Showing : Deseq2 • reset
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DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
updated 1 day ago by • 0 • written 4 days ago by • 0
0
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2
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216
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BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 18 days ago by 43k • written 20 days ago by • 0
3
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6
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851
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 4 weeks ago by • 0
0
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1
reply
163
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Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 24 days ago by ★ 5.0k • written 25 days ago by • 0
0
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2
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1.1k
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 4 weeks ago by ★ 4.0k • written 5 months ago by • 0
1
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11
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1.8k
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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 4 weeks ago by ★ 4.0k • written 4 months ago by • 0
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2
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308
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DESeq2 on non-RNASeq counts data
DESeq2
updated 3 days ago by • 0 • written 4 months ago by • 0
0
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2
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336
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 5 weeks ago by ★ 4.0k • written 3 months ago by • 0
0
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0
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132
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
0
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4
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221
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
5 weeks ago Denise • 0
0
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2
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239
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Setting up a DESeq2 Design with Paired Data
DESeq2
6 weeks ago Alexander • 0
2
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4
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503
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DESeq2 interactions
DESeq2
updated 8 weeks ago by 43k • written 3 months ago by • 0
3
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14
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1.2k
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 4 months ago by • 0
0
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3
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382
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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 3 months ago by • 0
0
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1
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721
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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 3 months ago by 43k • written 4 months ago by • 0
3
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5
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1.1k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 3 months ago by 68k • written 3 months ago by ▴ 200
17
votes
45
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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
683
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
4 months ago Denise • 0
2
votes
6
replies
621
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
4 months ago richardallenfriedmanbrooklyn ▴ 30
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3
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306
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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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920
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 4 months ago by 43k • written 5 months ago by • 0
1
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2
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430
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Differential expression on the transcript-level
DESeq2
updated 4 months ago by ★ 1.4k • written 5 months ago by • 0
3
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13
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2.2k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 14 months ago by • 0
4
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8
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2.0k
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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
5 months ago richardallenfriedmanbrooklyn ▴ 30
7
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9
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5.7k
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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
551
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 5 months ago by 68k • written 5 months ago by • 0
0
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2
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1.0k
views
gene detection across experiments
DESeq2 Normalization
5 months ago Mara • 0
5
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11
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3.4k
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 7 months ago by ▴ 10
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5
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4.7k
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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 6 months ago by • 0
1
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1
reply
2.2k
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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
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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 6 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 6 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 6 months ago by 43k • written 6 months ago by ▴ 10
0
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1
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621
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DESeq2 results
result DESeq2 subsetting
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
votes
1
reply
442
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 6 months ago by 43k • written 6 months ago by • 0
0
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1
reply
607
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
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2
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2.1k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
7 months ago • updated 6 months ago dudutchy ▴ 10
2
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3
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1.5k
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
7 months ago Paulito • 0
4
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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
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1
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442
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DESeq2 from phyloseq error
DESeq2 phyloseq
7 months ago asafpr • 0
3
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1
reply
667
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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
8
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3
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3.1k
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DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 6 months ago by 43k • written 7 months ago by ▴ 40
2
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4
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1.9k
views
Filtering after DESeq
DESeq2 IHW
written 8 months ago by ▴ 10
0
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4
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1.2k
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DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
7 months ago sk • 0
0
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6
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1.8k
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Discrepancies in normalised count data vs unnormalised
DESeq2
7 months ago AMgroup • 0
0
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2
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745
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Design formula for circadian time-course data for vst() function
DESeq2
7 months ago Vishnu • 0
0
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2
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881
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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 ...
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Comment: nice 3D displays for PCA analysis by adam80haynes • 0
That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
Comment: Bioinformatician at the Lausanne University Hospital by TikTsokaasocissalpc • 0
The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
Comment: DECIPHER DesignProbes unable to design FISH-probes by TikTsokaasocissalpc • 0
If you want to share your research progress and microbiome discoveries with colleagues or friends, [snaptroid android][1] download free mak…
Answer: Limma-voom sample weights and impact on DEG numbers by Gordon Smyth 53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
Answer: wgcna module preseravtion taking too long? by ATpoint ★ 5.0k
WGCNA is not a Bioconductor package, you won't get an answer here. Consider biostars.org or the r/bioinformatics reddit. Note that 10 sampl…
Votes
Limma-voom sample weights and impact on DEG numbers
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
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