Showing : deseq2 • reset
0
votes
3
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229
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DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
written 21 days ago by • 0
0
votes
2
replies
277
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 5 weeks ago by 43k • written 5 weeks ago by • 0
3
votes
6
replies
983
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 7 weeks ago by • 0
0
votes
1
reply
208
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 5 weeks ago by ★ 5.0k • written 6 weeks ago by • 0
0
votes
2
replies
1.2k
views
Install old version of DESeq2
apeglm Install DESeq2 version
updated 7 weeks ago by ★ 4.0k • written 6 months ago by • 0
1
vote
11
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2.0k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 7 weeks ago by ★ 4.0k • written 4 months ago by • 0
0
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2
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343
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DESeq2 on non-RNASeq counts data
DESeq2
written 4 months ago by • 0
0
votes
2
replies
351
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 7 weeks ago by ★ 4.0k • written 4 months ago by • 0
0
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0
replies
157
views
[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 7 weeks ago by ★ 4.0k • written 8 weeks ago by • 0
0
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4
replies
260
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
8 weeks ago • updated 7 weeks ago Denise • 0
0
votes
2
replies
275
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Setting up a DESeq2 Design with Paired Data
DESeq2
9 weeks ago Alexander • 0
2
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4
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528
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DESeq2 interactions
DESeq2
updated 10 weeks ago by 43k • written 3 months ago by • 0
3
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14
replies
1.3k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 5 months ago by • 0
0
votes
3
replies
403
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
758
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 4 months ago by • 0
3
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5
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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 4 months ago by ▴ 200
17
votes
45
replies
13k
views
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
0
votes
11
replies
724
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
4 months ago Denise • 0
2
votes
6
replies
653
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
4 months ago richardallenfriedmanbrooklyn ▴ 30
0
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3
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325
views
DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 4 months ago by ▴ 10
0
votes
4
replies
991
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
1
vote
2
replies
462
views
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
replies
2.2k
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 • updated 5 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 • updated 5 months ago bbao ▴ 10
0
votes
1
reply
576
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
votes
2
replies
1.0k
views
gene detection across experiments
DESeq2 Normalization
6 months ago Mara • 0
5
votes
11
replies
3.5k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 8 months ago by ▴ 10
1
vote
5
replies
5.0k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 5 months ago by 43k • written 7 months ago by • 0
1
vote
1
reply
2.2k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 6 months ago by 43k • written 6 months ago by • 0
0
votes
2
replies
1.2k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 6 months ago by 43k • written 6 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
2.7k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 7 months ago by • 0
3
votes
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
votes
1
reply
638
views
DESeq2 results
result DESeq2 subsetting
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
votes
1
reply
464
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
0
votes
1
reply
623
views
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
votes
2
replies
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
votes
3
replies
1.6k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
7 months ago Paulito • 0
4
votes
4
replies
2.1k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
7 months ago caroline.zanchi ▴ 10
0
votes
1
reply
456
views
DESeq2 from phyloseq error
DESeq2 phyloseq
7 months ago asafpr • 0
3
votes
1
reply
684
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
1.5k
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 7 months ago by 43k • written 8 months ago by ▴ 40
2
votes
4
replies
1.9k
views
Filtering after DESeq
DESeq2 IHW
written 8 months ago by ▴ 10
0
votes
4
replies
1.3k
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
8 months ago sk • 0
0
votes
6
replies
1.9k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
8 months ago • updated 7 months ago AMgroup • 0
0
votes
2
replies
763
views
Design formula for circadian time-course data for vst() function
DESeq2
8 months ago Vishnu • 0
0
votes
2
replies
917
views
Analyzing TnSeq data with DESeq2
DESeq2
written 8 months ago by • 0
0
votes
1
reply
1.2k
views
How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2 RUVSeq
updated 8 months ago by 43k • written 9 months ago by • 0
4,842 results • Page 1 of 97
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Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
Comment: Ensembl plants at annotationHub? by jwp48 • 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
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Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
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Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Votes
Answer: Where do the filename come from in the LOLA datasets?
Bioconductor Maintainer Application
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
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