Showing : DESeq2 • reset
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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
4 hours ago Simran • 0
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4
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
5 days ago • updated 4 hours ago Lennie • 0
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4
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 7 days ago by • 0
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755
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Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
updated 10 days ago by 68k • written 11 days ago by • 0
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
13 days ago • updated 12 days ago Luca • 0
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2
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405
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 8 days ago by 43k • written 16 days ago by ▴ 20
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5
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 6 days ago by • 0 • written 19 days ago by • 0
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186
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 18 days ago by 43k • written 19 days ago by • 0
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3
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how many significant figures are there in DESeq2 output
DESeq2
updated 23 days ago by ★ 4.7k • written 24 days ago by ▴ 180
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5
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984
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Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
27 days ago • updated 25 days ago picasa1983 • 0
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Vertical line at A=0, nothing else, on MA plot
deseq2
updated 26 days ago by ▴ 10 • written 6.0 years ago by ▴ 20
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1
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331
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How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData DESeq2 pseudobulk sing
updated 27 days ago by 68k • written 28 days ago by • 0
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456
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 28 days ago by ★ 1.4k • written 29 days ago by ▴ 10
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1
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287
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DEseq2 design for additive treatment
DESeq2
updated 29 days ago by ★ 4.7k • written 29 days ago by • 0
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Plot title for PCA in DESeq2
DESeq2
4 weeks ago • updated 28 days ago AL • 0
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 4 weeks ago by 43k • written 4 weeks ago by • 0
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 5 weeks ago by ★ 4.7k • written 5 weeks ago by • 0
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1
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158
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 6 weeks ago by 43k • written 6 weeks ago by • 0
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3
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524
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DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 6 weeks ago by • 0 • written 6 weeks ago by • 0
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382
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accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 6 weeks ago by • 0 • written 7 weeks ago by • 0
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3
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449
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 27 days ago by • 0 • written 7 weeks ago by • 0
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3
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418
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 7 weeks ago by • 0 • written 8 weeks ago by ▴ 10
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1
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233
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 7 weeks ago by 43k • written 8 weeks ago by • 0
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476
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 8 weeks ago by ★ 1.4k • written 8 weeks ago by • 0
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4
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977
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Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
8 weeks ago Quang NN ▴ 10
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
8 weeks ago Blandine • 0
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5
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359
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 8 weeks ago by • 0
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4
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530
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
9 weeks ago • updated 8 weeks ago Quang NN ▴ 10
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5
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Differential variability modelling with vst() expression
limma DESeq2
written 10 weeks ago by • 0
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3
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573
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 10 weeks ago by • 0
2
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9
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1.1k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
10 weeks ago • updated 9 weeks ago Quang NN ▴ 10
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1
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457
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 11 weeks ago by 43k • written 11 weeks ago by • 0
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1
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221
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 11 weeks ago by ★ 1.4k • written 11 weeks ago by • 0
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1
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414
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Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 11 weeks ago by 43k • written 3 months ago by • 0
2
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1
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415
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 11 weeks ago by 43k • written 12 weeks ago by • 0
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2
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408
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
12 weeks ago Kucsera • 0
1
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1
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429
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
1
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9
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975
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 3 months ago by ▴ 30
4
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2
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542
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 3 months ago by ★ 4.7k • written 3 months ago by ▴ 10
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5
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677
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Deseq2 Design
RNASeq DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
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5
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693
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p value is 0, padj is 0
DESeq2
3 months ago Wirayatida • 0
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2
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
3 months ago georgii.vdovin • 0
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7
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 3 months ago by • 0 • written 3 months ago by • 0
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1
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382
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 3 months ago by 43k • written 3 months ago by ▴ 20
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DESeq2 - Comparing Comparisons
DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
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4
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649
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lfcShrink and alpha value
lfcShrink DESeq2
3 months ago cropero • 0
2
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1
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413
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 3 months ago by 43k • written 3 months ago by • 0
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292
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
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330
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
3 months ago Anna • 0
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2
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Deseq2 res Function
DESeq2
updated 4 months ago by 68k • written 4 months ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: Error in cnetplot by Guido Hooiveld ★ 4.1k
Unfortunately you did not show how you generated your input data (object enrichment), nor did you show the output from `sessionInfo()`. To …
Answer: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
I think this is because Ensembl can assign different Gene IDs to "the same gene" if it is found both on a standard chromosome and a scaffol…
Comment: Explannation for ROAST results by Jay • 0
Yes! Tnx for your reply. I didn't notice the group design problem, so stupid. Thank you!
Answer: Explannation for ROAST results by ATpoint ★ 4.7k
The `contrast = 2` in an intercept-less design test whether the expression in the 2nd group is not 0. You can easily solve this by using `~…
Comment: Explannation for ROAST results by Jay • 0
BTW, AP1 is a character, composed of gene entrez ID, so is HIF1, UPR, etc al. And the rownames of `expr.i` is also gene entrez ID.
Votes
Comment: Limma comparing gene expression between base line and one treatment
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
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