Showing : DeSeq2 • reset
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DESeq - help with pair wise comparisons
DESeq2
5 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
6 months ago • updated 5 months ago ktz • 0
0
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1
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724
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DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 6 months ago by ★ 4.9k • written 6 months ago by • 0
4
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6
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1.5k
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 6 months ago by ★ 4.9k • written 7 months ago by • 0
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4
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717
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
6 months ago Lennie • 0
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4
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1.1k
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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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1.1k
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Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
6 months ago • updated 4 months ago Erika • 0
1
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8
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2.6k
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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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680
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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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1
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411
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 7 months ago by 43k • written 7 months ago by • 0
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3
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940
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how many significant figures are there in DESeq2 output
DESeq2
updated 7 months ago by ★ 4.9k • written 7 months ago by ▴ 180
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5
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1.3k
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Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
7 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 7 months ago by ▴ 10 • written 6.6 years ago by ▴ 20
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1
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772
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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 7 months ago by 68k • written 7 months ago by • 0
1
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1
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624
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 7 months ago by ★ 1.4k • written 7 months ago by ▴ 10
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1
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415
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DEseq2 design for additive treatment
DESeq2
updated 7 months ago by ★ 4.9k • written 7 months ago by • 0
2
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2
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780
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Plot title for PCA in DESeq2
DESeq2
7 months ago AL • 0
0
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3
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871
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 7 months ago by 43k • written 7 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 7 months ago by ★ 4.9k • written 7 months ago by • 0
0
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1
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352
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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
0
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3
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754
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DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 7 months ago by • 0 • written 8 months ago by • 0
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2
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874
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accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 7 months ago by • 0 • written 8 months ago by • 0
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3
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585
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 7 months ago by • 0 • written 8 months ago by • 0
0
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3
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793
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 8 months ago by • 0 • written 8 months ago by ▴ 10
0
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1
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480
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 8 months ago by 43k • written 8 months ago by • 0
2
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2
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652
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 8 months ago by ★ 1.4k • written 8 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
8 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
8 months ago Blandine • 0
0
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5
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643
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 8 months ago by • 0
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4
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913
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
8 months ago Quang NN ▴ 10
2
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5
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740
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Differential variability modelling with vst() expression
limma DESeq2
written 8 months ago by • 0
0
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3
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846
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 8 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
8 months ago Quang NN ▴ 10
1
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1
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827
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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
0
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1
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331
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 9 months ago by ★ 1.4k • written 9 months ago by • 0
0
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1
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566
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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 9 months ago by 43k • written 9 months ago by • 0
2
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1
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598
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 9 months ago by 43k • written 9 months ago by • 0
0
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2
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685
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
9 months ago Kucsera • 0
1
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1
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536
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
1
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9
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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
4
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2
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937
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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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943
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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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1.1k
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p value is 0, padj is 0
DESeq2
9 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
9 months ago georgii.vdovin • 0
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7
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1.2k
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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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514
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 10 months ago by 43k • written 10 months ago by ▴ 20
0
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3
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709
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DESeq2 - Comparing Comparisons
DESeq2
updated 9 months ago by 68k • written 10 months ago by • 0
0
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4
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859
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lfcShrink and alpha value
lfcShrink DESeq2
10 months ago cropero • 0
2
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1
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663
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 10 months ago by 43k • written 10 months ago by • 0
0
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2
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462
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 10 months ago by 43k • written 10 months ago by • 0
4,835 results • Page 2 of 97
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Comment: R course in Boston December 19-20 by eja.gaasa2e.r.m • 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Comment: incomplete imputation of missing values with LEA impute() function by Gordon Smyth 53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub by Aaron Lun ★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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