Showing : DeSeq2 • reset
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Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 2 hours ago by 53k • written 1 day ago by • 0
0
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6
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530
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BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 2 days ago by 25k • written 7 weeks ago by • 0
0
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1
reply
202
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DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage DESeq2 contrast
updated 1 day ago by ★ 5.0k • written 5 days ago by • 0
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0
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55
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News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
9 days ago Frances Turner ▴ 20
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3
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329
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DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
4 weeks ago • updated 5 days ago ja569116 • 0
3
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6
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1.0k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 8 weeks ago by • 0
0
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1
reply
225
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Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 7 weeks ago by ★ 5.0k • written 7 weeks ago by • 0
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2
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1.2k
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 8 weeks ago by ★ 4.0k • written 6 months ago by • 0
1
vote
11
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2.1k
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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 weeks ago by ★ 4.0k • written 5 months ago by • 0
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2
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360
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DESeq2 on non-RNASeq counts data
DESeq2
written 5 months ago by • 0
0
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2
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365
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 9 weeks ago by ★ 4.0k • written 4 months ago by • 0
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0
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173
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 9 weeks ago by ★ 4.0k • written 9 weeks ago by • 0
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4
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284
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
9 weeks ago Denise • 0
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2
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304
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Setting up a DESeq2 Design with Paired Data
DESeq2
10 weeks ago Alexander • 0
2
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4
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547
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DESeq2 interactions
DESeq2
updated 12 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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3
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413
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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
0
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1
reply
800
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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
3
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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
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 4 months ago by 68k • written 6.5 years ago by ▴ 60
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11
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758
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
5 months ago Denise • 0
2
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6
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665
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
5 months ago richardallenfriedmanbrooklyn ▴ 30
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3
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342
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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
1
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2
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496
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Differential expression on the transcript-level
DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
3
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13
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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
4
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8
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2.0k
views
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
reply
589
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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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1.1k
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gene detection across experiments
DESeq2 Normalization
6 months ago Mara • 0
5
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11
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3.7k
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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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5.2k
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Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 6 months ago by 43k • written 7 months ago by • 0
1
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1
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2.3k
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DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 7 months ago by 43k • written 7 months ago by • 0
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2
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1.3k
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6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 7 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
1
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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
reply
3.8k
views
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
0
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1
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654
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DESeq2 results
result DESeq2 subsetting
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
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1
reply
475
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
0
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1
reply
634
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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
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
8 months ago • updated 7 months ago dudutchy ▴ 10
2
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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
8 months ago Paulito • 0
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4
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2.2k
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Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
8 months ago caroline.zanchi ▴ 10
0
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1
reply
470
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DESeq2 from phyloseq error
DESeq2 phyloseq
8 months ago asafpr • 0
3
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1
reply
695
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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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3.3k
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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 9 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
0
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6
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1.9k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
8 months ago • updated 7 months ago AMgroup • 0
4,845 results • Page 1 of 97
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Replies
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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