Showing : deseq2 • reset
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New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 2 days ago by ▴ 210 • written 3 days ago by • 0
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1
reply
125
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
4 days ago • updated 8 hours ago Ben ▴ 10
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1
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134
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DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 3 days ago by ★ 1.4k • written 6 days ago by • 0
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1
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174
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 7 days ago by 42k • written 7 days ago by • 0
17
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6.7k
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How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 11 days ago by 67k • written 8.3 years ago by ▴ 10
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1
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179
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DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 3 days ago by ★ 1.4k • written 11 days ago by ▴ 10
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174
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 12 days ago by 42k • written 12 days ago by • 0
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2
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424
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 18 days ago by ★ 1.4k • written 23 days ago by • 0
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5
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1.5k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.4 years ago by • 0
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6
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1.3k
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[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 19 days ago by 42k • written 22 days ago by • 0
3
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6
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26k
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Deseq: What does "BaseMean" mean?
deseq2
written 6.0 years ago by • 0
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2
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742
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 28 days ago by ★ 1.4k • written 29 days ago by • 0
4
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11
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628
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Size factor normalized counts for between sample comparisons - correct?
DESeq2
4 weeks ago • updated 28 days ago boczniak767 ▴ 740
3
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4
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335
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Gene filtering in DESeq2
DESeq2
updated 4 weeks ago by ★ 4.4k • written 4 weeks ago by • 0
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2
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315
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Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 4 weeks ago by • 0
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230
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Deseq2 - differenc in results
DESeq2
written 4 weeks ago by • 0
0
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7
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511
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DESeq design with and without intercept is giving different results
DESeq2
written 4 weeks ago by • 0
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5
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657
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 4 weeks ago by 51k • written 5 weeks ago by • 0
0
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3
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364
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More significant genes after lfcShrink in DEseq2?
DESeq2
written 5 weeks ago by • 0
0
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3
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422
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 5 weeks ago by 51k • written 5 weeks ago by • 0
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2
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260
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 5 weeks ago by • 0
6
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3
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874
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What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
3
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3
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479
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 6 weeks ago by 67k • written 6 weeks ago by • 0
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2
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463
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R is Removing the Gene Names in My Count Data
DESeq2
updated 6 weeks ago by ▴ 70 • written 6 weeks ago by • 0
1
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4
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748
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Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2 independentfiltering glmGamPoi
7 weeks ago • updated 24 days ago Bob • 0
0
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1
reply
266
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Using DESeq2 for Analyzing AMR Gene Variations in Water Samples Post-Treatment
DESeq2 NanoporeRNASeq DNASeq
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
0
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3
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368
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 6 weeks ago by • 0
3
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5
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694
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 6 weeks ago by ★ 1.4k • written 7 weeks ago by • 0
2
votes
1
reply
296
views
DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 6 weeks ago by ★ 4.4k • written 6 weeks ago by • 0
2
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2
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394
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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
6 weeks ago BioinfGuru ▴ 70
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2
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494
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Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
7 weeks ago • updated 6 weeks ago DL • 0
0
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3
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370
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 7 weeks ago by 67k • written 7 weeks ago by • 0
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15
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Deseq2 design formula and analysis with internal controls
DESeq2
updated 6 weeks ago by ★ 1.4k • written 8 weeks ago by • 0
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2
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651
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How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
8 weeks ago • updated 7 weeks ago grothmn • 0
0
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1
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490
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HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 8 weeks ago by 67k • written 8 weeks ago by • 0
4
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7
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933
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What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 7 weeks ago by ▴ 10 • written 12 weeks ago by ▴ 70
0
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1
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467
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DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 8 weeks ago by 42k • written 10 weeks ago by • 0
0
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1
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555
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DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 8 weeks ago by 42k • written 9 weeks ago by • 0
2
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3
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658
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Comparing one group against multiple groups in DESeq2
DESeq2
written 8 months ago by • 0
2
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3
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775
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Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 8 weeks ago by • 0
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6
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693
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 9 weeks ago by • 0
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DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 10 weeks ago by ▴ 10
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3
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472
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Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 9 weeks ago by ★ 4.4k • written 9 weeks ago by • 0
1
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3
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500
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Doubt about model in paired samples (intercept ?)
DESeq2
updated 9 weeks ago by 42k • written 9 weeks ago by • 0
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10
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947
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Two treatments, one control
DESeq2 stageR
11 weeks ago • updated 9 weeks ago alephreish • 0
0
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2
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957
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How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
10 weeks ago • updated 9 weeks ago Fiona • 0
2
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3
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464
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DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 10 weeks ago by • 0
0
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1
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300
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How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 10 weeks ago by ★ 4.4k • written 10 weeks ago by • 0
4
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12
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857
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DGE with a Continuous Variable
DESeq2 model
updated 9 weeks ago by 42k • written 10 weeks ago by • 0
1
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2
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419
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DESeq2: two conditions two genotypes
DESeq2
11 weeks ago • updated 10 weeks ago Rocio • 0
50 results • Page 1 of 1
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Comment: How should I run ssGSEA Hallmark Enrichment Analysis? by Ginny • 0
I think the other side of this question is that the non protein coding genes would be in the "background", they would influence the ranking…
Comment: ISO a solution to rank-order introns by transcript by James W. MacDonald 67k
There's an error in the last line. Note that `sapply(lengths(z), seq_len)` will return a `list` because the lengths vary. We need a vector,…
Comment: BiomaRt - improved access to Ensembl ? by Mike Smith ★ 6.5k
Why do you want to use `useMart()` rather than `useEnsembl()`? They are essentially the same (`useEnsembl()` will eventually call `useMart(…
Comment: Installing Bioconductor packages in Docker by devarti.mahakalkar • 0
I have installed BiocManager on my base image rather than having it as base image. RUN Rscript -e "install.packages('BiocManager', re…
Comment: Meta-analysis on RNA-seq data sets by Travis • 0
Thank you for your suggestions and explanation of your approach!
Votes
Answer: ISO a solution to rank-order introns by transcript
Answer: ISO a solution to rank-order introns by transcript
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: addPatternDensity in 'qsea' takes too much time
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