Showing : DEseq2 • reset
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News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
2 days ago Frances Turner ▴ 20
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3
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244
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DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
written 26 days ago by • 0
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2
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284
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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 7 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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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 4 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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163
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 8 weeks ago by ★ 4.0k • written 8 weeks ago by • 0
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4
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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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282
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Setting up a DESeq2 Design with Paired Data
DESeq2
9 weeks ago Alexander • 0
2
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4
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535
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DESeq2 interactions
DESeq2
updated 11 weeks ago by 43k • written 4 months ago by • 0
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14
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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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408
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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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1.2k
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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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736
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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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330
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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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2.3k
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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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584
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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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5
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5.0k
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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 6 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
3
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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
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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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1
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646
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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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470
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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
3
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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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1.6k
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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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4
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Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
7 months ago caroline.zanchi ▴ 10
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1
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460
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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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689
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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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5
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1.5k
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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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3
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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
2
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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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768
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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
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Comment: Quality control of shotgun metagenomics data by elonlilx54 • 0
If you are a fan of word guessing games like Wordle, then you definitely cannot ignore [Octordle][1] - a more challenging and attractive ex…
Answer: Incosistencies in buildSNNGraph() function by stephengriffin04 • 0
Thank you for shedding light on the inconsistencies in the `buildSNNGraph()` function. It's crucial for users to address these issues as th…
Answer: A problem occurs when running the monocle2 by stephengriffin04 • 0
I totally feel you on the monocle2 issues! I had a similar run-in with unexpected errors last week that had me pulling my hair out. Did you…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
limpa reads standard feature-level output from Spectronaut. You do not need to make any changes to the output before reading it into limpa.…
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
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