Showing : DEseq2 • reset
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DESeq2 contrast cleaning problem
software error bugs deseq2
written 10.0 years ago by • 0
0
votes
1
reply
126
views
DESeq2 for 16S rRNA Analysis
DESeq2
updated 8 days ago by 68k • written 9 days ago by • 0
0
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5
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244
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Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 11 days ago by 43k • written 11 days ago by • 0
0
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2
replies
193
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lfc shrinkage estimator in DESeq2
DESeq2
written 12 days ago by • 0
0
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13
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818
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Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 12 days ago by 53k • written 18 days ago by • 0
0
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6
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620
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BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 19 days ago by 25k • written 9 weeks ago by • 0
0
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1
reply
271
views
DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage DESeq2 contrast
updated 18 days ago by ★ 5.0k • written 22 days ago by • 0
0
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1
reply
135
views
News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
written 26 days ago by ▴ 20
0
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3
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399
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
7 weeks ago • updated 22 days ago ja569116 • 0
3
votes
6
replies
1.1k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 11 weeks ago by • 0
0
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1
reply
242
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 9 weeks ago by ★ 5.0k • written 10 weeks ago by • 0
0
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2
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1.3k
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 11 weeks ago by ★ 4.0k • written 7 months ago by • 0
1
vote
11
replies
2.3k
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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 11 weeks ago by ★ 4.0k • written 5 months ago by • 0
0
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2
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402
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DESeq2 on non-RNASeq counts data
DESeq2
written 5 months ago by • 0
0
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2
replies
387
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 11 weeks ago by ★ 4.0k • written 5 months ago by • 0
0
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0
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189
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 11 weeks ago by ★ 4.0k • written 12 weeks ago by • 0
0
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4
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328
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
12 weeks ago • updated 11 weeks ago Denise • 0
0
votes
2
replies
365
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Setting up a DESeq2 Design with Paired Data
DESeq2
3 months ago Alexander • 0
2
votes
4
replies
578
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DESeq2 interactions
DESeq2
updated 3 months ago by 43k • written 4 months ago by • 0
3
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14
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1.4k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 6 months ago by • 0
0
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3
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438
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 4 months ago by 43k • written 5 months ago by • 0
0
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1
reply
869
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
3
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5
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1.2k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 5 months ago by 68k • written 5 months ago by ▴ 200
17
votes
45
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13k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 5 months ago by 68k • written 6.5 years ago by ▴ 60
0
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11
replies
806
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
5 months ago Denise • 0
2
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6
replies
689
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
5 months ago richardallenfriedmanbrooklyn ▴ 30
0
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3
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358
views
DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 5 months ago by ▴ 10
0
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4
replies
1.1k
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 6 months ago by 43k • written 6 months ago by • 0
1
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2
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543
views
Differential expression on the transcript-level
DESeq2
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
3
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13
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2.4k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 16 months ago by • 0
4
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8
replies
2.0k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
6 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
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5.8k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
7 months ago • updated 6 months ago bbao ▴ 10
0
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1
reply
605
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 7 months ago by 68k • written 7 months ago by • 0
0
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2
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1.1k
views
gene detection across experiments
DESeq2 Normalization
7 months ago Mara • 0
5
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11
replies
3.9k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 9 months ago by ▴ 10
1
vote
5
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5.3k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 6 months ago by 43k • written 8 months ago by • 0
1
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1
reply
2.3k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 7 months ago by 43k • written 7 months ago by • 0
0
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2
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1.3k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
3
votes
2
replies
1.6k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 8 months ago by ▴ 20
1
vote
2
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2.8k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 8 months ago by • 0
3
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1
reply
3.9k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 8 months ago by 43k • written 8 months ago by ▴ 10
0
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1
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676
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DESeq2 results
result DESeq2 subsetting
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
0
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1
reply
492
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
1
reply
662
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 8 months ago by 43k • written 9 months ago by • 0
3
votes
2
replies
2.1k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
9 months ago • updated 8 months ago dudutchy ▴ 10
2
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3
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1.6k
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
8 months ago Paulito • 0
4
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4
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2.2k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
8 months ago caroline.zanchi ▴ 10
0
votes
1
reply
504
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DESeq2 from phyloseq error
DESeq2 phyloseq
8 months ago asafpr • 0
3
votes
1
reply
725
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 9 months ago by 68k • written 9 months ago by • 0
1
vote
5
replies
1.7k
views
Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 9 months ago by 68k • written 9 months ago by ▴ 10
4,848 results • Page 1 of 97
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No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
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Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
Comment: using limma trend workflow in CAMERA
C: z-score with DESeq2?
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