Showing : DESEQ2 • reset
0
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3
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
updated 1 day ago by 43k • written 1 day ago by • 0
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0
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38
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
2 days ago colinmccornack • 0
0
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2
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160
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Setting up a DESeq2 Design with Paired Data
DESeq2
9 days ago • updated 8 days ago Alexander • 0
2
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4
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442
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DESeq2 interactions
DESeq2
updated 18 days ago by 43k • written 8 weeks ago by • 0
3
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14
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1.1k
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 3 months ago by • 0
0
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2
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230
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3-factor DESeq2 trime-series analysis
time-series DESeq2
9 weeks ago gogeni5529 • 0
0
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3
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355
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 9 weeks ago by 43k • written 10 weeks ago by • 0
0
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1
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658
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Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 9 weeks ago by 43k • written 11 weeks ago by • 0
3
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5
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1.1k
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How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 10 weeks ago by 68k • written 11 weeks ago by ▴ 200
17
votes
45
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13k
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Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 11 weeks ago by 68k • written 6.3 years ago by ▴ 60
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0
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153
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DESeq2 on non-RNASeq counts data
DESeq2
12 weeks ago vs • 0
1
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10
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1.1k
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Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 7 weeks ago by • 0 • written 12 weeks ago by • 0
0
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11
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598
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
3 months ago • updated 12 weeks ago Denise • 0
2
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6
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555
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
3 months ago richardallenfriedmanbrooklyn ▴ 30
0
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3
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255
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 3 months ago by ▴ 10
0
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4
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847
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 3 months ago by 43k • written 4 months ago by • 0
1
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2
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394
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Differential expression on the transcript-level
DESeq2
updated 3 months ago by ★ 1.4k • written 3 months ago by • 0
3
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13
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2.1k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 13 months ago by • 0
4
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8
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1.9k
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Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
4 months ago richardallenfriedmanbrooklyn ▴ 30
7
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9
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5.6k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
4 months ago bbao ▴ 10
0
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2
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956
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 4 months ago by 68k • written 4 months ago by • 0
0
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1
reply
510
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 4 months ago by 68k • written 4 months ago by • 0
0
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2
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965
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gene detection across experiments
DESeq2 Normalization
4 months ago Mara • 0
5
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11
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3.2k
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 6 months ago by ▴ 10
1
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5
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4.3k
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Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 3 months ago by 43k • written 5 months ago by • 0
1
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1
reply
2.2k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 4 months ago by 43k • written 4 months ago by • 0
0
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2
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1.2k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 4 months ago by 43k • written 5 months ago by • 0
3
votes
2
replies
1.4k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 5 months ago by ▴ 20
1
vote
2
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2.6k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 5 months ago by • 0
3
votes
1
reply
3.7k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 5 months ago by 43k • written 5 months ago by ▴ 10
0
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1
reply
576
views
DESeq2 results
result DESeq2 subsetting
updated 5 months ago by ★ 5.0k • written 5 months ago by • 0
0
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1
reply
411
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
0
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1
reply
554
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 5 months ago by 43k • written 6 months ago by • 0
3
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2
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2.0k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
6 months ago • updated 5 months ago dudutchy ▴ 10
2
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3
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1.4k
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
5 months ago Paulito • 0
4
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4
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2.0k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
5 months ago caroline.zanchi ▴ 10
0
votes
1
reply
403
views
DESeq2 from phyloseq error
DESeq2 phyloseq
6 months ago asafpr • 0
3
votes
1
reply
624
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 6 months ago by 68k • written 6 months ago by • 0
1
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5
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1.4k
views
Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 6 months ago by 68k • written 6 months ago by ▴ 10
8
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3
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3.0k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 5 months ago by 43k • written 6 months ago by ▴ 40
2
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4
replies
1.8k
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Filtering after DESeq
DESeq2 IHW
written 6 months ago by ▴ 10
0
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4
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1.2k
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
6 months ago sk • 0
0
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6
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1.8k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
6 months ago • updated 5 months ago AMgroup • 0
0
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2
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680
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Design formula for circadian time-course data for vst() function
DESeq2
6 months ago Vishnu • 0
0
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2
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815
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Analyzing TnSeq data with DESeq2
DESeq2
written 6 months ago by • 0
0
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1
reply
1.2k
views
How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2 RUVSeq
updated 6 months ago by 43k • written 7 months ago by • 0
0
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2
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712
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Differing results with DESeq2
DESeq2
updated 6 months ago by • 0 • written 7 months ago by • 0
0
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2
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590
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RNA Seq using Lrt
DESeq2
6 months ago Rob • 0
0
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3
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1.0k
views
Log2foldchange strange behavior
DESeq2
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
votes
1
reply
889
views
WGCNA
WGCNA DESeq2
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
4,838 results • Page 1 of 97
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Using biomaRt to extract SNP information from genomic regions is as simple as setting the correct dataset in this case, and defining your …
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I am answering my own question. I found the solution thanks to [this post][1], and I am writing here the very simple procedure: 1) Instal…
Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
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Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Issues with downloading biomaRt - SeqInfo and S4 Vectors
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