Showing : DEseq2 • reset
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WGCNA
WGCNA DESeq2
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
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1.1k
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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 7 months ago by ★ 1.4k • written 7 months ago by ▴ 20
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1.3k
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PhD scholar
RNASeqAnalysis DESeq2
updated 7 months ago by 4.2k • written 7 months ago by • 0
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489
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DESeq2 - am I extracting results incorrectly?
DESeq2
updated 7 months ago by 68k • written 7 months ago by ▴ 30
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3
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1.0k
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DESeq - help with pair wise comparisons
DESeq2
7 months ago bd2000 ▴ 30
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8
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3.0k
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
7 months ago ktz • 0
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1
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756
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DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 7 months ago by ★ 5.0k • written 8 months ago by • 0
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6
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1.6k
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
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4
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755
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
8 months ago Lennie • 0
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4
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1.2k
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 8 months ago by • 0
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2
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Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
8 months ago • updated 6 months ago Erika • 0
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8
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
8 months ago • updated 7 months ago Luca • 0
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2
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731
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 8 months ago by 43k • written 8 months ago by ▴ 20
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452
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 8 months ago by 43k • written 8 months ago by • 0
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979
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how many significant figures are there in DESeq2 output
DESeq2
updated 8 months ago by ★ 5.0k • written 8 months ago by ▴ 180
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5
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1.4k
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Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
9 months ago • updated 8 months ago picasa1983 • 0
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2.4k
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Vertical line at A=0, nothing else, on MA plot
deseq2
updated 8 months ago by ▴ 10 • written 6.7 years ago by ▴ 20
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1
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868
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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 9 months ago by 68k • written 9 months ago by • 0
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648
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 9 months ago by ★ 1.4k • written 9 months ago by ▴ 10
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1
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448
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DEseq2 design for additive treatment
DESeq2
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
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2
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814
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Plot title for PCA in DESeq2
DESeq2
9 months ago AL • 0
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3
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982
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 months ago by 43k • written 9 months ago by • 0
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2
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1.3k
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
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1
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397
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 9 months ago by 43k • written 9 months ago by • 0
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3
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809
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DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 9 months ago by • 0 • written 9 months ago by • 0
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2
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918
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accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 9 months ago by • 0 • written 9 months ago by • 0
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3
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608
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 9 months ago by • 0 • written 9 months ago by • 0
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3
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859
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 9 months ago by • 0 • written 10 months ago by ▴ 10
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1
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636
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
2
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2
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693
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 10 months ago by ★ 1.4k • written 10 months ago by • 0
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4
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1.4k
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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
10 months ago • updated 9 months ago Quang NN ▴ 10
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1.3k
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
10 months ago Blandine • 0
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5
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704
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 10 months ago by • 0
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4
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959
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
10 months ago Quang NN ▴ 10
2
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5
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790
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Differential variability modelling with vst() expression
limma DESeq2
written 10 months ago by • 0
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3
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900
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 10 months ago by • 0
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9
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1.7k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
10 months ago Quang NN ▴ 10
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1
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882
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 10 months ago by 43k • written 10 months ago by • 0
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339
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 10 months ago by ★ 1.4k • written 10 months ago by • 0
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1
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594
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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 months ago by 43k • written 11 months ago by • 0
2
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715
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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 months ago by 43k • written 11 months ago by • 0
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2
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709
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
11 months ago • updated 10 months ago Kucsera • 0
1
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1
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550
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
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9
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1.5k
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 11 months ago by ▴ 40
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2
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986
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 11 months ago by ★ 5.0k • written 11 months ago by ▴ 10
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5
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1.0k
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Deseq2 Design
RNASeq DESeq2
updated 11 months ago by 68k • written 11 months ago by • 0
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5
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1.1k
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p value is 0, padj is 0
DESeq2
11 months ago Wirayatida • 0
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2
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1.1k
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
11 months 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 11 months ago by • 0 • written 11 months ago by • 0
0
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542
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 11 months ago by 43k • written 11 months ago by ▴ 20
4,839 results • Page 2 of 97
Recent ...
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Comment: gene Set with high AUC score but no cells assigned to cell type by gogeni5529 • 0
THIS is spam. How Do I delete it?
Comment: limpa - drivers for unusually high standard error? by Julia Broadbent • 0
Apologies for not being clearer in my initial question, but thank you for answering regardless! The large SE values I am looking at appear …
Answer: limpa - drivers for unusually high standard error? by Gordon Smyth 53k
Hi Julia, I am going to assume that you mean standard errors (SEs) returned by `dpcQuant()`, because later stages in the limpa pipeline do…
Comment: gene Set with high AUC score but no cells assigned to cell type by e.j.aaw.g.erm • 0
It sounds like AUCell is struggling with thresholding because your cDC2 gene set doesn t show a clear bimodal distribution. While a high AU…
Comment: featureCounts -L: high unassigned:mapq fraction by insurancetaaddddaxrealty • 0
FeatureCounts can behave differently with ONT cDNA BAM files due to long read splice patterns, and many users compare settings or presets m…
Votes
Answer: gene Set with high AUC score but no cells assigned to cell type
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
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