Showing : DESEQ2 • reset
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DESeq - help with pair wise comparisons
DESeq2
5 months ago bd2000 ▴ 30
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8
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
5 months ago ktz • 0
0
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1
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714
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DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
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1.5k
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 5 months ago by ★ 4.9k • written 6 months ago by • 0
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
5 months ago Lennie • 0
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4
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 6 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
6 months ago • updated 3 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
6 months ago • updated 5 months ago Luca • 0
0
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2
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663
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 6 months ago by 43k • written 6 months ago by ▴ 20
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394
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 6 months ago by 43k • written 6 months ago by • 0
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3
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927
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how many significant figures are there in DESeq2 output
DESeq2
updated 6 months ago by ★ 4.9k • written 6 months ago by ▴ 180
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5
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Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
6 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 6 months ago by ▴ 10 • written 6.5 years ago by ▴ 20
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1
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751
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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 6 months ago by 68k • written 6 months ago by • 0
1
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614
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 6 months ago by ★ 1.4k • written 6 months ago by ▴ 10
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408
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DEseq2 design for additive treatment
DESeq2
updated 6 months ago by ★ 4.9k • written 6 months ago by • 0
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2
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768
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Plot title for PCA in DESeq2
DESeq2
6 months ago AL • 0
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3
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834
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 6 months ago by 43k • written 6 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 7 months ago by ★ 4.9k • written 7 months ago by • 0
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1
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331
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 7 months ago by 43k • written 7 months ago by • 0
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732
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DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 7 months ago by • 0 • written 7 months ago by • 0
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2
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854
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accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 7 months ago by • 0 • written 7 months ago by • 0
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570
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 6 months ago by • 0 • written 7 months ago by • 0
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3
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 7 months ago by • 0 • written 7 months ago by ▴ 10
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1
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459
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
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2
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632
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 7 months ago by ★ 1.4k • written 7 months ago by • 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
7 months ago Quang NN ▴ 10
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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
7 months ago Blandine • 0
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5
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613
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 7 months ago by • 0
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4
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884
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
7 months ago Quang NN ▴ 10
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5
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716
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Differential variability modelling with vst() expression
limma DESeq2
written 8 months ago by • 0
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3
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823
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 8 months ago by • 0
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1.5k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
8 months ago • updated 7 months ago Quang NN ▴ 10
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807
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 8 months ago by 43k • written 8 months ago by • 0
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321
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
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1
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556
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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 8 months ago by 43k • written 8 months ago by • 0
2
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1
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578
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 8 months ago by 43k • written 8 months ago by • 0
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2
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670
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
8 months ago Kucsera • 0
1
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1
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525
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 8 months ago by 43k • written 9 months ago by • 0
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1.4k
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 9 months ago by ▴ 30
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2
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915
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 9 months ago by ★ 4.9k • written 9 months ago by ▴ 10
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5
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907
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Deseq2 Design
RNASeq DESeq2
updated 9 months ago by 68k • written 9 months ago by • 0
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5
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1.0k
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p value is 0, padj is 0
DESeq2
9 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
9 months ago georgii.vdovin • 0
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7
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 9 months ago by • 0 • written 9 months ago by • 0
0
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1
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506
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 9 months ago by 43k • written 9 months ago by ▴ 20
0
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3
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691
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DESeq2 - Comparing Comparisons
DESeq2
updated 9 months ago by 68k • written 9 months ago by • 0
0
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4
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844
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lfcShrink and alpha value
lfcShrink DESeq2
9 months ago cropero • 0
2
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1
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649
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 9 months ago by 43k • written 9 months ago by • 0
0
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2
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451
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
4,835 results • Page 2 of 97
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Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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