Showing : DEseq2 • reset
0
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1.2k
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 20 months ago by 43k • written 20 months ago by • 0
0
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4
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877
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DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
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10
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1.7k
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DESeq2 filtering vs edgeR filtering
DESeq2
written 20 months ago by • 0
0
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2
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3.0k
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
20 months ago kcarey • 0
1
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1
reply
586
views
i'm not getting any differentially expressed genes.
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
2
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1
reply
811
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Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
1
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1
reply
520
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
1
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3
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1.0k
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 22 months ago by • 0
0
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2
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947
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DESeq2: Comparing A Knockout to a Strain
DESeq2
20 months ago Viktor Thiel • 0
0
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1
reply
842
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2 scCITE-seq
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
0
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8
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1.5k
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
20 months ago michelafrancesconi8 • 0
0
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1
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664
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Unusually large fold-changes in Deseq2 results
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
1
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4
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909
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DESeq2 Replicates
DESeq2 RNASeq
20 months ago kcarey • 0
2
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6
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1.0k
views
Factor vs Character in design
DESeq2
20 months ago James Aiden • 0
1
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3
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1.0k
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2 glmGamPoi
21 months ago • updated 20 months ago I-Hsuan Lin ▴ 10
4
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7
replies
1.8k
views
weird volcano plot
DESeq2
updated 20 months ago by • 0 • written 2.0 years ago by ▴ 10
0
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1
reply
729
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DEseq2 dispersion plot
DESeq2
updated 20 months ago by 43k • written 21 months ago by • 0
1
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3
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1.1k
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 21 months ago by ★ 1.4k • written 21 months ago by ▴ 10
0
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2
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1.1k
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Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
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3
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941
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 21 months ago by 68k • written 21 months ago by ▴ 10
0
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1
reply
697
views
Changed DESeq2 comparison value but the heatmap is still the same
DESeq2 pheatmap
updated 21 months ago by 68k • written 21 months ago by • 0
1
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4
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996
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Further clarification of unbalanced group sizes DESeq2
DESeq2
21 months ago hmillike • 0
0
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1
reply
476
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few significant genes from DESeq2 analysis
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
1
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4
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1.5k
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DEseq2 coefficient
DESeq2 coefficient
21 months ago • updated 19 months ago JKim • 0
3
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5
replies
1.7k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 21 months ago by 43k • written 21 months ago by ▴ 10
2
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1
reply
742
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 21 months ago by 43k • written 21 months ago by ▴ 10
2
votes
2
replies
824
views
locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
21 months ago Hope ▴ 10
1
vote
2
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849
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evaluate the variable importance on genes
DESeq2 deseq
21 months ago Meme • 0
0
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3
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828
views
library sizes differ extremely after dds
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
1
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4
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1.5k
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Comparing gene expression across three tissue types to identify any difference.
DESeq2
21 months ago James Aiden • 0
0
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13
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1.9k
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Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2 SmallRNA
updated 21 months ago by 43k • written 21 months ago by • 0
1
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5
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983
views
vst transformation and zero counts
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by ▴ 740
1
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12
replies
2.7k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
21 months ago paria.alipour • 0
0
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3
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1.4k
views
utf-8 codec can't decode byte 0xd5
importr DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
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1
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484
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Problems with filtering DESeq Results (log2fold change)
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
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3
replies
1.2k
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DESeq2: Adjust for treatment effect patient vs control
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
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1
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1.9k
views
Pseudobulk-DESeq2 analyze multiple cell types at once?
pseudobulk DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
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7
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1.3k
views
DESeq filtering specific to contrasts
DESeq2
updated 19 months ago by 43k • written 21 months ago by • 0
0
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2
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846
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help checking the design matrix and contrast in DESeq2 "not full rank" scenario
DESeq2
21 months ago ccshao ▴ 70
0
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1
reply
663
views
Double batch effect (Individuals nested within blocks in DESeq2)
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
1
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2
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955
views
DESeq2 issue: can't create DESeq2 object
DESeq2 RBioinf
21 months ago Magdalena • 0
0
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1
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453
views
Inconsistency in DESeq2 Log fold change
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
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3
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761
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DESeq2 Results in Different Pvalue & Log2FC using the same code and data
DESeq2 dese
written 21 months ago by • 0
0
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5
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1.1k
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DESEQ2 Repeated Measures-like design error help
DESeq2
updated 21 months ago by 43k • written 21 months ago by ▴ 10
0
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3
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1.1k
views
DESeq2 interaction terms RIPseq analysis
DESeq2 RIPSeq
updated 21 months ago by 43k • written 21 months ago by • 0
2
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2
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1.7k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
21 months ago jackafiore • 0
4
votes
2
replies
2.7k
views
How to do DESeq2 on Kallisto Data
DESeq2 Kallisto
updated 21 months ago by ▴ 40 • written 21 months ago by • 0
1
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2
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2.4k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.6 years ago by • 0
0
votes
2
replies
728
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
21 months ago Lily Cheang ▴ 10
0
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4
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870
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DESeq2 nomalize value
DESeq2
21 months ago 史哲 • 0
4,839 results • Page 7 of 97
Recent ...
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Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Answer: p.adjust BH Question by Gordon Smyth 53k
Duplicate of https://support.bioconductor.org/p/41077/
Answer: Large logFC but somewhat high FDR by Gordon Smyth 53k
Glad you're getting good use out of the package. The results that you show seem pretty much as one would expect, with nothing surprising. …
Comment: After running samtools, the featureCounts command crashed. by MarcHintz99 • 0
Thanks for shairng https://subread.sourceforge.net/
Votes
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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
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