Showing : Deseq2 • reset
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Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 1 hour ago by ★ 5.0k • written 23 hours ago by • 0
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2
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1.0k
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 8 days ago by ★ 4.0k • written 4 months ago by • 0
1
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11
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1.3k
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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 8 days ago by ★ 4.0k • written 3 months ago by • 0
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1
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218
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DESeq2 on non-RNASeq counts data
DESeq2
updated 9 days ago by ★ 4.0k • written 3 months ago by • 0
3
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5
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353
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
10 days ago • updated 4 days ago Ahmed Salah • 0
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2
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285
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 11 days ago by ★ 4.0k • written 11 weeks ago by • 0
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0
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92
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 11 days ago by ★ 4.0k • written 17 days ago by • 0
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4
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181
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
16 days ago • updated 13 days ago Denise • 0
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2
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193
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Setting up a DESeq2 Design with Paired Data
DESeq2
23 days ago Alexander • 0
2
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4
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464
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DESeq2 interactions
DESeq2
updated 4 weeks ago by 43k • written 10 weeks ago by • 0
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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 4 months ago by • 0
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3
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363
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 11 weeks ago by 43k • written 12 weeks ago by • 0
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1
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678
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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 11 weeks ago by 43k • written 3 months ago by • 0
3
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5
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1.1k
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How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 12 weeks ago by 68k • written 3 months 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 3 months ago by 68k • written 6.3 years ago by ▴ 60
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11
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618
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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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572
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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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271
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 3 months ago by ▴ 10
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4
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863
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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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402
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Differential expression on the transcript-level
DESeq2
updated 4 months ago by ★ 1.4k • written 4 months ago by • 0
3
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13
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2.1k
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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
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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
4 months ago richardallenfriedmanbrooklyn ▴ 30
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9
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5.6k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
4 months ago bbao ▴ 10
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1
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521
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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
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2
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978
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gene detection across experiments
DESeq2 Normalization
5 months ago Mara • 0
5
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11
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3.2k
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 7 months ago by ▴ 10
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5
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4.5k
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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
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2.2k
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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
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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
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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 5 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 5 months ago by 43k • written 5 months ago by ▴ 10
0
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1
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597
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DESeq2 results
result DESeq2 subsetting
updated 5 months ago by ★ 5.0k • written 5 months ago by • 0
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1
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421
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Unclear DEseq2 replaceOutliers error message
DESeq2
updated 6 months ago by 43k • written 6 months ago by • 0
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1
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571
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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
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Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
6 months ago dudutchy ▴ 10
2
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3
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1.5k
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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
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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
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417
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DESeq2 from phyloseq error
DESeq2 phyloseq
6 months ago asafpr • 0
3
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1
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639
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DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 6 months ago by 68k • written 6 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 6 months ago by 68k • written 6 months ago by ▴ 10
8
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3
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3.1k
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DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 6 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
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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
7 months ago • updated 6 months ago sk • 0
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6
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1.8k
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Discrepancies in normalised count data vs unnormalised
DESeq2
7 months ago • updated 6 months ago AMgroup • 0
0
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2
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701
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Design formula for circadian time-course data for vst() function
DESeq2
7 months ago Vishnu • 0
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2
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827
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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
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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 7 months ago by 43k • written 8 months ago by • 0
0
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2
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723
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Differing results with DESeq2
DESeq2
updated 7 months ago by • 0 • written 8 months ago by • 0
0
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2
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600
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RNA Seq using Lrt
DESeq2
7 months ago Rob • 0
4,840 results • Page 1 of 97
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Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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