Showing : DEseq2 • reset
2
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RNAseq high padj value from validated samples?
DESeq2
2.7 years ago DJ_Han • 0
0
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7
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2.2k
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LRT test followed by filtering based on LFC
deseq2 LFC LRT
written 6.8 years ago by • 0
7
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7
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1.7k
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Potential problem with independent filtering in DESeq2
DESeq2
2.8 years ago • updated 2.7 years ago Stepan • 0
1
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1
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1.6k
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Deseq2: Technical replicates for differential expression analysis
DESeq2
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
0
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1
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920
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Processing after adding Pseudocounts
DESeq2
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
2
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4
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1.2k
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Model comparison in mean-dispersion trend in DESeq2
DESeq2 StatisticalMethod
2.8 years ago Loïc • 0
2
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1
reply
3.2k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
0
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1
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1.2k
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How to use DESeq2 for just two samples ?
DESeq2
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
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1
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802
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Analysis with Batch correction
DESeq2 BatchEffect
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
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1
reply
624
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Strange Cook's Values with DESeq2
DESeq2
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
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1
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918
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DeSeq2 time series data
DESeq2 l
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
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4
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935
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Differences in sample size between conditions - pairwise comparison
DESeq2
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
2
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6
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2.6k
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Help me find the bug
DESeq2 HELP
2.8 years ago Michael • 0
0
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4
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1.9k
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DESeq2 installation error
DESeq2
updated 2.8 years ago by • 0 • written 2.8 years ago by ▴ 10
0
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4
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2.6k
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Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
0
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2
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1.8k
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Why is my log fold change not centered around 0 and lower?
DESeq2 MAplot
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
0
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4
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3.9k
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DESeq2 and heatmap for multiple comparisons
DESeq2
2.8 years ago artem.vorobyev • 0
0
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1
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4.8k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
0
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5
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1.8k
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What happens to genes with low dispersion during dispersion shrinkage in DESeq2
DESeq2
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
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4
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1.7k
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Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
2.8 years ago Dr. • 0
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2
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1.1k
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Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
DESeq2 RNAseq123
2.8 years ago fatemeh.peimani • 0
1
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6
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3.0k
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PlotCounts DESeq2 - how to plot count s for specific samples?
DESeq2 PlotCounts
2.8 years ago annamariabugaj ▴ 10
0
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2
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4.6k
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Conducting pair-wise comparison in DESeq2?
DESeq2 deseq2 biocondu Bioconductor RNASeq
written 2.8 years ago by • 0
2
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2
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1.4k
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Updating DESeq2 object's design with sva output
DESeq2 design sva
2.8 years ago Hatchet • 0
2
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2
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1.0k
views
DE Analysis on cells from a patient derived mouse xenograft with high levels of mouse count "contamination"
DESeq2
2.8 years ago jropa ▴ 10
0
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1
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1.2k
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Differential expression analysis with global differences among samples (tissues)
DESeq2 qsmooth edgeR limma
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
0
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2
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853
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Does DESeq2 work for investigating the gene differential expression before and after the treat but in the same sample?
DESeq2
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
1
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2
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4.6k
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DESeq2::plotPCA()
DESeq2
2.8 years ago Kai Hu ▴ 70
1
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1
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1.4k
views
Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 2.8 years ago by ★ 13k • written 2.8 years ago by ▴ 70
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2
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1.3k
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Log2Fold change interpretation - Continuous predictor variable
DESeq2
2.8 years ago m.c.stanley • 0
2
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1
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701
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Joining different datasets and analyzing using the group-specific condition effects strategy (DESeq2)
DESeq2
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
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2
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1.7k
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Adding gene names to DESeq result
DESeq2
updated 2.8 years ago by • 0 • written 2.8 years ago by • 0
0
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1
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1.3k
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struggling to create a heatmap
DESeq2 heatmaps
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 10
1
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3
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1.4k
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collapseReplicates error after tximeta
fishpond tximeta DESeq2
updated 2.2 years ago by 43k • written 2.8 years ago by • 0
0
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2
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2.0k
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Which genes are outliers in DESeq2?
DESeq2 RNAseq outlier
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
6
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2
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4.2k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 10
3
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1
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3.1k
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log2 of normalized counts for further analyzes
DESeq2 log2 normalized counts
updated 2.8 years ago by 68k • written 2.8 years ago by ▴ 10
0
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2
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799
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DESeq2 parameter infernce
DESeq2
2.8 years ago BioEpi • 0
0
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1
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1.0k
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DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2 LRT continuous coeficients
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 10
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1
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614
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DESeq2 with sample effect, unequal sample sizes
DESeq2
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
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1
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1.1k
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DEG analysis with Paired-end RNA-seq data using DESeq2, do I need to contain the library type when I using DESeq() function if I already using featur…
DESeq2 featurecounts
updated 2.8 years ago by ★ 1.4k • written 2.8 years ago by • 0
1
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1
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4.8k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 50
3
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6
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1.9k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
2.8 years ago • updated 2.7 years ago Zainab ▴ 20
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3
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3.0k
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Which version of DESeq2 for R 4.1.2 64bit
DESeq2
written 3.8 years ago by • 0
3
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2
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3.5k
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I cannot install annotables package in Rstudio (macOS)
DESeq2 PackageTypeData package Annotation
2.8 years ago m-bihie ▴ 10
3
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5
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1.7k
views
Design for DE analysis in tidybulk
DESeq2 designmatrix edgeR limma tidybulk
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 10
0
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1
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3.4k
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DESeq2 in R 4.2.2
DESeq2 SummarizedExperiment DelayedArray
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
0
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1
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1.1k
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Libraries loading error
DESeq2 clusterProfiler enrichplot
updated 2.8 years ago by 43k • written 2.9 years ago by • 0
0
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2
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2.9k
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 18 months ago by • 0 • written 2.8 years ago by ▴ 10
2
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2
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1.2k
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[DESeq2] There is no difference in expression in my heatmap
DESeq2 heatmaps
2.8 years ago Sooni ▴ 10
4,839 results • Page 15 of 97
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
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.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
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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