Showing : DEseq2 • reset
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
0
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2
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761
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 12 months ago by ★ 1.4k • written 12 months ago by • 0
0
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5
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2.2k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.4 years ago by • 0
3
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6
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1.9k
views
[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
3
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6
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31k
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Deseq: What does "BaseMean" mean?
deseq2
written 7.0 years ago by • 0
0
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2
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1.5k
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 12 months ago by ★ 1.4k • written 12 months ago by • 0
4
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11
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1.4k
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Size factor normalized counts for between sample comparisons - correct?
DESeq2
13 months ago • updated 12 months ago boczniak767 ▴ 740
3
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4
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756
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Gene filtering in DESeq2
DESeq2
updated 13 months ago by ★ 4.9k • written 13 months ago by • 0
0
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2
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698
views
Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 13 months ago by • 0
1
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2
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461
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Deseq2 - differenc in results
DESeq2
written 13 months ago by • 0
0
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7
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1.0k
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DESeq design with and without intercept is giving different results
DESeq2
written 13 months ago by • 0
1
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5
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1.4k
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 13 months ago by 53k • written 13 months ago by • 0
0
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3
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1.0k
views
More significant genes after lfcShrink in DEseq2?
DESeq2
written 13 months ago by • 0
0
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3
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863
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 13 months ago by 53k • written 13 months ago by • 0
0
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2
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609
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 13 months ago by • 0
6
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5
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4.0k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 8 months ago by ▴ 20 • written 13 months ago by • 0
3
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3
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1.5k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 13 months ago by 68k • written 13 months ago by • 0
0
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2
replies
1.1k
views
R is Removing the Gene Names in My Count Data
DESeq2
updated 13 months ago by ▴ 70 • written 13 months ago by • 0
1
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4
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1.4k
views
Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2 independentfiltering glmGamPoi
13 months ago • updated 12 months ago Bob ▴ 30
0
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1
reply
538
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Using DESeq2 for Analyzing AMR Gene Variations in Water Samples Post-Treatment
DESeq2 NanoporeRNASeq DNASeq
updated 13 months ago by 43k • written 13 months ago by • 0
0
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3
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953
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 13 months ago by • 0
3
votes
5
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2.2k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
2
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1
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1.5k
views
DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 13 months ago by ★ 4.9k • written 13 months ago by • 0
2
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2
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788
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Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
13 months ago BioinfGuru ▴ 70
1
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2
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758
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Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
13 months ago DL • 0
0
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3
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808
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 13 months ago by 68k • written 13 months ago by • 0
6
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15
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2.3k
views
Deseq2 design formula and analysis with internal controls
DESeq2
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
1
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2
replies
1.2k
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
13 months ago grothmn • 0
0
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1
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1.1k
views
HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 13 months ago by 68k • written 13 months ago by • 0
4
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7
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2.1k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 13 months ago by ▴ 10 • written 14 months ago by ▴ 70
0
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1
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774
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DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 13 months ago by 43k • written 14 months ago by • 0
0
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1
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939
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DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 13 months ago by 43k • written 14 months ago by • 0
2
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3
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938
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Comparing one group against multiple groups in DESeq2
DESeq2
written 20 months ago by • 0
2
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3
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2.8k
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Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 14 months ago by • 0
3
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6
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1.2k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 14 months ago by • 0
4
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3
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1.5k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 14 months ago by ▴ 10
0
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3
replies
909
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 14 months ago by ★ 4.9k • written 14 months ago by • 0
1
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3
replies
875
views
Doubt about model in paired samples (intercept ?)
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
0
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10
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1.9k
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Two treatments, one control
DESeq2 stageR
14 months ago alephreish • 0
0
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2
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1.9k
views
How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
14 months ago Fiona • 0
2
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3
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873
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 14 months ago by • 0
0
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1
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1.1k
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How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 14 months ago by ★ 4.9k • written 14 months ago by • 0
4
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12
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1.7k
views
DGE with a Continuous Variable
DESeq2 model
updated 14 months ago by 43k • written 14 months ago by • 0
1
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2
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716
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DESeq2: two conditions two genotypes
DESeq2
14 months ago Rocio • 0
2
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4
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1.2k
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DESeq normalized counts vs CQN and statistics
DESeq2 cqn
written 14 months ago by • 0
0
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1
reply
897
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 14 months ago by 43k • written 14 months ago by • 0
0
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1
reply
461
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unreal negative log2fc values
DESeq2 des
updated 14 months ago by 68k • written 14 months ago by • 0
0
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1
reply
505
views
LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
1
vote
8
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1.7k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 14 months ago by 53k • written 15 months ago by • 0
1
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2
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3.1k
views
Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
15 months ago sropri • 0
4,835 results • Page 4 of 97
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Comment: DiffBind - question on the use of filtered or unfiltered input data by deltaexecutor4 • 0
FFH4X is a [Free Fire mod][1] menu APK that offers cheats like auto headshot, aimbot, ESP, wallhack, and unlimited skins. Players use it to…
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 …
Comment: GO.db and others package Download failure by Skyler • 0
Am I using Bioc-devel?
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Is there a reason to use Bioc-devel? If not, you should be using the release version (which I am, and which installs `GO.db` without compla…
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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
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