Showing : deseq2 • reset
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532
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DESeq2 from phyloseq error
DESeq2 phyloseq
9 months ago asafpr • 0
3
votes
1
reply
750
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DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 9 months ago by 68k • written 9 months ago by • 0
1
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5
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1.8k
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Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 9 months ago by 68k • written 9 months ago by ▴ 10
9
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3
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3.4k
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DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 8 months ago by 43k • written 9 months ago by ▴ 40
2
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4
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2.0k
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Filtering after DESeq
DESeq2 IHW
written 10 months ago by ▴ 10
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4
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1.3k
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DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
9 months ago sk • 0
0
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6
replies
1.9k
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Discrepancies in normalised count data vs unnormalised
DESeq2
9 months ago AMgroup • 0
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2
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818
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Design formula for circadian time-course data for vst() function
DESeq2
10 months ago Vishnu • 0
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2
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983
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Analyzing TnSeq data with DESeq2
DESeq2
written 10 months ago by • 0
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1
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1.3k
views
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 10 months ago by 43k • written 11 months ago by • 0
0
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2
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795
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Differing results with DESeq2
DESeq2
updated 10 months ago by • 0 • written 10 months ago by • 0
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2
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646
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RNA Seq using Lrt
DESeq2
10 months ago Rob • 0
0
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3
replies
1.1k
views
Log2foldchange strange behavior
DESeq2
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
0
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1
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1.1k
views
WGCNA
WGCNA DESeq2
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
0
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1
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1.1k
views
Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 10 months ago by ★ 1.4k • written 10 months ago by ▴ 20
1
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1
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1.4k
views
PhD scholar
RNASeqAnalysis DESeq2
updated 10 months ago by 4.3k • written 10 months ago by • 0
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1
reply
536
views
DESeq2 - am I extracting results incorrectly?
DESeq2
updated 10 months ago by 68k • written 10 months ago by ▴ 30
1
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3
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1.1k
views
DESeq - help with pair wise comparisons
DESeq2
10 months ago bd2000 ▴ 30
1
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8
replies
3.1k
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
10 months ago ktz • 0
0
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1
reply
840
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
4
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6
replies
1.7k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
1
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4
replies
858
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
11 months ago Lennie • 0
0
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4
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1.6k
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 11 months ago by • 0
1
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2
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1.3k
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
11 months ago • updated 9 months ago Erika • 0
1
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8
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2.9k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
11 months ago • updated 10 months ago Luca • 0
0
votes
2
replies
871
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 11 months ago by 43k • written 11 months ago by ▴ 20
0
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1
reply
514
views
DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 11 months ago by 43k • written 11 months ago by • 0
0
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3
replies
1.1k
views
how many significant figures are there in DESeq2 output
DESeq2
updated 11 months ago by ★ 5.0k • written 11 months ago by ▴ 180
2
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5
replies
1.5k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
12 months ago picasa1983 • 0
3
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7
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2.5k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 12 months ago by ▴ 10 • written 7.0 years ago by ▴ 20
0
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1
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1.6k
views
How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData DESeq2 pseudobulk sing
updated 12 months ago by 68k • written 12 months ago by • 0
1
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1
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786
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 12 months ago by ★ 1.4k • written 12 months ago by ▴ 10
1
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1
reply
492
views
DEseq2 design for additive treatment
DESeq2
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
2
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2
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974
views
Plot title for PCA in DESeq2
DESeq2
12 months ago AL • 0
0
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3
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1.2k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 12 months ago by 43k • written 12 months ago by • 0
1
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2
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1.5k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
0
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1
reply
513
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 12 months ago by 43k • written 12 months ago by • 0
0
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3
replies
940
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 12 months ago by • 0 • written 12 months ago by • 0
0
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2
replies
983
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 12 months ago by • 0 • written 12 months ago by • 0
0
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3
replies
659
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 12 months ago by • 0 • written 12 months ago by • 0
0
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3
replies
1.2k
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 12 months ago by • 0 • written 13 months ago by ▴ 10
0
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1
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785
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
2
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2
replies
808
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
0
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4
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1.5k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
13 months ago Quang NN ▴ 10
0
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2
replies
1.8k
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
13 months ago Blandine • 0
0
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5
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837
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 13 months ago by • 0
0
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4
replies
1.4k
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
13 months ago Quang NN ▴ 10
2
votes
5
replies
1.0k
views
Differential variability modelling with vst() expression
limma DESeq2
written 13 months ago by • 0
0
votes
3
replies
1.1k
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 13 months ago by • 0
2
votes
9
replies
2.1k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
13 months ago Quang NN ▴ 10
4,851 results • Page 2 of 98
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Comment: Question on processing compound protein groups in limpa by JKim • 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa by Gordon Smyth 53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input by Gordon Smyth 53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2 by a2a2hset32aa • 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Comment: Deadline Extended: EuroBioC2026 Call for Abstracts by a2a2hset32aa • 0
Attending EuroBioC2026 is an excellent way for researchers to explore the intersection of technology and biology. For those seeking high qu…
Votes
Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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