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Diffbind
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0
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4
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194
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
8 days ago • updated 5 days ago
lonn
• 0
2
votes
2
replies
353
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
13 days ago • updated 12 days ago
Henry
▴ 10
2
votes
2
replies
146
views
[DiffBind] Obtaining normalization factors
DiffBind
12 days ago • updated 9 days ago
Henry
▴ 10
0
votes
0
replies
98
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
27 days ago
feather-W
• 0
0
votes
0
replies
18
views
ATACseq merge peaks
DiffBind
22 hours ago
Shloka
• 0
0
votes
0
replies
76
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
9 days ago
Virangika
• 0
0
votes
0
replies
83
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
28 days ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
96
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
27 days ago
Ankit
▴ 20
8 results • Page
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Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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James W. MacDonald
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Gordon Smyth
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Chris
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Jonathan
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