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DEseq
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What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 13 hours ago by
ATpoint
★ 2.0k • written 1 day ago by
m-bihie
• 0
0
votes
1
reply
104
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 9 days ago by
Dario Strbenac
★ 1.5k • written 11 days ago by
Hicham
• 0
0
votes
2
replies
759
views
suggestions/comments on DESeq transcript wise analysis
convert
DESeq
convert
DESeq
written 11.0 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190
1
vote
1
reply
173
views
How to design multifactor DESEQ2 formula?
DESEQ
DESEQ2
updated 4 months ago by
ATpoint
★ 2.0k • written 4 months ago by
barrypraveen
• 0
3
votes
2
replies
285
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq
DESeq2
6 months ago
manwar
• 0
1
vote
1
reply
278
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 7 months ago by
Michael Love
39k • written 7 months ago by
stew
• 0
1
vote
5
replies
404
views
Error in DEseq
DEseq
RNASeqData
updated 7 months ago by
ATpoint
★ 2.0k • written 7 months ago by
Sanatan
• 0
2
votes
1
reply
442
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 8 months ago by
swbarnes2
★ 1.2k • written 8 months ago by
Hicham
• 0
1
vote
5
replies
583
views
Potential outlier/high variance
deseq
DESeq2
updated 9 months ago by
Michael Love
39k • written 9 months ago by
Amali Thrimawithana
• 0
1
vote
2
replies
330
views
Deseq2 with imbalanced design
Deseq
10 months ago
Alex
• 0
2
votes
4
replies
2.4k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’
DESeq
updated 11 months ago by
Nicola
• 0 • written 2.8 years ago by
krunal.24.6
▴ 10
0
votes
1
reply
2.3k
views
voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Normalization
graph
limma
convert
edgeR
DESeq
Rsubread
Normalization
graph
limma
convert
updated 27 days ago by
Gordon Smyth
47k • written 10.7 years ago by
Kasper Daniel Hansen
6.5k
12 results • Page
1 of 1
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Replies
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
Sorry, I don't understand your experiment. You are reading the edgeR Section on on what to do without replicates, but your experiment appe…
Answer: MA plot
by
Nathalie
• 0
Thank you very much for your help and comments. There is errors in my file. BaseMean is BaseMeanLog2. I don't know how insert a file.
Comment: Design for DE analysis in tidybulk
by
Michael Love
39k
The mapping from what you want to a contrast is a long conversation. You can make pairwise comparisons or numeric contrasts or really anyth…
Votes
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: MA plot
Answer: MA plot
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Michael Love
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62k
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Assa Yeroslaviz
★ 1.5k
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ATpoint
★ 2.0k
Popular Question
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