Showing : DEseq2 • reset
1
vote
3
replies
990
views
DESeq - help with pair wise comparisons
DESeq2
5 months ago bd2000 ▴ 30
1
vote
8
replies
2.8k
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
5 months ago ktz • 0
0
votes
1
reply
717
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
4
votes
6
replies
1.5k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 5 months ago by ★ 4.9k • written 6 months ago by • 0
1
vote
4
replies
708
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
6 months ago • updated 5 months ago Lennie • 0
0
votes
4
replies
1.1k
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 6 months ago by • 0
1
vote
2
replies
1.1k
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
6 months ago • updated 3 months ago Erika • 0
1
vote
8
replies
2.6k
views
[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
votes
2
replies
668
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 6 months ago by 43k • written 6 months ago by ▴ 20
0
votes
1
reply
399
views
DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 6 months ago by 43k • written 6 months ago by • 0
0
votes
3
replies
931
views
how many significant figures are there in DESeq2 output
DESeq2
updated 6 months ago by ★ 4.9k • written 6 months ago by ▴ 180
2
votes
5
replies
1.3k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
6 months ago picasa1983 • 0
3
votes
7
replies
2.3k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 6 months ago by ▴ 10 • written 6.5 years ago by ▴ 20
0
votes
1
reply
758
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 6 months ago by 68k • written 6 months ago by • 0
1
vote
1
reply
615
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 6 months ago by ★ 1.4k • written 6 months ago by ▴ 10
1
vote
1
reply
409
views
DEseq2 design for additive treatment
DESeq2
updated 6 months ago by ★ 4.9k • written 6 months ago by • 0
2
votes
2
replies
772
views
Plot title for PCA in DESeq2
DESeq2
6 months ago AL • 0
0
votes
3
replies
842
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 6 months ago by 43k • written 7 months ago by • 0
1
vote
2
replies
1.3k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 7 months ago by ★ 4.9k • written 7 months ago by • 0
0
votes
1
reply
334
views
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
votes
3
replies
733
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 7 months ago by • 0 • written 7 months ago by • 0
0
votes
2
replies
856
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 7 months ago by • 0 • written 7 months ago by • 0
0
votes
3
replies
570
views
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
0
votes
3
replies
772
views
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
0
votes
1
reply
464
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
2
votes
2
replies
635
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 7 months ago by ★ 1.4k • written 7 months ago by • 0
0
votes
4
replies
1.3k
views
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
0
votes
2
replies
1.2k
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
7 months ago Blandine • 0
0
votes
5
replies
616
views
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
0
votes
4
replies
889
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
8 months ago • updated 7 months ago Quang NN ▴ 10
2
votes
5
replies
717
views
Differential variability modelling with vst() expression
limma DESeq2
written 8 months ago by • 0
0
votes
3
replies
826
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 8 months ago by • 0
2
votes
9
replies
1.5k
views
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
vote
1
reply
809
views
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
votes
1
reply
322
views
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
0
votes
1
reply
557
views
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
votes
1
reply
582
views
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
0
votes
2
replies
670
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
8 months ago Kucsera • 0
1
vote
1
reply
530
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
1
vote
9
replies
1.4k
views
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
votes
2
replies
918
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 9 months ago by ★ 4.9k • written 9 months ago by ▴ 10
1
vote
5
replies
912
views
Deseq2 Design
RNASeq DESeq2
updated 9 months ago by 68k • written 9 months ago by • 0
0
votes
5
replies
1.0k
views
p value is 0, padj is 0
DESeq2
9 months ago Wirayatida • 0
1
vote
2
replies
1.1k
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
9 months ago georgii.vdovin • 0
0
votes
7
replies
1.2k
views
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
votes
1
reply
506
views
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
votes
3
replies
695
views
DESeq2 - Comparing Comparisons
DESeq2
updated 9 months ago by 68k • written 9 months ago by • 0
0
votes
4
replies
846
views
lfcShrink and alpha value
lfcShrink DESeq2
9 months ago cropero • 0
2
votes
1
reply
654
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
2
replies
452
views
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
Recent ...
Replies
Comment: Visualization of Functional Enrichment Result with enrichplot: How to control la by zhaoqiansun0592 • 0
Wow, this is super helpful! I always struggle with label sizes in enrichplot. Glad to see a solution using gginnards([Pasjans][1]) and ggre…
Comment: Could we detect difference at pathway level but not significant different at gen by zhaoqiansun0592 • 0
Interesting question! It's cool that ChatGPT4 gave such a helpful answer. I've also been wondering if pathways([space waves][1]) can show d…
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by zhaoqiansun0592 • 0
Good to know there are workarounds for these tricky [doodle baseball][1]! Thanks for sharing the tips! [1]: https://doodle-baseball.cc/
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Awards • All
Popular Question to Paulito • 0
Popular Question to geneprophet • 0
Popular Question to Hervé Pagès 16k
Teacher to Gordon Smyth 53k
Popular Question to Vincent J. Carey, Jr. 6.7k
Locations • All
WEHI, Melbourne, Australia, 21 minutes ago
Germany, 1 hour ago
Italy, 1 hour ago
The city by the bay, 3 hours ago
San Diego, 4 hours ago
Traffic: 1287 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6