Showing : deseq2 • reset
0
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2
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177
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 5 hours ago by ★ 1.4k • written 5 days ago by • 0
0
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5
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1.4k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.3 years ago by • 0
3
votes
6
replies
1.1k
views
[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 1 day ago by 42k • written 4 days ago by • 0
3
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6
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25k
views
Deseq: What does "BaseMean" mean?
deseq2
written 6.0 years ago by • 0
0
votes
2
replies
616
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 10 days ago by ★ 1.4k • written 11 days ago by • 0
4
votes
11
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525
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Size factor normalized counts for between sample comparisons - correct?
DESeq2
12 days ago • updated 10 days ago boczniak767 ▴ 740
3
votes
4
replies
269
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Gene filtering in DESeq2
DESeq2
updated 13 days ago by ★ 4.4k • written 13 days ago by • 0
0
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2
replies
214
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Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 13 days ago by • 0
1
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2
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176
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Deseq2 - differenc in results
DESeq2
written 13 days ago by • 0
0
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7
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422
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DESeq design with and without intercept is giving different results
DESeq2
written 16 days ago by • 0
1
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5
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592
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 15 days ago by 51k • written 18 days ago by • 0
0
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3
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295
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More significant genes after lfcShrink in DEseq2?
DESeq2
written 17 days ago by • 0
0
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3
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393
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 18 days ago by 51k • written 19 days ago by • 0
0
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2
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239
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 20 days ago by • 0
6
votes
3
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819
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What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 20 days ago by 67k • written 21 days ago by • 0
3
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3
replies
421
views
the count matrix have decimal values
DESeq2 DifferentialExpression
updated 25 days ago by 67k • written 26 days ago by • 0
0
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2
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422
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R is Removing the Gene Names in My Count Data
DESeq2
updated 25 days ago by ▴ 70 • written 26 days ago by • 0
1
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4
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702
views
Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2 independentfiltering glmGamPoi
4 weeks ago • updated 6 days ago Bob • 0
0
votes
1
reply
248
views
Using DESeq2 for Analyzing AMR Gene Variations in Water Samples Post-Treatment
DESeq2 NanoporeRNASeq DNASeq
updated 26 days ago by 42k • written 28 days ago by • 0
0
votes
3
replies
334
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 28 days ago by • 0
3
votes
5
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648
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 28 days ago by ★ 1.4k • written 4 weeks ago by • 0
2
votes
1
reply
253
views
DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 28 days ago by ★ 4.4k • written 28 days ago by • 0
2
votes
2
replies
367
views
Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
29 days ago • updated 28 days ago BioinfGuru ▴ 70
1
vote
2
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473
views
Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
5 weeks ago • updated 28 days ago DL • 0
0
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3
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344
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 4 weeks ago by 67k • written 4 weeks ago by • 0
6
votes
15
replies
1.1k
views
Deseq2 design formula and analysis with internal controls
DESeq2
updated 29 days ago by ★ 1.4k • written 5 weeks ago by • 0
1
vote
2
replies
626
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
5 weeks ago grothmn • 0
0
votes
1
reply
474
views
HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
4
votes
7
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892
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 5 weeks ago by ▴ 10 • written 9 weeks ago by ▴ 70
0
votes
1
reply
449
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 6 weeks ago by 42k • written 7 weeks ago by • 0
0
votes
1
reply
535
views
DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
2
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3
replies
634
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Comparing one group against multiple groups in DESeq2
DESeq2
written 7 months ago by • 0
2
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3
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680
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Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 6 weeks ago by • 0
3
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6
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664
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 6 weeks ago by • 0
4
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3
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1.1k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 7 weeks ago by ▴ 10
0
votes
3
replies
450
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 6 weeks ago by ★ 4.4k • written 6 weeks ago by • 0
1
vote
3
replies
480
views
Doubt about model in paired samples (intercept ?)
DESeq2
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
0
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10
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900
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Two treatments, one control
DESeq2 stageR
8 weeks ago • updated 7 weeks ago alephreish • 0
0
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2
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920
views
How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
7 weeks ago Fiona • 0
2
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3
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437
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 7 weeks ago by • 0
0
votes
1
reply
253
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How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 7 weeks ago by ★ 4.4k • written 7 weeks ago by • 0
4
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12
replies
822
views
DGE with a Continuous Variable
DESeq2 model
updated 6 weeks ago by 42k • written 7 weeks ago by • 0
1
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2
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405
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DESeq2: two conditions two genotypes
DESeq2
8 weeks ago Rocio • 0
2
votes
4
replies
559
views
DESeq normalized counts vs CQN and statistics
DESeq2 cqn
written 8 weeks ago by • 0
0
votes
1
reply
309
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 8 weeks ago by 42k • written 9 weeks ago by • 0
0
votes
1
reply
216
views
unreal negative log2fc values
DESeq2 des
updated 9 weeks ago by 67k • written 9 weeks ago by • 0
0
votes
1
reply
302
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LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 9 weeks ago by 42k • written 9 weeks ago by • 0
1
vote
8
replies
683
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 9 weeks ago by 51k • written 10 weeks ago by • 0
1
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2
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1.2k
views
Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
10 weeks ago sropri • 0
0
votes
1
reply
235
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Deseq2 design matrix
DESeq2 Designmatrix limma
updated 11 weeks ago by 67k • written 11 weeks ago by • 0
50 results • Page 1 of 1
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Comment: ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS by semra • 0
install(Biostrings, force = TRUE) Error in install(Biostrings, force = TRUE) : install fonksiyonu bulunamadı > library(Biostrings) Erro…
Comment: AffylmGUI does not start wit R 4.4.1 by richardallenfriedmanbrooklyn ▴ 20
Dear List, AffylmGUI works fine with R 4.4.1 on Windows. However most of my students have macs. I have installed BWidget and Tktable in the…
Answer: PCA analysis RNA-Seq QC looks strange? by swbarnes2 ★ 1.4k
In my experience, when the first PC is 91% of the difference, its because you are looking at two different tissues. Check to see what gene…
Comment: ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS by James W. MacDonald 67k
What is the output from ``` install("Biostrings, force = TRUE) library(Biostrings) ```
Comment: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic by Michael Love 42k
I request the post here, so not a problem.
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Time course experiment using limma
DEXseq: How to do differential exon usage of genes with overlapping exons
A: Moderated F-test followed by moderated t-test in limma
Answer: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic
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