by
Ειρήνη
• 0
0
votes
0
replies
293
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
8 months ago
Virangika
• 0
1
vote
2
replies
792
views
DiffBind spike-in lib.sizes confusion
SpikeIn
DiffBind
22 months ago
Weisheng
• 0
6
votes
2
replies
3.0k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2
SpikeIn
Normalization
DifferentialExpression
updated 23 months ago by
ATpoint
★ 4.6k • written 23 months ago by
kalavattam
▴ 10
0
votes
2
replies
2.3k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 7 months ago by
maria.soler
• 0 • written 23 months ago by
kalavattam
▴ 10
3
votes
4
replies
2.3k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
2.1 years ago • updated 24 months ago
spg
• 0
0
votes
0
replies
1.1k
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind
ChIPSeq
Normalization
SpikeIn
3.2 years ago
Drew
• 0
0
votes
0
replies
896
views
Spike-In Cells for Normalization?
SpikeIn
SingleCell
3.4 years ago
mb1996
• 0
0
votes
2
replies
1.4k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq
SpikeIn
edgeR
Normalization
3.4 years ago
maria.soler
• 0
7
votes
12
replies
4.8k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
updated 15 months ago by
Miguel
• 0 • written 3.9 years ago by
robert.chen
• 0
1
vote
9
replies
3.8k
views
Spike-in normalization in EdgeR
CUTandRUN
edgeR
Normalization
SpikeIn
ChIPSeq
updated 2.1 years ago by
Bogdan
▴ 670 • written 4.2 years ago by
Hesh
▴ 10
13 results • Page
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Comment: How do I fix an odd voom plot in a combined dataset?
by
1sunmic2
• 0
Thanks for responding! I did change the code slightly: dge1 <- DGEList(counts = combined_data_counts) keep <- rowSums(cpm(dge1)…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Andre
• 0
The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1). If I use estimateGLMRobustDisp(), like…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Gordon Smyth
52k
Here, estimateGLMRobustDisp() was used just to get the diagnostic BCV plot by plotBCV(y). The robust NB dispersions were not used for the D…
Answer: Please, I desperately need help with DESeq2. Three groups of repeated measures w
by
Michael Love
43k
I have to reserve my time on the support site for software related questions. I recommend working with a local statistician or someone fami…
Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a
by
Michael Love
43k
I would probably just do the M vs M analysis. You could instead include a term for sex and have a model with all 45 samples, but the M vs M…
Votes
Answer: How do I fix an odd voom plot in a combined dataset?
Answer: How do I fix an odd voom plot in a combined dataset?
Comment: How do I fix an odd voom plot in a combined dataset?
C: How does edgeR cpm function calculate log(CPM) values?
C: How does edgeR cpm function calculate log(CPM) values?
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