Showing : Deseq2 • reset
0
votes
1
reply
498
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 5 days ago by ★ 4.8k • written 6 days ago by • 0
4
votes
6
replies
1.1k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 6 days ago by ★ 4.8k • written 29 days ago by • 0
0
votes
0
replies
160
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
9 days ago Simran • 0
1
vote
4
replies
368
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
14 days ago • updated 9 days ago Lennie • 0
0
votes
4
replies
468
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 17 days ago by • 0
1
vote
1
reply
772
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
updated 20 days ago by 68k • written 20 days ago by • 0
1
vote
2
replies
1.2k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
23 days ago • updated 22 days ago Luca • 0
0
votes
2
replies
421
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 17 days ago by 43k • written 25 days ago by ▴ 20
0
votes
1
reply
200
views
DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 28 days ago by 43k • written 29 days ago by • 0
0
votes
3
replies
633
views
how many significant figures are there in DESeq2 output
DESeq2
updated 4 weeks ago by ★ 4.8k • written 4 weeks ago by ▴ 180
2
votes
5
replies
1.0k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
5 weeks ago picasa1983 • 0
3
votes
7
replies
2.0k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 5 weeks ago by ▴ 10 • written 6.1 years ago by ▴ 20
0
votes
1
reply
359
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 5 weeks ago by 68k • written 5 weeks ago by • 0
1
vote
1
reply
474
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 5 weeks ago by ★ 1.4k • written 5 weeks ago by ▴ 10
1
vote
1
reply
304
views
DEseq2 design for additive treatment
DESeq2
updated 5 weeks ago by ★ 4.8k • written 5 weeks ago by • 0
2
votes
2
replies
555
views
Plot title for PCA in DESeq2
DESeq2
5 weeks ago AL • 0
0
votes
3
replies
577
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 5 weeks ago by 43k • written 6 weeks ago by • 0
1
vote
2
replies
1.1k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 6 weeks ago by ★ 4.8k • written 6 weeks ago by • 0
0
votes
1
reply
166
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 7 weeks ago by 43k • written 8 weeks ago by • 0
0
votes
3
replies
537
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 7 weeks ago by • 0 • written 8 weeks ago by • 0
0
votes
2
replies
393
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 7 weeks ago by • 0 • written 8 weeks ago by • 0
0
votes
3
replies
455
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 5 weeks ago by • 0 • written 8 weeks ago by • 0
0
votes
3
replies
439
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 8 weeks ago by • 0 • written 9 weeks ago by ▴ 10
0
votes
1
reply
244
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
2
votes
2
replies
477
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 9 weeks ago by ★ 1.4k • written 9 weeks ago by • 0
0
votes
4
replies
997
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
9 weeks ago Quang NN ▴ 10
0
votes
2
replies
627
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
10 weeks ago • updated 9 weeks ago Blandine • 0
0
votes
5
replies
383
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 10 weeks ago by • 0
0
votes
4
replies
573
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
10 weeks ago Quang NN ▴ 10
2
votes
5
replies
465
views
Differential variability modelling with vst() expression
limma DESeq2
written 12 weeks ago by • 0
0
votes
3
replies
598
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 12 weeks ago by • 0
2
votes
9
replies
1.1k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
12 weeks ago • updated 10 weeks ago Quang NN ▴ 10
1
vote
1
reply
478
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
0
votes
1
reply
226
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 12 weeks ago by ★ 1.4k • written 12 weeks ago by • 0
0
votes
1
reply
423
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 3 months ago by • 0
2
votes
1
reply
428
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 3 months ago by • 0
0
votes
2
replies
430
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
3 months ago Kucsera • 0
1
vote
1
reply
440
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
1
vote
9
replies
999
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 3 months ago by ▴ 30
4
votes
2
replies
569
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 3 months ago by ★ 4.8k • written 3 months ago by ▴ 10
1
vote
5
replies
695
views
Deseq2 Design
RNASeq DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
0
votes
5
replies
716
views
p value is 0, padj is 0
DESeq2
3 months ago Wirayatida • 0
1
vote
2
replies
688
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
3 months ago georgii.vdovin • 0
0
votes
7
replies
1.0k
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 3 months ago by • 0 • written 3 months ago by • 0
0
votes
1
reply
390
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 3 months ago by 43k • written 3 months ago by ▴ 20
0
votes
3
replies
533
views
DESeq2 - Comparing Comparisons
DESeq2
updated 3 months ago by 68k • written 4 months ago by • 0
0
votes
4
replies
664
views
lfcShrink and alpha value
lfcShrink DESeq2
4 months ago cropero • 0
2
votes
1
reply
436
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 4 months ago by 43k • written 4 months ago by • 0
0
votes
2
replies
309
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
0
votes
2
replies
340
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
4 months ago Anna • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Comment: Question on displaying color photo as Greyscale in EBImage by Albert • 0
great and very nice
Comment: European Bioconductor Conference 2023 planning by Pandora • 0
The [Tag Game][1] is not just a simple chase; it involves strategy and tactics as players must think quickly to avoid being tagged. Various…
Comment: Generalized edgeR functions by bukarimanches • 0
I have estimated the new parameter set, it doesn't seem as useful as I thought [geometry dash lite][1] [1]: https://geometry-lite.com/
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by Morse • 0
[Geometry Dash Lite][1] is the free version of the famous Geometry Dash series. It was made by RobTop Games and lets players enjoy the thri…
Votes
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
what the test method for enrichGO in clusterProfiler?
Awards • All
Scholar to Michael Love 43k
Popular Question to Rob • 0
Popular Question to shepherl 4.1k
Popular Question to Gordon Smyth 52k
Popular Question to Le • 0
Locations • All
United States, just now
United States, 1 minute ago
Italy, 7 minutes ago
United States, 32 minutes ago
Canada, 34 minutes ago
Traffic: 857 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