Showing : Deseq2 • reset
0
votes
0
replies
16
views
Filtering after DESeq
DESeq2 IHW
16 hours ago caroline.zanchi • 0
0
votes
1
reply
205
views
Analyzing TnSeq data with DESeq2
DESeq2
updated 2 days ago by • 0 • written 2 days ago by • 0
0
votes
1
reply
586
views
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 3 days ago by 43k • written 4 weeks ago by • 0
0
votes
2
replies
440
views
Differing results with DESeq2
DESeq2
updated 1 day ago by • 0 • written 21 days ago by • 0
0
votes
2
replies
299
views
RNA Seq using Lrt
DESeq2
3 days ago • updated 2 days ago Rob • 0
0
votes
3
replies
714
views
Log2foldchange strange behavior
DESeq2
updated 11 days ago by ★ 4.8k • written 11 days ago by • 0
0
votes
1
reply
530
views
WGCNA
WGCNA DESeq2
updated 14 days ago by ★ 4.8k • written 17 days ago by • 0
0
votes
1
reply
827
views
Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 14 days ago by ★ 1.4k • written 15 days ago by ▴ 20
1
vote
1
reply
1.1k
views
PhD scholar
RNASeqAnalysis DESeq2
updated 14 days ago by 4.1k • written 15 days ago by • 0
0
votes
1
reply
280
views
DESeq2 - am I extracting results incorrectly?
DESeq2
updated 17 days ago by 68k • written 17 days ago by ▴ 30
1
vote
3
replies
781
views
DESeq - help with pair wise comparisons
DESeq2
18 days ago bd2000 ▴ 30
1
vote
8
replies
2.5k
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
21 days ago • updated 18 days ago ktz • 0
0
votes
1
reply
562
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 27 days ago by ★ 4.8k • written 28 days ago by • 0
4
votes
6
replies
1.2k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 28 days ago by ★ 4.8k • written 7 weeks ago by • 0
1
vote
4
replies
451
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
5 weeks ago • updated 4 weeks ago Lennie • 0
0
votes
4
replies
614
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 5 weeks ago by • 0
1
vote
1
reply
805
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
updated 6 weeks ago by 68k • written 6 weeks ago by • 0
1
vote
8
replies
2.3k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
6 weeks ago • updated 16 days ago Luca • 0
0
votes
2
replies
465
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 5 weeks ago by 43k • written 6 weeks ago by ▴ 20
0
votes
1
reply
229
views
DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
0
votes
3
replies
675
views
how many significant figures are there in DESeq2 output
DESeq2
updated 7 weeks ago by ★ 4.8k • written 8 weeks ago by ▴ 180
2
votes
5
replies
1.0k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
8 weeks ago picasa1983 • 0
3
votes
7
replies
2.1k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 8 weeks ago by ▴ 10 • written 6.1 years ago by ▴ 20
0
votes
1
reply
452
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 8 weeks ago by 68k • written 8 weeks ago by • 0
1
vote
1
reply
503
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 8 weeks ago by ★ 1.4k • written 8 weeks ago by ▴ 10
1
vote
1
reply
321
views
DEseq2 design for additive treatment
DESeq2
updated 8 weeks ago by ★ 4.8k • written 8 weeks ago by • 0
2
votes
2
replies
608
views
Plot title for PCA in DESeq2
DESeq2
9 weeks ago • updated 8 weeks ago AL • 0
0
votes
3
replies
615
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
1
vote
2
replies
1.1k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 10 weeks ago by ★ 4.8k • written 10 weeks ago by • 0
0
votes
1
reply
194
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 10 weeks ago by 43k • written 11 weeks ago by • 0
0
votes
3
replies
574
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 10 weeks ago by • 0 • written 11 weeks ago by • 0
0
votes
2
replies
428
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 10 weeks ago by • 0 • written 11 weeks ago by • 0
0
votes
3
replies
488
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 8 weeks ago by • 0 • written 11 weeks ago by • 0
0
votes
3
replies
502
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 11 weeks ago by • 0 • written 3 months ago by ▴ 10
0
votes
1
reply
282
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
2
votes
2
replies
507
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 12 weeks ago by ★ 1.4k • written 3 months ago by • 0
0
votes
4
replies
1.0k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
3 months ago • updated 12 weeks ago Quang NN ▴ 10
0
votes
2
replies
824
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
3 months ago Blandine • 0
0
votes
5
replies
424
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 3 months ago by • 0
0
votes
4
replies
664
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
3 months ago Quang NN ▴ 10
2
votes
5
replies
517
views
Differential variability modelling with vst() expression
limma DESeq2
written 3 months ago by • 0
0
votes
3
replies
652
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 3 months ago by • 0
2
votes
9
replies
1.2k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
3 months ago Quang NN ▴ 10
1
vote
1
reply
549
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 3 months ago by 43k • written 3 months ago by • 0
0
votes
1
reply
247
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 3 months ago by ★ 1.4k • written 3 months ago by • 0
0
votes
1
reply
445
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 3 months ago by 43k • written 4 months ago by • 0
2
votes
1
reply
452
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 3 months ago by 43k • written 4 months ago by • 0
0
votes
2
replies
495
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
3 months ago Kucsera • 0
1
vote
1
reply
467
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
1
vote
9
replies
1.1k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 4 months ago by ▴ 30
50 results • Page 1 of 1
Recent ...
Replies
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
Awards • All
Popular Question to etiennedanis • 0
Popular Question to javier.ruizramirez • 0
Autobiographer to Paul Harrison ▴ 100
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to Kinnary ▴ 20
Locations • All
Netherlands, 21 minutes ago
The city by the bay, 48 minutes ago
WEHI, Melbourne, Australia, 56 minutes ago
Seattle, WA, United States, 1 hour ago
Australia/Melbourne, 3 hours ago
Traffic: 818 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