Showing : DESeq2 • reset
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
updated 19 hours ago by 68k • written 1 day ago by • 0
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4
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369
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 3 days ago by • 0
0
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1
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392
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Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
updated 6 days ago by 68k • written 6 days ago by • 0
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2
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1.2k
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
9 days ago • updated 8 days ago Luca • 0
0
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2
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371
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 3 days ago by 43k • written 12 days ago by ▴ 20
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913
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 2 days ago by • 0 • written 15 days ago by • 0
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1
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174
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 14 days ago by 43k • written 15 days ago by • 0
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3
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596
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how many significant figures are there in DESeq2 output
DESeq2
updated 19 days ago by ★ 4.7k • written 20 days ago by ▴ 180
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5
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980
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Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
23 days ago • updated 21 days ago picasa1983 • 0
3
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7
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2.0k
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Vertical line at A=0, nothing else, on MA plot
deseq2
updated 22 days ago by ▴ 10 • written 6.0 years ago by ▴ 20
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1
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325
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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 23 days ago by 68k • written 23 days ago by • 0
1
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1
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451
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 24 days ago by ★ 1.4k • written 24 days ago by ▴ 10
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1
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283
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DEseq2 design for additive treatment
DESeq2
updated 25 days ago by ★ 4.7k • written 25 days ago by • 0
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505
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Plot title for PCA in DESeq2
DESeq2
27 days ago • updated 24 days ago AL • 0
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3
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547
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 28 days ago by 43k • written 4 weeks ago by • 0
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 4 weeks ago by ★ 4.7k • written 5 weeks ago by • 0
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1
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156
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 5 weeks ago by 43k • written 6 weeks ago by • 0
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3
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517
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DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 5 weeks ago by • 0 • written 6 weeks ago by • 0
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2
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380
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accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 5 weeks ago by • 0 • written 6 weeks ago by • 0
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3
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447
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 23 days ago by • 0 • written 6 weeks ago by • 0
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3
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415
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 6 weeks ago by • 0 • written 7 weeks ago by ▴ 10
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1
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229
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
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2
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475
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 7 weeks ago by ★ 1.4k • written 8 weeks ago by • 0
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4
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972
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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
7 weeks ago Quang NN ▴ 10
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2
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543
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
8 weeks ago • updated 7 weeks ago Blandine • 0
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5
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357
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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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521
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
8 weeks ago Quang NN ▴ 10
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5
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427
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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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569
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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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1.0k
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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 8 weeks ago Quang NN ▴ 10
1
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1
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451
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
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1
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217
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 10 weeks ago by ★ 1.4k • written 10 weeks ago by • 0
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1
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411
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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 10 weeks ago by 43k • written 12 weeks ago by • 0
2
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1
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413
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 10 weeks ago by 43k • written 12 weeks ago by • 0
0
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2
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406
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
11 weeks ago Kucsera • 0
1
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1
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422
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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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968
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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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530
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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
1
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5
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673
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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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680
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p value is 0, padj is 0
DESeq2
3 months ago Wirayatida • 0
1
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2
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654
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
3 months ago georgii.vdovin • 0
0
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7
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996
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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
0
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1
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375
views
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
0
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3
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512
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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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2
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288
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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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2
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329
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
3 months ago Anna • 0
1
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2
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634
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Deseq2 res Function
DESeq2
updated 3 months ago by 68k • written 3 months ago by ▴ 10
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4
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538
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
3 months ago NB • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Comment: deseq2 lfc shrinkage with few DEGs by Michael Love 43k
Agree with your edit.
Comment: DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling) by Michael Love 43k
See above about my recommendation to collaborate with someone familiar with linear models represented in R. I have to limit my time on the …
Votes
Comment: Using TPM from tximport of Salmon output for singscore
Answer: Using TPM from tximport of Salmon output for singscore
Comment: deseq2 lfc shrinkage with few DEGs
Answer: DESEQ2 looking at main effects while controlling for a continuous variable
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
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