Showing : Deseq2 • reset
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3
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212
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DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
written 18 days ago by • 0
0
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2
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259
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BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 4 weeks ago by 43k • written 4 weeks ago by • 0
3
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6
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968
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 6 weeks ago by • 0
0
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1
reply
192
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Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 5 weeks ago by ★ 5.0k • written 5 weeks ago by • 0
0
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2
replies
1.1k
views
Install old version of DESeq2
apeglm Install DESeq2 version
updated 6 weeks ago by ★ 4.0k • written 6 months ago by • 0
1
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11
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1.9k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 6 weeks ago by ★ 4.0k • written 4 months ago by • 0
0
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2
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338
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DESeq2 on non-RNASeq counts data
DESeq2
written 4 months ago by • 0
0
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2
replies
344
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 7 weeks ago by ★ 4.0k • written 3 months ago by • 0
0
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0
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155
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 7 weeks ago by ★ 4.0k • written 7 weeks ago by • 0
0
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4
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246
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
7 weeks ago Denise • 0
0
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2
replies
263
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Setting up a DESeq2 Design with Paired Data
DESeq2
8 weeks ago Alexander • 0
2
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4
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520
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DESeq2 interactions
DESeq2
updated 9 weeks ago by 43k • written 3 months ago by • 0
3
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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
0
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3
replies
394
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 3 months ago by 43k • written 4 months ago by • 0
0
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1
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743
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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
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
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Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 4 months ago by 68k • written 6.4 years ago by ▴ 60
0
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11
replies
714
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
4 months ago Denise • 0
2
votes
6
replies
647
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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320
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 4 months ago by ▴ 10
0
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4
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972
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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 5 months ago by • 0
1
vote
2
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451
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
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2.2k
views
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
5 months ago richardallenfriedmanbrooklyn ▴ 30
7
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9
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5.7k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
5 months ago bbao ▴ 10
0
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1
reply
570
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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1.0k
views
gene detection across experiments
DESeq2 Normalization
6 months ago Mara • 0
5
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11
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3.5k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 8 months ago by ▴ 10
1
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5
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4.9k
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
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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
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2
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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
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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
reply
634
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
456
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
620
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 7 months ago by 43k • written 7 months ago by • 0
3
votes
2
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2.1k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
7 months ago dudutchy ▴ 10
2
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3
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1.6k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
7 months ago Paulito • 0
4
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4
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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
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1
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455
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DESeq2 from phyloseq error
DESeq2 phyloseq
7 months ago asafpr • 0
3
votes
1
reply
678
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DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 7 months ago by 68k • written 7 months ago by • 0
1
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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 7 months ago by 68k • written 7 months ago by ▴ 10
9
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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 8 months ago by ▴ 10
0
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4
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1.3k
views
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
0
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2
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760
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Design formula for circadian time-course data for vst() function
DESeq2
8 months ago Vishnu • 0
0
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2
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907
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Analyzing TnSeq data with DESeq2
DESeq2
written 8 months ago by • 0
0
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1
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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
Recent ...
Replies
Comment: Converting Probe IDs to HGNC symbols by nana • 0
Converting probe IDs to HGNC gene symbols depends on the platform the probes come from (Affymetrix, Illumina, Agilent, etc.). Below are the…
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…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub? by jwp48 • 0
Dear Johannes, Would it be possible to generate a EnsDb for the newest Medicago V5 genome release? Medicago truncatula A17 r5.0 This woul…
Votes
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
how to control age and gender effect in expression data using DESeq2
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
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