Showing : DEseq2 • reset
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Filtering after DESeq
DESeq2 IHW
4 hours ago caroline.zanchi • 0
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Analyzing TnSeq data with DESeq2
DESeq2
updated 1 day ago by • 0 • written 2 days ago by • 0
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579
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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 3 days ago by 43k • written 4 weeks ago by • 0
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Differing results with DESeq2
DESeq2
updated 1 day ago by • 0 • written 21 days ago by • 0
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293
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RNA Seq using Lrt
DESeq2
3 days ago • updated 2 days ago Rob • 0
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Log2foldchange strange behavior
DESeq2
updated 11 days ago by ★ 4.8k • written 11 days ago by • 0
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530
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WGCNA
WGCNA DESeq2
updated 13 days ago by ★ 4.8k • written 17 days ago by • 0
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824
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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 14 days ago by ★ 1.4k • written 15 days ago by ▴ 20
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PhD scholar
RNASeqAnalysis DESeq2
updated 14 days ago by 4.1k • written 14 days ago by • 0
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278
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DESeq2 - am I extracting results incorrectly?
DESeq2
updated 17 days ago by 68k • written 17 days ago by ▴ 30
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779
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DESeq - help with pair wise comparisons
DESeq2
18 days ago bd2000 ▴ 30
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
21 days ago • updated 18 days ago ktz • 0
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DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 27 days ago by ★ 4.8k • written 27 days ago by • 0
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6
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1.2k
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 28 days ago by ★ 4.8k • written 7 weeks ago by • 0
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450
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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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4
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614
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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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805
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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 6 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 16 days ago Luca • 0
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2
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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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226
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
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673
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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 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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450
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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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502
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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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321
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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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608
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Plot title for PCA in DESeq2
DESeq2
8 weeks ago AL • 0
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3
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615
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
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1.1k
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 10 weeks ago by ★ 4.8k • written 10 weeks ago by • 0
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194
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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 11 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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2
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428
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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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488
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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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3
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500
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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 3 months 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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2
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506
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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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4
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1.0k
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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
3 months ago • updated 12 weeks ago Quang NN ▴ 10
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819
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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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5
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423
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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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4
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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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516
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Differential variability modelling with vst() expression
limma DESeq2
written 3 months ago by • 0
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652
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 3 months ago by • 0
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1.2k
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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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548
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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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1
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445
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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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1
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452
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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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2
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494
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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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1
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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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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
50 results • Page 1 of 1
Recent ...
Replies
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by donnycrimson • 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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