Showing : DEseq2 • reset
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 3 hours ago by ★ 1.4k • written 3 days ago by • 0
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1
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165
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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
updated 16 hours ago by ★ 4.6k • written 2 days ago by ▴ 10
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
2 days ago • updated 12 hours ago Quang NN ▴ 10
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
5 days ago • updated 3 days ago Blandine • 0
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4
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190
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
6 days ago georgeyu703 • 0
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4
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369
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
7 days ago • updated 5 days ago Quang NN ▴ 10
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5
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Differential variability modelling with vst() expression
limma DESeq2
written 18 days ago by • 0
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368
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
19 days ago • updated 16 days ago sindhuri • 0
2
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9
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767
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
19 days ago • updated 7 days ago Quang NN ▴ 10
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295
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 20 days ago by 43k • written 20 days ago by • 0
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170
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 21 days ago by ★ 1.4k • written 21 days ago by • 0
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1
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355
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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 24 days ago by 43k • written 4 weeks ago by • 0
2
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1
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349
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 24 days ago by 43k • written 4 weeks ago by • 0
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2
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
4 weeks ago • updated 28 days ago Kucsera • 0
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 5 weeks ago by 43k • written 6 weeks ago by • 0
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833
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 5 weeks ago by ▴ 30
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2
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323
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 5 weeks ago by ★ 4.6k • written 6 weeks ago by • 0
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5
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566
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Deseq2 Design
RNASeq DESeq2
updated 6 weeks ago by 67k • written 6 weeks ago by • 0
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5
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516
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p value is 0, padj is 0
DESeq2
6 weeks ago Wirayatida • 0
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
6 weeks ago georgii.vdovin • 0
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 6 weeks ago by • 0 • written 7 weeks ago by • 0
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287
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 7 weeks ago by 43k • written 7 weeks ago by ▴ 20
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DESeq2 - Comparing Comparisons
DESeq2
updated 6 weeks ago by 67k • written 7 weeks ago by • 0
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553
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lfcShrink and alpha value
lfcShrink DESeq2
8 weeks ago • updated 7 weeks ago cropero • 0
2
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1
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307
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
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231
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
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274
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
8 weeks ago Anna • 0
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560
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Deseq2 res Function
DESeq2
updated 9 weeks ago by 67k • written 9 weeks ago by ▴ 10
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452
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
9 weeks ago NB • 0
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470
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Identical samples after deseq2 batch effect removal
DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
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262
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 9 weeks ago by 67k • written 9 weeks ago by • 0
1
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319
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
9 weeks ago Denise • 0
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173
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eRNAs count
RNASeq DESeq2
updated 10 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
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415
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DESeq2 rerun returns different results
DESeq2
updated 10 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
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268
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
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250
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 10 weeks ago by ★ 4.1k • written 10 weeks ago by • 0
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652
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Handling biological replicates in DESeq2
DESeq2
updated 10 weeks ago by ★ 4.6k • written 11 weeks ago by • 0
5
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 1 day ago by • 0 • written 6.0 years ago by ▴ 30
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1.0k
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 11 weeks ago by 43k • written 11 weeks ago by ▴ 10
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400
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 11 weeks ago by • 0
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
12 weeks ago • updated 11 weeks ago LuciaNhu • 0
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427
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Average expression of genes across replicates
DESeq2
updated 12 weeks ago by ★ 4.6k • written 12 weeks ago by • 0
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
12 weeks ago info ▴ 10
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1.4k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
3 months ago • updated 11 weeks ago Denise • 0
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1
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375
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Deseq to output continous sequencing data
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
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4
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881
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Adjusted p-values become NA when sub-setting samples
DESeq2
3 months ago • updated 11 weeks ago txema.heredia • 0
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3
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955
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 3 months ago by • 0
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385
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 3 months ago by • 0
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337
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
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3
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Analysis of large RNA-Seq Datasets
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Selection of correct coefficients or contrasts in DESeq2 by swbarnes2 ★ 1.4k
I think you need to include the design you used, and the command you used to call it. The simplest answer is that your two ways of doing t…
Comment: Csaw normalization strategies - general inquiry by Luca • 0
Hello Aaron, About the IP efficiencies, yes definitely and for us, to complicate this experiment further, these batches were generated by …
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by Quang NN ▴ 10
Thank you ATpoint for your response. In bulkRNAseq, I did have two cell types to compare. But, I want to also see if bulkRNAseq might have …
Answer: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
The choice of variable genes is typically part of a QC process. You select genes that in an unbiased fashion (unbiased because variance cal…
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by ATpoint ★ 4.6k
My take is that RNA-seq (be it bulk or single-cell) is inherently relative. I don't think you can really "compare" the absolute expression …
Votes
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
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