Showing : DEseq2 • reset
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Design formula for circadian time-course data for vst() function
DESeq2
8 months ago Vishnu • 0
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2
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932
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Analyzing TnSeq data with DESeq2
DESeq2
written 9 months ago by • 0
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1
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1.3k
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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 9 months ago by 43k • written 10 months ago by • 0
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2
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770
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Differing results with DESeq2
DESeq2
updated 9 months ago by • 0 • written 9 months ago by • 0
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2
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635
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RNA Seq using Lrt
DESeq2
9 months ago Rob • 0
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3
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1.1k
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Log2foldchange strange behavior
DESeq2
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
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1
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995
views
WGCNA
WGCNA DESeq2
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
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1
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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 9 months ago by ★ 1.4k • written 9 months ago by ▴ 20
1
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1
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1.4k
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PhD scholar
RNASeqAnalysis DESeq2
updated 9 months ago by 4.3k • written 9 months ago by • 0
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1
reply
520
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DESeq2 - am I extracting results incorrectly?
DESeq2
updated 9 months ago by 68k • written 9 months ago by ▴ 30
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3
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1.1k
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DESeq - help with pair wise comparisons
DESeq2
9 months ago bd2000 ▴ 30
1
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8
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3.1k
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
9 months ago ktz • 0
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1
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809
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DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
4
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6
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1.7k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 9 months ago by ★ 5.0k • written 10 months ago by • 0
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4
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833
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
10 months ago Lennie • 0
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4
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1.4k
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 10 months ago by • 0
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2
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1.2k
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Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
10 months ago • updated 7 months ago Erika • 0
1
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8
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2.8k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
10 months ago • updated 9 months ago Luca • 0
0
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2
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826
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 10 months ago by 43k • written 10 months ago by ▴ 20
0
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1
reply
495
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 10 months ago by 43k • written 10 months ago by • 0
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3
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1.0k
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how many significant figures are there in DESeq2 output
DESeq2
updated 10 months ago by ★ 5.0k • written 10 months ago by ▴ 180
2
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5
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1.5k
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Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
10 months ago picasa1983 • 0
3
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7
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2.5k
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Vertical line at A=0, nothing else, on MA plot
deseq2
updated 10 months ago by ▴ 10 • written 6.9 years ago by ▴ 20
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1
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1.2k
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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 10 months ago by 68k • written 10 months ago by • 0
1
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1
reply
724
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 11 months ago by ★ 1.4k • written 11 months ago by ▴ 10
1
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1
reply
472
views
DEseq2 design for additive treatment
DESeq2
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
2
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2
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909
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Plot title for PCA in DESeq2
DESeq2
11 months ago • updated 10 months ago AL • 0
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3
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1.1k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 11 months ago by 43k • written 11 months ago by • 0
1
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2
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1.4k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
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1
reply
469
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 11 months ago by 43k • written 11 months ago by • 0
0
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3
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894
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 11 months ago by • 0 • written 11 months ago by • 0
0
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2
replies
956
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 11 months ago by • 0 • written 11 months ago by • 0
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3
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649
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 10 months ago by • 0 • written 11 months ago by • 0
0
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3
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1.0k
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 11 months ago by • 0 • written 12 months ago by ▴ 10
0
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1
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722
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
2
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2
replies
756
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 11 months ago by ★ 1.4k • written 12 months ago by • 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
12 months ago • updated 11 months ago Quang NN ▴ 10
0
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2
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1.6k
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
12 months ago Blandine • 0
0
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5
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797
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 12 months ago by • 0
0
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4
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1.2k
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
12 months ago Quang NN ▴ 10
2
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5
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954
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Differential variability modelling with vst() expression
limma DESeq2
written 12 months ago by • 0
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3
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1.0k
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 12 months ago by • 0
2
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9
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1.9k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
12 months ago Quang NN ▴ 10
1
vote
1
reply
1.2k
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 12 months ago by 43k • written 12 months ago by • 0
0
votes
1
reply
371
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 12 months ago by ★ 1.4k • written 12 months ago by • 0
0
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1
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656
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 12 months ago by 43k • written 13 months ago by • 0
2
votes
1
reply
769
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 12 months ago by 43k • written 12 months ago by • 0
0
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2
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788
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
12 months ago Kucsera • 0
1
vote
1
reply
592
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
1
vote
9
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1.7k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 13 months ago by ▴ 40
4,845 results • Page 2 of 97
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Answer: Are individual-mouse-based statistics possible in CellChat? by ATpoint ★ 5.0k
Not a Bioconductor package, I commented on the crosspost at https://www.biostars.org/p/9617271/
Comment: DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups by ATpoint ★ 5.0k
apeglm is more cumbersome than ashr as with apeglm the coefficients need to be explicitely available in the resultsNames.So, you need to re…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Martin Morgan 25k
I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
Given that this is an issue with BiocParallel on your machine and we have a minimal reproducible example, you may want to repost the issue.…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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