Showing : DEseq2 • reset
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 2 days ago by ★ 4.0k • written 4 months ago by • 0
1
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11
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1.2k
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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 2 days ago by ★ 4.0k • written 3 months ago by • 0
0
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1
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197
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DESeq2 on non-RNASeq counts data
DESeq2
updated 3 days ago by ★ 4.0k • written 3 months ago by • 0
2
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3
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134
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
3 days ago • updated 2 days ago Ahmed Salah • 0
0
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2
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268
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 5 days ago by ★ 4.0k • written 10 weeks ago by • 0
0
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0
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81
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 5 days ago by ★ 4.0k • written 10 days ago by • 0
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4
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153
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
9 days ago • updated 6 days ago Denise • 0
0
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2
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178
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Setting up a DESeq2 Design with Paired Data
DESeq2
17 days ago • updated 16 days ago Alexander • 0
2
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4
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455
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DESeq2 interactions
DESeq2
updated 25 days ago by 43k • written 10 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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3
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358
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 10 weeks ago by 43k • written 11 weeks ago by • 0
0
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1
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670
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 10 weeks ago by 43k • written 3 months ago by • 0
3
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5
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1.1k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 11 weeks ago by 68k • written 12 weeks ago by ▴ 200
17
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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 12 weeks ago by 68k • written 6.3 years ago by ▴ 60
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11
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610
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
3 months ago Denise • 0
2
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6
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566
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
3 months ago richardallenfriedmanbrooklyn ▴ 30
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3
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266
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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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852
views
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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396
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Differential expression on the transcript-level
DESeq2
updated 3 months ago by ★ 1.4k • written 4 months ago by • 0
3
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13
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2.1k
views
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
views
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
views
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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1
reply
513
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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971
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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
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 6 months ago by ▴ 10
1
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5
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4.4k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 4 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 5 months ago by 43k • written 5 months ago by • 0
0
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2
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1.2k
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6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
3
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2
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1.4k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 5 months ago by ▴ 20
1
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2
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2.7k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 5 months ago by • 0
3
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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
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590
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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
416
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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
566
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 6 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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1.5k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
6 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
6 months ago caroline.zanchi ▴ 10
0
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1
reply
411
views
DESeq2 from phyloseq error
DESeq2 phyloseq
6 months ago asafpr • 0
3
votes
1
reply
631
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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1.5k
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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
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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
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1.8k
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Filtering after DESeq
DESeq2 IHW
written 7 months ago by ▴ 10
0
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4
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1.2k
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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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692
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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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823
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Analyzing TnSeq data with DESeq2
DESeq2
written 7 months ago by • 0
0
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1
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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 7 months ago by 43k • written 8 months ago by • 0
0
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2
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718
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Differing results with DESeq2
DESeq2
updated 7 months ago by • 0 • written 7 months ago by • 0
0
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2
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592
views
RNA Seq using Lrt
DESeq2
7 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
4,839 results • Page 1 of 97
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Comment: limpa - drivers for unusually high standard error? by Julia Broadbent • 0
Apologies for not being clearer in my initial question, but thank you for answering regardless! The large SE values I am looking at appear …
Answer: limpa - drivers for unusually high standard error? by Gordon Smyth 53k
Hi Julia, I am going to assume that you mean standard errors (SEs) returned by `dpcQuant()`, because later stages in the limpa pipeline do…
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It sounds like AUCell is struggling with thresholding because your cDC2 gene set doesn t show a clear bimodal distribution. While a high AU…
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FeatureCounts can behave differently with ONT cDNA BAM files due to long read splice patterns, and many users compare settings or presets m…
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For gamers facing technical issues or errors in complex scripts, the Redz Hub script download provides a reliable tool to optimize performa…
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Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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