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0
votes
1
answer
39
views
1
answer
Normalization and Quality Control for Multiple scRNAseq Data Sets
rnaseq genetics normalization batch effect dropout written 4 days ago by lmm278 • 0 • updated 4 days ago by Steve Lianoglou ♦ 12k
0
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1
answer
49
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1
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Strange lfcShrink plot when running DESeq2 workflow
rnaseq deseq deseq2 rna-seq written 4 days ago by Ben Gabriel • 0
0
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1
answer
63
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1
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how to make gene cluster from RNA-Seq counts?
rnaseq deseq2 R written 4 days ago by ahmad.moousavi • 0 • updated 4 days ago by Michael Love ♦ 19k
2
votes
1
answer
64
views
1
answer
DESeq2 design with multiple factors
rnaseq deseq2 multiple factor design written 6 days ago by Vanilla • 0 • updated 6 days ago by Michael Love ♦ 19k
1
vote
1
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57
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1
answer
newSCESet and SingleCellExperiment basic differences and TMM Normalization
rnaseq single-cell scater seurat singlecellexperiment written 7 days ago by hamza_karakurt • 0
2
votes
1
answer
70
views
1
answer
How to block for a subject in a 2 factor design formula
rnaseq deseq2 differential gene expression written 7 days ago by Onyi Ukay • 0
0
votes
1
answer
43
views
1
answer
DESeq2 got stuck for one night, restarting?
rnaseq deseq2 written 12 days ago by Raymond • 0 • updated 12 days ago by Michael Love ♦ 19k
1
vote
1
answer
59
views
1
answer
EdgeR between unequal group sizes?
rnaseq edger differential gene expression written 16 days ago by rina • 0 • updated 16 days ago by Gordon Smyth ♦ 35k
0
votes
1
answer
95
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1
answer
Large fold changes after deseq2 when one condition has two zeros and small number the other condition has two zeros and a large number
rnaseq deseq2 rsem written 21 days ago by loliveira • 0
5
votes
1
answer
100
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1
answer
Voom transformation from counts and normalization to negative values
rnaseq limma statistics voom tcga written 22 days ago by Beginner • 50 • updated 22 days ago by Ryan C. Thompson ♦ 6.9k
2
votes
1
answer
113
views
1
answer
Correct formulation of contrasts of interest regarding an RNA-Seq gene expression analysis with edgeR
rnaseq edger design and contrast matrix multifactorial design written 29 days ago by fotakisg • 0 • updated 27 days ago by Aaron Lun • 21k
0
votes
1
answer
67
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1
answer
Limma analysis combining twins pairs and unpaired controls
rnaseq limma twin analysis written 4 weeks ago by kalletrontti • 0 • updated 4 weeks ago by Aaron Lun • 21k
2
votes
1
answer
102
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1
answer
Visualise and remove batch effects in DESeq2
rnaseq deseq2 written 4 weeks ago by Tash. • 0 • updated 4 weeks ago by Michael Love ♦ 19k
8
votes
1
answer
73
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1
answer
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect written 4 weeks ago by Laura • 20 • updated 4 weeks ago by Aaron Lun • 21k
3
votes
1
answer
104
views
1
answer
edgeR analysis of cells treated with either drug1, drug2, or a time matched control at two different time points, did I set this up correctly?
rnaseq edger bioinformatics gene expression written 5 weeks ago by brett.vanderwerff • 0 • updated 5 weeks ago by Gordon Smyth ♦ 35k
0
votes
1
answer
98
views
1
answer
RNA-seq unbalanced batch effect correction
rnaseq edger batch effect written 6 weeks ago by sckinta • 0 • updated 5 weeks ago by James W. MacDonald ♦ 48k
0
votes
0
answers
67
views
0
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Problem running (loading) systemPipeR package after downloading
rnaseq systempiper written 6 weeks ago by rj.innet • 0
3
votes
1
answer
124
views
1
answer
Help with multi-factor Deseq analysis
rnaseq deseq deseq2 written 6 weeks ago by MAPK • 0 • updated 6 weeks ago by Michael Love ♦ 19k
1
vote
1
answer
90
views
1
answer
Problem with finding mitochondrial genes in a human single cell RNA-Seq readCounts file
rnaseq mitochondria single-cell written 6 weeks ago by es.azadian • 0 • updated 6 weeks ago by Aaron Lun • 21k
4
votes
2
answers
119
views
2
answers
Perfectly aligning sequences not mapping to worm genome with Subread-align?
rnaseq featurecounts subread written 7 weeks ago by rogangrant • 0 • updated 7 weeks ago by Gordon Smyth ♦ 35k
0
votes
0
answers
79
views
0
answers
Evaluating Hub genes in WGCNA and role of using Signed network
rnaseq wgcna written 9 weeks ago by dorothy.jrobbert • 10
0
votes
1
answer
110
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1
answer
A few up-regulated genes using an extravagant number of reads - effect on DE analysis
rnaseq deseq2 written 10 weeks ago by Poikilo • 0 • updated 10 weeks ago by Michael Love ♦ 19k
2
votes
1
answer
137
views
1
answer
Adding gene names (or symbols) in my DESeq result
rnaseq deseq2 gene names written 10 weeks ago by ytlin610 • 10 • updated 10 weeks ago by Michael Love ♦ 19k
1
vote
1
answer
130
views
1
answer
DESeq2 Normalized Counts for Mfuzz
rnaseq mfuzz deseq2 written 12 weeks ago by rbenel • 0 • updated 12 weeks ago by Michael Love ♦ 19k
0
votes
1
answer
85
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1
answer
single cell RNA-seq pipeline
rnaseq scrna-seq written 3 months ago by Bogdan • 520 • updated 3 months ago by Aaron Lun • 21k
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