Showing : DeSeq2 • reset
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
16 months ago paul.meraner • 0
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673
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
16 months ago • updated 15 months ago info ▴ 10
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6
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1.6k
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heatmap with batch effect
DESeq2 BatchEffect
written 16 months ago by • 0
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2
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820
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How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
1
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1
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1.3k
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 16 months ago by 68k • written 16 months ago by • 0
1
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1
reply
756
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 16 months ago by ★ 5.0k • written 16 months ago by • 0
1
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1
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626
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DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 16 months ago by ★ 5.0k • written 16 months ago by • 0
1
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2
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965
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 16 months ago by 43k • written 16 months ago by ▴ 10
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2
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1.1k
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DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
1
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2
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1.1k
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DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 16 months ago by 43k • written 16 months ago by ▴ 10
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6
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2.1k
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New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 15 months ago by ★ 5.0k • written 16 months ago by • 0
0
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1
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504
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
17
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9
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8.5k
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How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 16 months ago by 68k • written 9.7 years ago by ▴ 10
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1
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685
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
0
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2
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890
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 16 months ago by ★ 1.4k • written 17 months ago by • 0
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5
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2.4k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.7 years ago by • 0
3
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6
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2.1k
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[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 17 months ago by 43k • written 17 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 7.4 years ago by • 0
0
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2
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1.8k
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
4
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11
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1.9k
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Size factor normalized counts for between sample comparisons - correct?
DESeq2
17 months ago boczniak767 ▴ 740
3
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4
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901
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Gene filtering in DESeq2
DESeq2
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
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2
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889
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Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 17 months ago by • 0
1
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2
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528
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Deseq2 - differenc in results
DESeq2
written 17 months ago by • 0
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7
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1.2k
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DESeq design with and without intercept is giving different results
DESeq2
written 17 months ago by • 0
1
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5
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1.7k
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 17 months ago by 53k • written 17 months ago by • 0
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3
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1.2k
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More significant genes after lfcShrink in DEseq2?
DESeq2
written 17 months ago by • 0
0
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3
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1.0k
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 17 months ago by 53k • written 17 months ago by • 0
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2
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737
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 17 months ago by • 0
6
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5
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4.8k
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What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 13 months ago by ▴ 20 • written 17 months ago by • 0
3
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3
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1.9k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
0
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2
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1.3k
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R is Removing the Gene Names in My Count Data
DESeq2
updated 17 months ago by ▴ 70 • written 17 months ago by • 0
1
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4
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1.7k
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Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2 independentfiltering glmGamPoi
18 months ago • updated 17 months ago Bob ▴ 30
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1
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656
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Using DESeq2 for Analyzing AMR Gene Variations in Water Samples Post-Treatment
DESeq2 NanoporeRNASeq DNASeq
updated 17 months ago by 43k • written 17 months ago by • 0
0
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3
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1.2k
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 17 months ago by • 0
3
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5
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2.7k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 17 months ago by ★ 1.4k • written 18 months ago by • 0
2
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1
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1.9k
views
DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
2
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2
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951
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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
17 months ago BioinfGuru ▴ 70
1
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2
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840
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Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
18 months ago • updated 17 months ago DL • 0
0
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3
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987
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 18 months ago by 68k • written 18 months ago by • 0
6
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15
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2.7k
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Deseq2 design formula and analysis with internal controls
DESeq2
updated 17 months ago by ★ 1.4k • written 18 months ago by • 0
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2
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1.4k
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How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
18 months ago grothmn • 0
0
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1
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1.4k
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HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 18 months ago by 68k • written 18 months ago by • 0
4
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7
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2.6k
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What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 18 months ago by ▴ 10 • written 19 months ago by ▴ 70
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1
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942
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DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 18 months ago by 43k • written 18 months ago by • 0
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1
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1.1k
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DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 18 months ago by 43k • written 18 months ago by • 0
2
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3
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1.1k
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Comparing one group against multiple groups in DESeq2
DESeq2
written 2.0 years ago by • 0
2
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3
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3.3k
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Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 18 months ago by • 0
3
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6
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1.4k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 18 months ago by • 0
4
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3
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1.7k
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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 18 months ago by ▴ 10
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3
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views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
4,848 results • Page 4 of 97
Recent ...
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Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Votes
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
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