Showing : desEQ2 • reset
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DESeq2 - am I extracting results incorrectly?
DESeq2
updated 7 months ago by 68k • written 7 months ago by ▴ 30
1
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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
1
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8
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2.9k
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
7 months ago ktz • 0
0
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1
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741
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
4
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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 7 months ago by ★ 5.0k • written 8 months ago by • 0
1
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4
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731
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
7 months ago Lennie • 0
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 7 months ago by • 0
1
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2
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1.1k
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Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
7 months ago • updated 5 months ago Erika • 0
1
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8
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2.7k
views
[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
0
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2
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722
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 7 months ago by 43k • written 8 months ago by ▴ 20
0
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1
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448
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 8 months ago by 43k • written 8 months ago by • 0
0
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3
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967
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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
2
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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
8 months ago picasa1983 • 0
3
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7
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2.3k
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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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852
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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 months ago by 68k • written 8 months ago by • 0
1
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1
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641
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 8 months ago by ★ 1.4k • written 8 months ago by ▴ 10
1
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1
reply
443
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DEseq2 design for additive treatment
DESeq2
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
2
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2
replies
802
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Plot title for PCA in DESeq2
DESeq2
8 months ago AL • 0
0
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3
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960
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 8 months ago by 43k • written 8 months ago by • 0
1
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2
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1.3k
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
0
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1
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386
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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
0
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3
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791
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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
0
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2
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909
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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
0
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3
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600
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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 months ago by • 0 • written 9 months ago by • 0
0
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3
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838
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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 9 months ago by ▴ 10
0
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1
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581
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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
replies
679
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 9 months ago by ★ 1.4k • written 9 months ago by • 0
0
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4
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1.3k
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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
9 months ago Quang NN ▴ 10
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2
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1.2k
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
9 months ago Blandine • 0
0
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5
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686
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 9 months ago by • 0
0
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4
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942
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
9 months ago Quang NN ▴ 10
2
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5
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772
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Differential variability modelling with vst() expression
limma DESeq2
written 10 months ago by • 0
0
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3
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883
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 10 months ago by • 0
2
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9
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1.6k
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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 • updated 9 months ago Quang NN ▴ 10
1
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1
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865
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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
0
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1
reply
336
views
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
0
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1
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589
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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 10 months ago by • 0
2
votes
1
reply
672
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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 10 months ago by • 0
0
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2
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702
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
10 months ago Kucsera • 0
1
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1
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549
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 10 months ago by 43k • written 11 months ago by • 0
1
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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 10 months ago by ▴ 40
4
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2
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963
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 10 months ago by ★ 5.0k • written 11 months ago by ▴ 10
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5
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1.0k
views
Deseq2 Design
RNASeq DESeq2
updated 10 months ago by 68k • written 11 months ago by • 0
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
1
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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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7
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1.3k
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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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1
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530
views
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
0
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3
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726
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DESeq2 - Comparing Comparisons
DESeq2
updated 11 months ago by 68k • written 11 months ago by • 0
0
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4
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908
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lfcShrink and alpha value
lfcShrink DESeq2
11 months ago anon • 0
2
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1
reply
691
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 11 months ago by 43k • written 11 months ago by • 0
4,836 results • Page 2 of 97
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Replies
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Answer: Streamlining the computing time for MiloDE p-value correction in large dataset? by Kevin Blighe ★ 4.0k
Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be far…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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