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spikein
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Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
2 days ago
Virangika
• 0
4
votes
12
replies
3.7k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
updated 6 months ago by
Miguel
• 0 • written 3.1 years ago by
robert.chen
• 0
1
vote
2
replies
574
views
DiffBind spike-in lib.sizes confusion
SpikeIn
DiffBind
13 months ago
Weisheng
• 0
4
votes
2
replies
1.7k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2
SpikeIn
Normalization
DifferentialExpression
updated 14 months ago by
ATpoint
★ 4.0k • written 14 months ago by
kalavattam
▴ 10
0
votes
1
reply
1.2k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 15 months ago by
Michael Love
41k • written 15 months ago by
kalavattam
▴ 10
3
votes
4
replies
1.6k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
16 months ago • updated 15 months ago
spg
• 0
1
vote
9
replies
2.9k
views
Spike-in normalization in EdgeR
CUTandRUN
edgeR
Normalization
SpikeIn
ChIPSeq
updated 16 months ago by
Bogdan
▴ 670 • written 3.5 years ago by
Hesh
▴ 10
0
votes
0
replies
887
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind
ChIPSeq
Normalization
SpikeIn
2.5 years ago
Drew
• 0
0
votes
0
replies
688
views
Spike-In Cells for Normalization?
SpikeIn
SingleCell
2.6 years ago
mb1996
• 0
0
votes
2
replies
1.1k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq
SpikeIn
edgeR
Normalization
2.7 years ago
maria.soler
• 0
10 results • Page
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Comment: Input Question for deseq.r
by
ATpoint
★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present
by
ATpoint
★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded
by
ATpoint
★ 4.0k
```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…
Comment: DESeq2 setting significant p-value
by
Dev
• 0
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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