Showing : DeSeq2 • reset
0
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5
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164
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Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 1 day ago by 43k • written 1 day ago by • 0
0
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2
replies
110
views
lfc shrinkage estimator in DESeq2
DESeq2
written 2 days ago by • 0
0
votes
13
replies
725
views
Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 2 days ago by 53k • written 8 days ago by • 0
0
votes
6
replies
589
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BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 9 days ago by 25k • written 7 weeks ago by • 0
0
votes
1
reply
245
views
DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage DESeq2 contrast
updated 8 days ago by ★ 5.0k • written 11 days ago by • 0
0
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1
reply
88
views
News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
written 16 days ago by ▴ 20
0
votes
3
replies
363
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
5 weeks ago • updated 12 days ago ja569116 • 0
3
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6
replies
1.0k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 9 weeks ago by • 0
0
votes
1
reply
233
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 8 weeks ago by ★ 5.0k • written 8 weeks ago by • 0
0
votes
2
replies
1.2k
views
Install old version of DESeq2
apeglm Install DESeq2 version
updated 9 weeks ago by ★ 4.0k • written 6 months ago by • 0
1
vote
11
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2.2k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 9 weeks ago by ★ 4.0k • written 5 months ago by • 0
0
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2
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372
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DESeq2 on non-RNASeq counts data
DESeq2
written 5 months ago by • 0
0
votes
2
replies
374
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 10 weeks ago by ★ 4.0k • written 4 months ago by • 0
0
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0
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176
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 10 weeks ago by ★ 4.0k • written 10 weeks ago by • 0
0
votes
4
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300
views
Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
10 weeks ago Denise • 0
0
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2
replies
324
views
Setting up a DESeq2 Design with Paired Data
DESeq2
11 weeks ago Alexander • 0
2
votes
4
replies
561
views
DESeq2 interactions
DESeq2
updated 3 months ago by 43k • written 4 months ago by • 0
3
votes
14
replies
1.4k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 6 months ago by • 0
0
votes
3
replies
420
views
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
votes
1
reply
827
views
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 5 months ago by • 0
3
votes
5
replies
1.2k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 4 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
780
views
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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673
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
5 months ago richardallenfriedmanbrooklyn ▴ 30
0
votes
3
replies
347
views
DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 5 months ago by ▴ 10
0
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4
replies
1.1k
views
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
vote
2
replies
510
views
Differential expression on the transcript-level
DESeq2
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
3
votes
13
replies
2.3k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 15 months ago by • 0
4
votes
8
replies
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
7
votes
9
replies
5.8k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
6 months ago bbao ▴ 10
0
votes
1
reply
593
views
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
0
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2
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1.1k
views
gene detection across experiments
DESeq2 Normalization
7 months ago Mara • 0
5
votes
11
replies
3.8k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 9 months ago by ▴ 10
1
vote
5
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5.2k
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 7 months ago by • 0
1
vote
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
replies
1.5k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 7 months ago by ▴ 20
1
vote
2
replies
2.8k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 7 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 7 months ago by 43k • written 7 months ago by ▴ 10
0
votes
1
reply
662
views
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
479
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
1
reply
646
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 8 months ago by 43k • written 8 months ago by • 0
3
votes
2
replies
2.1k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
8 months ago dudutchy ▴ 10
2
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3
replies
1.6k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
8 months ago Paulito • 0
4
votes
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
483
views
DESeq2 from phyloseq error
DESeq2 phyloseq
8 months ago asafpr • 0
3
votes
1
reply
706
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 8 months ago by 68k • written 8 months ago by • 0
1
vote
5
replies
1.6k
views
Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 8 months ago by 68k • written 8 months ago by ▴ 10
9
votes
3
replies
3.3k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 8 months ago by 43k • written 8 months ago by ▴ 40
2
votes
4
replies
1.9k
views
Filtering after DESeq
DESeq2 IHW
written 9 months ago by ▴ 10
4,847 results • Page 1 of 97
Recent ...
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Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Comment: limpa analysis advice by Gordon Smyth 53k
I prefer for limpa to work on precursor intensities, because my understanding is that precursors are the basic unit of identification and q…
Answer: Confirm that OpenStats will not be archived (pryr dependency) by shepherl 4.3k
As long as OpenStats is building cleanly and all needed stated dependencies are on CRAN or Bioconductor, OpenStats will not be archived. I…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq by Michael Love 43k
Yes, I find that the LFC shrinkage and its corresponding stat `svalue` if you use lfcShrink with a threshold often returns more reliable ge…
Votes
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
Answer: Array weights in dpcDE
Answer: Array weights in dpcDE
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