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0
votes
2
answers
48
views
2
answers
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2 written 3 hours ago by Nik Tuzov • 50 • updated 45 minutes ago by Gordon Smyth ♦ 31k
0
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2
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43
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2
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DESeq2 Which gene used to normalize?
normalization deseq2 R written 11 hours ago by michi.s • 0 • updated 8 hours ago by Steve Lianoglou ♦ 12k
2
votes
1
answer
41
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1
answer
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
annotationdbi deseq2 tximport written 20 hours ago by prab4th • 0 • updated 20 hours ago by Johannes Rainer • 960
1
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1
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55
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1
answer
DESeq2 Dispersion Shrinkage - more samples is better?
deseq2 dds written 1 day ago by rrcutler • 30 • updated 1 day ago by Michael Love ♦ 13k
0
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1
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54
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1
answer
Different PCA plots using rlog and vsd on the same data set
deseq2 pca rlog variancestabilizingtransformation plotpca written 1 day ago by lirongrossmann • 0 • updated 1 day ago by Michael Love ♦ 13k
3
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1
answer
61
views
1
answer
DESeq2 Design Formula for Time Series Experiment
deseq2 written 3 days ago by gkuffel • 10 • updated 2 days ago by David Requena • 20
3
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2
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90
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2
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About the results and contrast (DESeq2)
deseq2 differential expression rna-seq written 6 days ago by David Requena • 20
10
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1
answer
1.5k
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5 follow
1
answer
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq limma edger deseq2 voom written 2.3 years ago by Sean Davis ♦ 20k • updated 3 days ago by Paul Harrison • 60
0
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1
answer
64
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1
answer
Sample-to-sample distance matrix using heatmap.2
deseq2 heatmap.2 gplots written 5 days ago by Jane Merlevede • 90
2
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1
answer
38
views
1
answer
problem with DESeq2 on metagenome analysis
deseq2 metagenome written 3 days ago by ghanbari.msc • 10 • updated 3 days ago by Michael Love ♦ 13k
0
votes
1
answer
70
views
1
answer
DESeq2 biological replicates and RIN values
rnaseq deseq2 differential gene expression covariates written 5 days ago by pmoranlosada • 0 • updated 3 days ago by Michael Love ♦ 13k
1
vote
1
answer
41
views
1
answer
[DESeq2] Slight difference between lfcMLE and my calculated log2 fold change
deseq2 written 3 days ago by Mike • 0 • updated 3 days ago by Michael Love ♦ 13k
0
votes
2
answers
67
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2
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paired design with continious covariate
deseq2 R written 6 days ago by fabian.roger • 0 • updated 4 days ago by Michael Love ♦ 13k
1
vote
1
answer
66
views
1
answer
DESeq2 for ASE
deseq2 ase diploid-genome written 5 days ago by gtechbio • 0 • updated 5 days ago by Michael Love ♦ 13k
1
vote
1
answer
61
views
1
answer
Effect of inclusion of patientID in the formula
deseq2 written 6 days ago by o.giannakopoulou • 0 • updated 6 days ago by James W. MacDonald ♦ 44k
0
votes
1
answer
60
views
1
answer
Importing kallisto's abundance files into DESeq2 pipeline
deseq2 kallisto written 7 days ago by deena • 0 • updated 7 days ago by Michael Love ♦ 13k
0
votes
1
answer
241
views
1
answer
Paired Difference Analysis
deseq2 R differential gene expression written 6 weeks ago by nhua • 0
1
vote
1
answer
55
views
1
answer
DESeq2 had non-zero exit status
deseq2 written 7 days ago by mdtorohernando • 0 • updated 7 days ago by Mike Smith • 2.0k
0
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2
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85
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2
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DESeq2 ComputeSumFactors extract normalized counts
normalization deseq2 counts written 9 days ago by herrmannmaria94 • 0 • updated 9 days ago by Michael Love ♦ 13k
1
vote
1
answer
157
views
1
answer
How to exactly replicate the results from plotMA in DESeq2 ?
deseq2 plotma written 11 days ago by Yvan Wenger • 50
0
votes
1
answer
229
views
1
answer
lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions
deseq2 rlog lfcshrink written 19 days ago by pecot • 0
1
vote
1
answer
122
views
1
answer
DESeq2: Is it necessary to include all terms and interactions in LRT tests?
deseq2 lrt written 12 days ago by chimeric • 0 • updated 11 days ago by Gavin Kelly • 320
0
votes
1
answer
150
views
1
answer
Looking at interaction term in DESeq2 while also controlling for individual variable
deseq2 written 13 days ago by hmgeiger • 0
0
votes
1
answer
114
views
1
answer
DESeq2 Design controlling for gender
deseq2 multiple factor design written 13 days ago by rejane.troudet • 0 • updated 12 days ago by Michael Love ♦ 13k
2
votes
1
answer
114
views
1
answer
deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq deseq2 differential gene expression wald lrt written 13 days ago by chrysanthi.taxiarchi12 • 0 • updated 12 days ago by Gavin Kelly • 320
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