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bayespeak
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[bug] BayesPeak cannot deal with RangedData input
BayesPeak
bug
9.1 years ago
balwierz
▴ 40
1
vote
3
replies
1.4k
views
Error in bayespeak function importing data
bayespeak
10.1 years ago
Reed
▴ 10
8
votes
9
replies
7.1k
views
ChIPseq-style peak calling for paired-end sequencing?
Chipseq
DNAseq
ATAC
bayespeak
narrowpeaks
updated 10.3 years ago by
Gordon Smyth
53k • written 10.3 years ago by
samuel collombet
▴ 140
0
votes
8
replies
2.4k
views
chip-seq data
ChIPSeq
chipseq
BayesPeak
ChIPSeq
chipseq
BayesPeak
13.0 years ago
John linux-user
▴ 210
0
votes
1
reply
1.4k
views
Question about ChIPpeakAnno R package
AnnotationData
annotate
ChIPpeakAnno
BayesPeak
AnnotationData
annotate
ChIPpeakAnno
13.1 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
1.2k
views
Upgrade bioconductor to version 2.6
BayesPeak
BayesPeak
14.0 years ago
Mary Ellen Fitzpatrick
▴ 20
0
votes
7
replies
2.4k
views
error in bayespeak function
ChIPSeq
GO
BSgenome
BSgenome
chipseq
BayesPeak
ChIPSeq
GO
BSgenome
BSgenome
chipseq
updated 14.1 years ago by
Jonathan Cairns
▴ 130 • written 14.1 years ago by
Andreia Fonseca
▴ 810
0
votes
1
reply
1.3k
views
BayesPeak and RangedData obj output
BayesPeak
BayesPeak
updated 14.8 years ago by
Jonathan Cairns
▴ 130 • written 14.8 years ago by
Binbin Liu
▴ 30
0
votes
4
replies
2.0k
views
BayesPeak segfault woes
BayesPeak
BayesPeak
updated 15.3 years ago by
Jonathan Cairns
▴ 130 • written 15.3 years ago by
Tim Rayner
▴ 270
9 results • Page
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Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
by
Michael Love
43k
I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …
Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi
by
Michael Love
43k
> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…
Comment: voomLmFit fitted log-CPM values
by
Gordon Smyth
53k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
Comment: voomLmFit fitted log-CPM values
by
Lina
▴ 10
Is the output from fitted(v) in the log2 CPM scale? or CPM scale?
Answer: voomLmFit fitted log-CPM values
by
Gordon Smyth
53k
Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```
Votes
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
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