Showing : desEQ2 • reset
17
votes
9
replies
8.2k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 13 months ago by 68k • written 9.4 years ago by ▴ 10
0
votes
1
reply
599
views
Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
0
votes
2
replies
796
views
PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 14 months ago by ★ 1.4k • written 14 months ago by • 0
0
votes
5
replies
2.3k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.5 years ago by • 0
3
votes
6
replies
1.9k
views
[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
3
votes
6
replies
32k
views
Deseq: What does "BaseMean" mean?
deseq2
written 7.1 years ago by • 0
0
votes
2
replies
1.5k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 14 months ago by ★ 1.4k • written 14 months ago by • 0
4
votes
11
replies
1.5k
views
Size factor normalized counts for between sample comparisons - correct?
DESeq2
14 months ago boczniak767 ▴ 740
3
votes
4
replies
806
views
Gene filtering in DESeq2
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
0
votes
2
replies
762
views
Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 14 months ago by • 0
1
vote
2
replies
485
views
Deseq2 - differenc in results
DESeq2
written 14 months ago by • 0
0
votes
7
replies
1.0k
views
DESeq design with and without intercept is giving different results
DESeq2
written 14 months ago by • 0
1
vote
5
replies
1.4k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 14 months ago by 53k • written 14 months ago by • 0
0
votes
3
replies
1.1k
views
More significant genes after lfcShrink in DEseq2?
DESeq2
written 14 months ago by • 0
0
votes
3
replies
943
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 14 months ago by 53k • written 14 months ago by • 0
0
votes
2
replies
664
views
Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 14 months ago by • 0
6
votes
5
replies
4.1k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 10 months ago by ▴ 20 • written 14 months ago by • 0
3
votes
3
replies
1.6k
views
the count matrix have decimal values
DESeq2 DifferentialExpression
updated 15 months ago by 68k • written 15 months ago by • 0
0
votes
2
replies
1.2k
views
R is Removing the Gene Names in My Count Data
DESeq2
updated 15 months ago by ▴ 70 • written 15 months ago by • 0
1
vote
4
replies
1.5k
views
Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2 independentfiltering glmGamPoi
15 months ago • updated 14 months ago Bob ▴ 30
0
votes
1
reply
608
views
Using DESeq2 for Analyzing AMR Gene Variations in Water Samples Post-Treatment
DESeq2 NanoporeRNASeq DNASeq
updated 15 months ago by 43k • written 15 months ago by • 0
0
votes
3
replies
1.0k
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 15 months ago by • 0
3
votes
5
replies
2.2k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
2
votes
1
reply
1.5k
views
DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
2
votes
2
replies
861
views
Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
15 months ago BioinfGuru ▴ 70
1
vote
2
replies
786
views
Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
15 months ago DL • 0
0
votes
3
replies
867
views
RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 15 months ago by 68k • written 15 months ago by • 0
6
votes
15
replies
2.5k
views
Deseq2 design formula and analysis with internal controls
DESeq2
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
1
vote
2
replies
1.3k
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
15 months ago grothmn • 0
0
votes
1
reply
1.2k
views
HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 15 months ago by 68k • written 15 months ago by • 0
4
votes
7
replies
2.2k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 15 months ago by ▴ 10 • written 16 months ago by ▴ 70
0
votes
1
reply
820
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 15 months ago by 43k • written 15 months ago by • 0
0
votes
1
reply
959
views
DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 15 months ago by 43k • written 15 months ago by • 0
2
votes
3
replies
988
views
Comparing one group against multiple groups in DESeq2
DESeq2
written 21 months ago by • 0
2
votes
3
replies
2.9k
views
Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 15 months ago by • 0
3
votes
6
replies
1.3k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 15 months ago by • 0
4
votes
3
replies
1.6k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 15 months ago by ▴ 10
0
votes
3
replies
969
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
1
vote
3
replies
913
views
Doubt about model in paired samples (intercept ?)
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
0
votes
10
replies
2.0k
views
Two treatments, one control
DESeq2 stageR
16 months ago • updated 15 months ago alephreish • 0
0
votes
2
replies
1.9k
views
How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
15 months ago Fiona • 0
2
votes
3
replies
941
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 15 months ago by • 0
0
votes
1
reply
1.1k
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
4
votes
12
replies
1.8k
views
DGE with a Continuous Variable
DESeq2 model
updated 15 months ago by 43k • written 16 months ago by • 0
1
vote
2
replies
738
views
DESeq2: two conditions two genotypes
DESeq2
16 months ago Rocio • 0
2
votes
4
replies
1.2k
views
DESeq normalized counts vs CQN and statistics
DESeq2 cqn
written 16 months ago by • 0
0
votes
1
reply
969
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 16 months ago by 43k • written 16 months ago by • 0
0
votes
1
reply
573
views
unreal negative log2fc values
DESeq2 des
updated 16 months ago by 68k • written 16 months ago by • 0
0
votes
1
reply
544
views
LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
1
vote
8
replies
1.8k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 16 months ago by 53k • written 16 months ago by • 0
4,836 results • Page 4 of 97
Recent ...
Replies
Comment: Save the Date: BioC2026 by eja.gsssssswwse.r.m • 0
Que notícia incrivel sobre o BioC2026 Para quem gosta de aproveitar o conteudo online, também e possvel Baixar [snaptube versão antiga][1] …
Comment: Ensembl 115 has been released! by eja.gsssssswwse.r.m • 0
Keeping up with Ensembls latest release ensures access to cutting-edge genomic information. For those balancing research and leisure, a mob…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
Awards • All
Scholar to shepherl 4.2k
Scholar to James W. MacDonald 68k
Popular Question to Daniel Cameron ▴ 40
Popular Question to Peter Hickey ▴ 760
Popular Question to edward.esiribloom • 0
Locations • All
The Cave, 181 Longwood Avenue, Boston, USA, 37 minutes ago
Pittsburgh, United States, 1 hour ago
The city by the bay, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
Pakistan, 2 hours ago
Traffic: 809 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