Showing : DEseq2 • reset
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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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465
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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
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9
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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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602
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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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808
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 14 months ago by ★ 1.4k • written 14 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
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6
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[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
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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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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
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4
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824
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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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773
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Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 15 months ago by • 0
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495
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Deseq2 - differenc in results
DESeq2
written 15 months ago by • 0
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7
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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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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
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3
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960
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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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677
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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 10 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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Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2 independentfiltering glmGamPoi
15 months ago • updated 14 months ago Bob ▴ 30
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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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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 15 months ago by • 0
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5
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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 15 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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876
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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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805
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Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
15 months ago DL • 0
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3
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892
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 15 months ago by 68k • written 15 months ago by • 0
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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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1.3k
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How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
15 months ago grothmn • 0
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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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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
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837
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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
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970
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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
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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
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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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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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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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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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1.9k
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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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DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 16 months ago by • 0
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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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753
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DESeq2: two conditions two genotypes
DESeq2
16 months ago Rocio • 0
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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
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1.0k
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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
4,839 results • Page 4 of 97
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Comment: Senior Teaching Fellow (MSc Computational Biomedicine) by eja.ger.m • 0
Opportunities like this remind me how digital learning is evolving, much like modern mobile games. With programmes becoming fully online an…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by ATpoint ★ 5.0k
Since the donor effect is so clear I assume that a paired analysis within donor is strictly necessary to get DEGs, and therefore one would …
Comment: Large logFC but somewhat high FDR by JKim • 0
forgot to attach some other plots, which may be informative... RLE plot ![enter image description here][1] pvalue distribution ![enter …
Comment: upstream git branches of bioc-release by andres.wokaty ▴ 70
Yes, all packages in https://bioconductor.org/packages/json/3.22bioc/packages.json have a `RELEASE_3_22` branch.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
Can we assume that each package git repo will have a `RELEASE_3_22` branch, even when they had "a build error in release"?
Votes
Comment: upstream git branches of bioc-release
A: p.adjust BH generates duplicate values
Answer: gene Set with high AUC score but no cells assigned to cell type
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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