Showing : Deseq2 • reset
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News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
4 days ago Frances Turner ▴ 20
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3
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DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
written 27 days ago by • 0
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2
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286
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BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 5 weeks ago by 43k • written 6 weeks ago by • 0
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6
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1.0k
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 8 weeks ago by • 0
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1
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215
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Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 6 weeks ago by ★ 5.0k • written 6 weeks ago by • 0
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2
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1.2k
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 7 weeks ago by ★ 4.0k • written 6 months ago by • 0
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11
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2.0k
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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 ★ 4.0k • written 5 months ago by • 0
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2
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DESeq2 on non-RNASeq counts data
DESeq2
written 4 months ago by • 0
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2
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359
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 8 weeks ago by ★ 4.0k • written 4 months ago by • 0
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166
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 8 weeks ago by ★ 4.0k • written 9 weeks ago by • 0
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4
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270
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
8 weeks ago Denise • 0
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2
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283
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Setting up a DESeq2 Design with Paired Data
DESeq2
10 weeks ago Alexander • 0
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4
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536
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DESeq2 interactions
DESeq2
updated 11 weeks ago by 43k • written 4 months ago by • 0
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1.3k
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 5 months ago by • 0
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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 4 months ago by • 0
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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 4 months ago by 43k • written 4 months ago by • 0
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5
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How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 4 months ago by 68k • written 4 months ago by ▴ 200
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45
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13k
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Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 4 months ago by 68k • written 6.5 years ago by ▴ 60
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11
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743
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
5 months ago • updated 4 months ago Denise • 0
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6
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655
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
5 months ago richardallenfriedmanbrooklyn ▴ 30
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332
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 5 months ago by ▴ 10
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4
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1.0k
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 5 months ago by 43k • written 6 months ago by • 0
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Differential expression on the transcript-level
DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 15 months ago by • 0
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8
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2.0k
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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
6 months ago richardallenfriedmanbrooklyn ▴ 30
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9
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5.8k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
6 months ago bbao ▴ 10
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1
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585
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discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 6 months ago by 68k • written 6 months ago by • 0
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2
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1.0k
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gene detection across experiments
DESeq2 Normalization
6 months ago Mara • 0
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11
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3.6k
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 8 months ago by ▴ 10
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Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 5 months ago by 43k • written 7 months ago by • 0
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DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 6 months ago by 43k • written 7 months ago by • 0
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6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 6 months ago by 43k • written 7 months ago by • 0
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2
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1.5k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 7 months ago by ▴ 20
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2.7k
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Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 7 months ago by • 0
3
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1
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3.8k
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DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 7 months ago by 43k • written 7 months ago by ▴ 10
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647
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DESeq2 results
result DESeq2 subsetting
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
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1
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471
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Unclear DEseq2 replaceOutliers error message
DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
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1
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625
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 7 months ago by 43k • written 8 months ago by • 0
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2
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2.1k
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Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
8 months ago • updated 7 months ago dudutchy ▴ 10
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3
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
7 months ago Paulito • 0
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Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
8 months ago • updated 7 months ago caroline.zanchi ▴ 10
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463
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DESeq2 from phyloseq error
DESeq2 phyloseq
8 months ago asafpr • 0
3
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1
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691
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DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 8 months ago by 68k • written 8 months ago by • 0
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Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 8 months ago by 68k • written 8 months ago by ▴ 10
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DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 7 months ago by 43k • written 8 months ago by ▴ 40
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4
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1.9k
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Filtering after DESeq
DESeq2 IHW
written 8 months ago by ▴ 10
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4
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1.3k
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DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
8 months ago sk • 0
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6
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1.9k
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Discrepancies in normalised count data vs unnormalised
DESeq2
8 months ago • updated 7 months ago AMgroup • 0
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2
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769
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Design formula for circadian time-course data for vst() function
DESeq2
8 months ago Vishnu • 0
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2
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Analyzing TnSeq data with DESeq2
DESeq2
written 8 months ago by • 0
4,843 results • Page 1 of 97
Recent ...
Replies
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
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