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1
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95
views
1
answer
Controlling numerical covariates: differential gene expression with limma voom
rnaseq limma R voom differential gene expression written 8 days ago by Onyi Ukay • 0 • updated 8 days ago by mikhael.manurung • 10
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2
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2
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DESeq2 estimateSizeFactors with control genes
deseq2 differential gene expression controls references written 11 days ago by cris.kgs • 0 • updated 11 days ago by mahesh • 0
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45
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DESeq2 - shrunken log fold changes and threshold test
deseq2 differential gene expression lfcthreshold lfcshrink written 19 days ago by corentinrichard374369 • 0 • updated 18 days ago by Michael Love ♦ 20k
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Error while loading the data structrure in the ballgown tool
rnaseq differential gene expression ballgown new tuxedo pipleine written 29 days ago by Mithil Gaikwad • 0
2
votes
1
answer
98
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1
answer
Using LIMMA for differential gene analysis of microarray data
limma differential gene expression affymetrix microarrays ncbi geo written 4 weeks ago by Francesca McGrath • 0 • updated 4 weeks ago by Aaron Lun • 21k
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1
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103
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DESeq2 with several biological replicates
rnaseq deseq2 differential gene expression written 4 weeks ago by bharata1803 • 30
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votes
1
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109
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1
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Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysis
edger differential gene expression glmtreat written 6 weeks ago by svlachavas • 610 • updated 5 weeks ago by Gordon Smyth ♦ 35k
2
votes
1
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104
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1
answer
Multi-factor with interaction model in EdgeR and DESeq2
rnaseq edger deseq2 differential gene expression written 6 weeks ago by camilla.alves • 0 • updated 6 weeks ago by Michael Love ♦ 20k
9
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2
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156
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5 follow
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Finding DE genes from RNA-seq data
qvalue edger differential gene expression fpkm pvalue written 6 weeks ago by Harrisonesmith • 0 • updated 6 weeks ago by Steve Lianoglou ♦ 12k
0
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1
answer
83
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1
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Multiple factor design for differential expression with DESeq2
deseq2 differential gene expression multiple factor design written 7 weeks ago by galozs • 0 • updated 7 weeks ago by Michael Love ♦ 20k
0
votes
1
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89
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1
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DESEQ2 Finding Unchanged Genes
deseq2 differential gene expression written 7 weeks ago by tirza.doniger • 10 • updated 7 weeks ago by Michael Love ♦ 20k
5
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1
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146
views
1
answer
How to set up appropriate analysis using sample type and condition for DESeq2
deseq2 design differential gene expression written 7 weeks ago by newbio17 • 0 • updated 7 weeks ago by Michael Love ♦ 20k
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1
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115
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1
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deseq2 analysis multiple factor and 4 different time points
differential gene expression bias edger and deseq2 written 8 weeks ago by yusuf.zhc • 0 • updated 8 weeks ago by swbarnes2 • 50
2
votes
1
answer
154
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1
answer
How to block for a subject in a 2 factor design formula
rnaseq deseq2 differential gene expression written 9 weeks ago by Onyi Ukay • 0
1
vote
1
answer
113
views
1
answer
EdgeR between unequal group sizes?
rnaseq edger differential gene expression written 10 weeks ago by rina • 0 • updated 10 weeks ago by Gordon Smyth ♦ 35k
4
votes
1
answer
146
views
1
answer
EdgeR blocking and "All combinations of multiple factors"
edger differential gene expression written 12 weeks ago by rfenouil • 0 • updated 12 weeks ago by James W. MacDonald ♦ 48k
8
votes
1
answer
116
views
1
answer
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect written 3 months ago by Laura • 20 • updated 3 months ago by Aaron Lun • 21k
2
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1
answer
146
views
1
answer
EdgeR analysis batch effect
edger differential gene expression written 3 months ago by rfenouil • 0 • updated 3 months ago by Aaron Lun • 21k
0
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1
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95
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1
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Combining biological replicates from raw counts for use in differential gene expression/normalization (DESeq2 and edgeR)
differential gene expression biologicalreplicates raw_counts written 3 months ago by tasnif.rahman • 0 • updated 3 months ago by James W. MacDonald ♦ 48k
1
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1
answer
147
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1
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How do I discern if a magnitude difference in expression is up-regulation in one group or down-regulation in another?
edger R differential gene expression gene list up-regulation written 3 months ago by philip.freda • 0 • updated 3 months ago by Gordon Smyth ♦ 35k
0
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0
answers
97
views
0
answers
Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
timecourse differential gene expression edge interaction written 4 months ago by rubi • 90
1
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2
answers
144
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2
answers
skewed differentially expressed gene results - DESeq2
deseq2 differential gene expression outliers written 4 months ago by CE • 10 • updated 4 months ago by Ryan C. Thompson ♦ 7.0k
0
votes
0
answers
141
views
0
answers
Simple differential expression analysis for 2 groups
microarray limma differential gene expression agilent microarrays dea written 4 months ago by christiangriffioen • 0
1
vote
1
answer
139
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1
answer
Differentially expressed genes across multiple conditions
differential gene expression limma voom multiple treatments written 4 months ago by vam3002 • 0 • updated 4 months ago by James W. MacDonald ♦ 48k
3
votes
1
answer
283
views
1
answer
EdgeR for differential analysis between two cell lines without replication
rnaseq edger differential gene expression written 5 months ago by Biologist • 70 • updated 5 months ago by Gordon Smyth ♦ 35k
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