Showing : Deseq2 • reset
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Analyzing TnSeq data with DESeq2
DESeq2
updated 14 hours ago by • 0 • written 1 day ago by • 0
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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
updated 2 days ago by 43k • written 4 weeks ago by • 0
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Differing results with DESeq2
DESeq2
updated 2 hours ago by • 0 • written 20 days ago by • 0
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RNA Seq using Lrt
DESeq2
2 days ago • updated 1 day ago Rob • 0
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Log2foldchange strange behavior
DESeq2
updated 10 days ago by ★ 4.8k • written 10 days ago by • 0
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WGCNA
WGCNA DESeq2
updated 12 days ago by ★ 4.8k • written 16 days ago by • 0
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Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 13 days ago by ★ 1.4k • written 13 days ago by ▴ 20
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PhD scholar
RNASeqAnalysis DESeq2
updated 13 days ago by 4.1k • written 13 days ago by • 0
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DESeq2 - am I extracting results incorrectly?
DESeq2
updated 16 days ago by 68k • written 16 days ago by ▴ 30
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DESeq - help with pair wise comparisons
DESeq2
17 days ago bd2000 ▴ 30
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
20 days ago • updated 17 days ago ktz • 0
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DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 26 days ago by ★ 4.8k • written 26 days ago by • 0
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 27 days ago by ★ 4.8k • written 7 weeks ago by • 0
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
5 weeks ago • updated 4 weeks ago Lennie • 0
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 5 weeks ago by • 0
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Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
updated 5 weeks ago by 68k • written 5 weeks ago by • 0
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
6 weeks ago • updated 14 days ago Luca • 0
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 5 weeks ago by 43k • written 6 weeks ago by ▴ 20
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 6 weeks ago by 43k • written 7 weeks ago by • 0
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how many significant figures are there in DESeq2 output
DESeq2
updated 7 weeks ago by ★ 4.8k • written 7 weeks ago by ▴ 180
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Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
8 weeks ago • updated 7 weeks ago picasa1983 • 0
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Vertical line at A=0, nothing else, on MA plot
deseq2
updated 8 weeks ago by ▴ 10 • written 6.1 years ago by ▴ 20
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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 8 weeks ago by 68k • written 8 weeks ago by • 0
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 8 weeks ago by ★ 1.4k • written 8 weeks ago by ▴ 10
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DEseq2 design for additive treatment
DESeq2
updated 8 weeks ago by ★ 4.8k • written 8 weeks ago by • 0
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Plot title for PCA in DESeq2
DESeq2
8 weeks ago AL • 0
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 9 weeks ago by ★ 4.8k • written 9 weeks ago by • 0
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192
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
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DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 10 weeks ago by • 0 • written 11 weeks ago by • 0
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425
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accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 10 weeks ago by • 0 • written 11 weeks ago by • 0
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 8 weeks ago by • 0 • written 11 weeks ago by • 0
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 11 weeks ago by • 0 • written 12 weeks ago by ▴ 10
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281
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 12 weeks ago by ★ 1.4k • written 3 months ago by • 0
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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
12 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
3 months ago Blandine • 0
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421
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 3 months ago by • 0
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663
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
3 months ago Quang NN ▴ 10
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Differential variability modelling with vst() expression
limma DESeq2
written 3 months ago by • 0
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650
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 3 months ago by • 0
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
3 months ago Quang NN ▴ 10
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543
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 3 months ago by 43k • written 3 months ago by • 0
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246
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 3 months ago by ★ 1.4k • written 3 months ago by • 0
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443
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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 3 months ago by 43k • written 4 months ago by • 0
2
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450
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 3 months ago by 43k • written 3 months ago by • 0
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489
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
3 months ago Kucsera • 0
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467
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
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9
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1.1k
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 4 months ago by ▴ 30
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 4 months ago by ★ 4.8k • written 4 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
Votes
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
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