Showing : DESEQ2 • reset
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DESeq2 interactions
DESeq2
6 hours ago Michael • 0
3
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14
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728
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 6 weeks ago by • 0
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2
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111
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3-factor DESeq2 trime-series analysis
time-series DESeq2
4 days ago • updated 3 days ago gogeni5529 • 0
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3
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212
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 3 days ago by 43k • written 12 days ago by • 0
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1
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185
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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 6 days ago by 43k • written 20 days ago by • 0
3
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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 12 days ago by 68k • written 18 days ago by ▴ 200
17
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45
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12k
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Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 19 days ago by 68k • written 6.1 years ago by ▴ 60
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84
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DESeq2 on non-RNASeq counts data
DESeq2
25 days ago vs • 0
1
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9
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755
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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
27 days ago • updated 23 days ago Raya • 0
0
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11
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414
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
29 days ago • updated 24 days ago Denise • 0
2
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6
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371
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
4 weeks ago richardallenfriedmanbrooklyn ▴ 30
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3
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179
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 4 weeks ago by ▴ 10
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4
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777
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 5 weeks ago by 43k • written 8 weeks ago by • 0
1
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2
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326
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Differential expression on the transcript-level
DESeq2
updated 6 weeks ago by ★ 1.4k • written 7 weeks ago by • 0
3
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11
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1.8k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 11 months ago by • 0
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8
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1.7k
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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
9 weeks ago • updated 8 weeks ago richardallenfriedmanbrooklyn ▴ 30
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9
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5.3k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
9 weeks ago • updated 8 weeks ago bbao ▴ 10
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2
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895
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 9 weeks ago by 68k • written 9 weeks ago by • 0
0
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1
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427
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discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 9 weeks ago by 68k • written 9 weeks ago by • 0
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2
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893
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gene detection across experiments
DESeq2 Normalization
11 weeks ago • updated 10 weeks ago Mara • 0
5
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11
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3.0k
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 4 months ago by ▴ 10
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5
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3.7k
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Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 7 weeks ago by 43k • written 3 months ago by • 0
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1
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2.1k
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DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
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2
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1.1k
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6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
3
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2
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1.3k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 3 months ago by ▴ 20
1
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2
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2.5k
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Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 3 months ago by • 0
3
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1
reply
3.7k
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DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 3 months ago by 43k • written 3 months ago by ▴ 10
0
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1
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440
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DESeq2 results
result DESeq2 subsetting
updated 3 months ago by ★ 4.9k • written 3 months ago by • 0
0
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1
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355
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Unclear DEseq2 replaceOutliers error message
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
0
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1
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453
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 3 months ago by 43k • written 4 months ago by • 0
3
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2
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2.0k
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Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
4 months ago • updated 3 months ago dudutchy ▴ 10
2
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3
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1.2k
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
3 months ago Paulito • 0
4
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4
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1.9k
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Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
3 months ago caroline.zanchi ▴ 10
0
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1
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361
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DESeq2 from phyloseq error
DESeq2 phyloseq
3 months ago asafpr • 0
3
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1
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546
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DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 4 months ago by 68k • written 4 months ago by • 0
1
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5
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1.3k
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Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 4 months ago by 68k • written 4 months ago by ▴ 10
8
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3
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3.0k
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DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 3 months ago by 43k • written 4 months ago by ▴ 40
2
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4
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1.6k
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Filtering after DESeq
DESeq2 IHW
written 4 months ago by ▴ 10
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4
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1.1k
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DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
4 months ago sk • 0
0
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6
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1.7k
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Discrepancies in normalised count data vs unnormalised
DESeq2
4 months ago • updated 3 months ago AMgroup • 0
0
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2
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628
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Design formula for circadian time-course data for vst() function
DESeq2
4 months ago Vishnu • 0
0
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2
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765
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Analyzing TnSeq data with DESeq2
DESeq2
written 4 months ago by • 0
0
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1
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1.1k
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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 4 months ago by 43k • written 5 months ago by • 0
0
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2
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654
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Differing results with DESeq2
DESeq2
updated 4 months ago by • 0 • written 5 months ago by • 0
0
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2
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539
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RNA Seq using Lrt
DESeq2
4 months ago Rob • 0
0
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3
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937
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Log2foldchange strange behavior
DESeq2
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
0
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1
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834
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WGCNA
WGCNA DESeq2
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
0
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1
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1.0k
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Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by ▴ 20
1
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1
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1.3k
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PhD scholar
RNASeqAnalysis DESeq2
updated 5 months ago by 4.2k • written 5 months ago by • 0
0
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1
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447
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DESeq2 - am I extracting results incorrectly?
DESeq2
updated 5 months ago by 68k • written 5 months ago by ▴ 30
4,835 results • Page 1 of 97
Recent ...
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Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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