Showing : DeSeq2 • reset
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DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
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2
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1.0k
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DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 14 months ago by 43k • written 14 months ago by ▴ 10
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6
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1.8k
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New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 13 months ago by ★ 5.0k • written 14 months ago by • 0
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1
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469
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
17
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9
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8.3k
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How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 14 months ago by 68k • written 9.5 years ago by ▴ 10
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1
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606
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
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2
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810
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 14 months ago by ★ 1.4k • written 15 months ago by • 0
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5
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2.3k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.5 years ago by • 0
3
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6
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2.0k
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[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 14 months ago by 43k • written 15 months ago by • 0
3
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6
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32k
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Deseq: What does "BaseMean" mean?
deseq2
written 7.2 years ago by • 0
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2
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1.6k
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
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11
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1.6k
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Size factor normalized counts for between sample comparisons - correct?
DESeq2
15 months ago boczniak767 ▴ 740
3
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4
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830
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Gene filtering in DESeq2
DESeq2
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
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2
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776
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Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 15 months ago by • 0
1
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2
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496
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Deseq2 - differenc in results
DESeq2
written 15 months ago by • 0
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1.1k
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DESeq design with and without intercept is giving different results
DESeq2
written 15 months ago by • 0
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5
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1.5k
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 15 months ago by 53k • written 15 months ago by • 0
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3
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1.1k
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More significant genes after lfcShrink in DEseq2?
DESeq2
written 15 months ago by • 0
0
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3
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969
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 15 months ago by 53k • written 15 months ago by • 0
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2
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682
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 15 months ago by • 0
6
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5
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4.1k
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What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 11 months ago by ▴ 20 • written 15 months ago by • 0
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3
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1.6k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 15 months ago by 68k • written 15 months ago by • 0
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2
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1.2k
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R is Removing the Gene Names in My Count Data
DESeq2
updated 15 months ago by ▴ 70 • written 15 months ago by • 0
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4
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1.5k
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Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2 independentfiltering glmGamPoi
16 months ago • updated 15 months ago Bob ▴ 30
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1
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622
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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
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3
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1.0k
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 15 months ago by • 0
3
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5
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2.3k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 15 months ago by ★ 1.4k • written 16 months ago by • 0
2
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1
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1.6k
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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
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2
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881
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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
15 months ago BioinfGuru ▴ 70
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2
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807
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Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
16 months ago • updated 15 months ago DL • 0
0
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3
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899
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 16 months ago by 68k • written 16 months ago by • 0
6
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15
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2.5k
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Deseq2 design formula and analysis with internal controls
DESeq2
updated 15 months ago by ★ 1.4k • written 16 months ago by • 0
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2
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1.3k
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How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
16 months ago grothmn • 0
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1.2k
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HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 16 months ago by 68k • written 16 months ago by • 0
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7
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2.2k
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What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 16 months ago by ▴ 10 • written 17 months ago by ▴ 70
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1
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844
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DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 16 months ago by 43k • written 16 months ago by • 0
0
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1
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972
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DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 16 months ago by 43k • written 16 months ago by • 0
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3
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1.0k
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Comparing one group against multiple groups in DESeq2
DESeq2
written 22 months ago by • 0
2
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3
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3.0k
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Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 16 months ago by • 0
3
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6
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1.3k
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 16 months ago by • 0
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3
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1.6k
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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 16 months ago by ▴ 10
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3
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995
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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 16 months ago by ★ 5.0k • written 16 months ago by • 0
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3
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938
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Doubt about model in paired samples (intercept ?)
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
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10
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2.1k
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Two treatments, one control
DESeq2 stageR
16 months ago alephreish • 0
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2
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2.0k
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How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
16 months ago Fiona • 0
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3
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966
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DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 16 months ago by • 0
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1
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1.2k
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How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 16 months ago by ★ 5.0k • written 16 months ago by • 0
4
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12
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1.9k
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DGE with a Continuous Variable
DESeq2 model
updated 16 months ago by 43k • written 16 months ago by • 0
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2
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757
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DESeq2: two conditions two genotypes
DESeq2
16 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 16 months ago by • 0
4,840 results • Page 4 of 97
Recent ...
Replies
Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
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Popular Question to Gordon Smyth 53k
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