Showing : Deseq2 • reset
1
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4
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123
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Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
1 day ago • updated 4 hours ago Mariami • 0
0
votes
5
replies
2.3k
views
DESeq2 contrast cleaning problem
software error bugs deseq2
written 10.0 years ago by • 0
0
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1
reply
141
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DESeq2 for 16S rRNA Analysis
DESeq2
updated 11 days ago by 68k • written 11 days ago by • 0
0
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5
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256
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Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 14 days ago by 43k • written 14 days ago by • 0
0
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2
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203
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lfc shrinkage estimator in DESeq2
DESeq2
written 14 days ago by • 0
0
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13
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836
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Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 14 days ago by 53k • written 20 days ago by • 0
0
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6
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635
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BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 21 days ago by 25k • written 9 weeks ago by • 0
0
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1
reply
281
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DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage DESeq2 contrast
updated 21 days ago by ★ 5.0k • written 24 days ago by • 0
0
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1
reply
145
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News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
written 29 days ago by ▴ 20
0
votes
3
replies
408
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
7 weeks ago • updated 24 days ago ja569116 • 0
3
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6
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1.1k
views
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
reply
244
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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
0
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2
replies
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
1
vote
11
replies
2.3k
views
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
0
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2
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408
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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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391
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 11 weeks ago by ★ 4.0k • written 5 months ago by • 0
0
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0
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192
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 11 weeks ago by ★ 4.0k • written 12 weeks ago by • 0
0
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4
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333
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
12 weeks ago Denise • 0
0
votes
2
replies
370
views
Setting up a DESeq2 Design with Paired Data
DESeq2
3 months ago Alexander • 0
2
votes
4
replies
583
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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
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 6 months ago by • 0
0
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3
replies
439
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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
0
votes
1
reply
882
views
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
votes
5
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1.2k
views
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
votes
45
replies
13k
views
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
0
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11
replies
821
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
5 months ago Denise • 0
2
votes
6
replies
690
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
5 months ago richardallenfriedmanbrooklyn ▴ 30
0
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3
replies
361
views
DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 6 months ago by ▴ 10
0
votes
4
replies
1.1k
views
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
replies
549
views
Differential expression on the transcript-level
DESeq2
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
3
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13
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2.4k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 16 months ago by • 0
4
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8
replies
2.1k
views
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
7
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9
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5.8k
views
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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609
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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
replies
1.1k
views
gene detection across experiments
DESeq2 Normalization
7 months ago Mara • 0
5
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11
replies
4.0k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 9 months ago by ▴ 10
1
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5
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5.4k
views
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
1
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1
reply
2.3k
views
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
0
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2
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1.3k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
3
votes
2
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1.6k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 8 months ago by ▴ 20
1
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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
votes
1
reply
3.9k
views
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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677
views
DESeq2 results
result DESeq2 subsetting
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
0
votes
1
reply
493
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
1
reply
663
views
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
votes
2
replies
2.1k
views
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
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
8 months ago Paulito • 0
4
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4
replies
2.2k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
8 months ago caroline.zanchi ▴ 10
0
votes
1
reply
509
views
DESeq2 from phyloseq error
DESeq2 phyloseq
8 months ago asafpr • 0
3
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1
reply
731
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DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 9 months ago by 68k • written 9 months ago by • 0
4,849 results • Page 1 of 97
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Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you so much for your help! will try to proceed with the suggestion
Comment: GSEA in R/Bioconductor course by a2a2haa • 0
Academic researchers often share their breakthroughs and course updates through visual stories, making it essential to have tools that pres…
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 `…
Comment: Announcing a New Journal - Bioinformatics Methods and Applications - Now Open fo by a2a2haa • 0
By promoting reproducible analysis, the scientific community can better understand the precise mechanisms that make [Hydrogen inhalation sa…
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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