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DESeq2
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14
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
9 hours ago
lonn
• 0
0
votes
0
replies
23
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
9 hours ago • updated 7 hours ago
ussarizona
• 0
0
votes
0
replies
25
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
10 hours ago
quanah.hudson
• 0
0
votes
0
replies
38
views
covariate with negative and positive values
DESeq2
1 day ago
Brynn
• 0
0
votes
3
replies
125
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
andrebolerbarros
▴ 20
1
vote
1
reply
152
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 2 days ago by
Michael Love
41k • written 7 days ago by
Weiqian
▴ 10
0
votes
3
replies
151
views
DEG with low counts
DESeq2
3 days ago • updated 1 day ago
Rajat
• 0
0
votes
1
reply
78
views
Deseq2 Rlog transformation
DESeq2
updated 2 days ago by
ATpoint
★ 4.0k • written 3 days ago by
Sahar
• 0
1
vote
2
replies
140
views
Design Matrix within group comparison more than two groups
DESeq2
5 days ago • updated 4 days ago
hemantcnaik
• 0
0
votes
1
reply
100
views
Bioinformatics student
Des
DESeq2
updated 5 days ago by
hemantcnaik
• 0 • written 5 days ago by
Sahar
• 0
0
votes
1
reply
135
views
DESeq2 gives an error and R crashes
DESeq2
7 days ago • updated 6 days ago
Shefali
• 0
0
votes
4
replies
548
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 1 day ago by
Michael Love
41k • written 5 months ago by
Crystal571
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 11 hours ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
5
votes
12
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by
Seyram M.
• 0 • written 4.6 years ago by
hsbio
▴ 10
14 results • Page
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Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Comment: Methylation Analysis experiment design using Limma
by
hortense96
• 0
Hi, Thank you very much for your answer. It's true that I only used 6 samples for this analysis, which is consistent with your explanation…
Comment: Error using champ.import
by
shilpa
• 0
I'm having same issues too. Did anyone manage to resolve it?
Votes
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.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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