Showing : DeSeq2 • reset
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Subsetting data verses contrasts [DESeq2]?
DESeq2
updated 2 hours ago by ★ 5.0k • written 3 hours ago by • 0
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33
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How to start learning RNA sequence analysis with DESeq2
DESeq2
21 hours ago Syed • 0
1
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4
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170
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Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
2 days ago • updated 1 day ago Mariami • 0
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5
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2.3k
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DESeq2 contrast cleaning problem
software error bugs deseq2
written 10.0 years ago by • 0
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1
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153
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DESeq2 for 16S rRNA Analysis
DESeq2
updated 12 days ago by 68k • written 12 days ago by • 0
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5
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261
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Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 15 days ago by 43k • written 15 days ago by • 0
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2
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207
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lfc shrinkage estimator in DESeq2
DESeq2
written 15 days ago by • 0
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13
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843
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Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 15 days ago by 53k • written 21 days ago by • 0
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6
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643
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BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 22 days ago by 25k • written 9 weeks ago by • 0
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1
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291
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DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage DESeq2 contrast
updated 22 days ago by ★ 5.0k • written 25 days ago by • 0
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1
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149
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News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
written 4 weeks ago by ▴ 20
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3
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413
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DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
7 weeks ago • updated 25 days ago ja569116 • 0
3
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6
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1.1k
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 11 weeks ago by • 0
0
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1
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247
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Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 10 weeks ago by ★ 5.0k • written 10 weeks ago by • 0
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2
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1.3k
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 11 weeks ago by ★ 4.0k • written 7 months ago by • 0
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11
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2.3k
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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 11 weeks ago by ★ 4.0k • written 5 months ago by • 0
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2
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413
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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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394
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 12 weeks ago by ★ 4.0k • written 5 months ago by • 0
0
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0
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195
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 12 weeks ago by ★ 4.0k • written 3 months ago by • 0
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4
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339
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
12 weeks ago Denise • 0
0
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2
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378
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Setting up a DESeq2 Design with Paired Data
DESeq2
3 months ago Alexander • 0
2
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4
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586
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DESeq2 interactions
DESeq2
updated 3 months ago by 43k • written 4 months ago by • 0
3
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14
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1.5k
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 6 months ago by • 0
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3
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443
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
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1
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894
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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 5 months ago by 43k • written 5 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 5 months ago by 68k • written 5 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 5 months ago by 68k • written 6.5 years ago by ▴ 60
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11
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823
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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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691
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
6 months ago richardallenfriedmanbrooklyn ▴ 30
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3
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364
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 6 months ago by ▴ 10
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4
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1.1k
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 6 months ago by 43k • written 6 months ago by • 0
1
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2
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553
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Differential expression on the transcript-level
DESeq2
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
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13
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2.4k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 16 months ago by • 0
4
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8
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2.1k
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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
7 months ago richardallenfriedmanbrooklyn ▴ 30
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9
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5.9k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
7 months ago bbao ▴ 10
0
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1
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611
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discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 7 months ago by 68k • written 7 months ago by • 0
0
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2
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1.1k
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gene detection across experiments
DESeq2 Normalization
7 months ago Mara • 0
5
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11
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4.0k
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 9 months ago by ▴ 10
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5
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5.4k
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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 8 months ago by • 0
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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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1.6k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 8 months ago by ▴ 20
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2
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2.8k
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Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 8 months ago by • 0
3
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1
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3.9k
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DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 8 months ago by 43k • written 8 months ago by ▴ 10
0
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1
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680
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DESeq2 results
result DESeq2 subsetting
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
0
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1
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498
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Unclear DEseq2 replaceOutliers error message
DESeq2
updated 8 months ago by 43k • written 8 months ago by • 0
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1
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668
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 8 months ago by 43k • written 9 months ago by • 0
3
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2
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2.1k
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Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
9 months ago • updated 8 months ago dudutchy ▴ 10
2
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3
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1.7k
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
8 months ago Paulito • 0
4
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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
4,851 results • Page 1 of 98
Recent ...
Replies
Answer: Subsetting data verses contrasts [DESeq2]? by ATpoint ★ 5.0k
This has been asked many times before, please search for relevant posts. In short: Generally it is least tedious to not split the data and …
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you so much for your help! will try to proceed with the suggestion
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you for the explanation. I understand, although at the moment we are limited in our ability to increase N. My concern came from the o…
Answer: Bulk RNAseq analysis for by Gordon Smyth 53k
All three packages allow paired comparisons, where the clone is the "pair". limma moreover allows mixed models (just run `voomLmFit` with `…
Answer: Bulk RNAseq analysis for by James W. MacDonald 68k
In my experience, the within-clone variability of differentiated stem cells is often as large or larger than the between-clone variability,…
Votes
Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
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