Showing : desEQ2 • reset
0
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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
vote
1
reply
578
views
i'm not getting any differentially expressed genes.
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
2
votes
1
reply
794
views
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
513
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
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 21 months ago by • 0
0
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2
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927
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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
826
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
reply
653
views
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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894
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DESeq2 Replicates
DESeq2 RNASeq
20 months ago kcarey • 0
2
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6
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995
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Factor vs Character in design
DESeq2
20 months ago James Aiden • 0
1
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3
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1.0k
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Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2 glmGamPoi
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
712
views
DEseq2 dispersion plot
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
1
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3
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1.1k
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 20 months ago by ★ 1.4k • written 20 months ago by ▴ 10
0
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2
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1.1k
views
Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
0
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3
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927
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 20 months ago by 68k • written 20 months ago by ▴ 10
0
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1
reply
685
views
Changed DESeq2 comparison value but the heatmap is still the same
DESeq2 pheatmap
updated 20 months ago by 68k • written 20 months ago by • 0
1
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4
replies
982
views
Further clarification of unbalanced group sizes DESeq2
DESeq2
20 months ago hmillike • 0
0
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1
reply
465
views
few significant genes from DESeq2 analysis
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
1
vote
4
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1.5k
views
DEseq2 coefficient
DESeq2 coefficient
20 months ago • updated 18 months ago JKim • 0
3
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5
replies
1.7k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 20 months ago by 43k • written 20 months ago by ▴ 10
2
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1
reply
731
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 20 months ago by 43k • written 20 months ago by ▴ 10
2
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2
replies
812
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locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
20 months ago Hope ▴ 10
1
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2
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836
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evaluate the variable importance on genes
DESeq2 deseq
20 months ago Meme • 0
0
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3
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815
views
library sizes differ extremely after dds
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
1
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4
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1.5k
views
Comparing gene expression across three tissue types to identify any difference.
DESeq2
20 months ago James Aiden • 0
0
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13
replies
1.8k
views
Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2 SmallRNA
updated 20 months ago by 43k • written 20 months ago by • 0
1
vote
5
replies
964
views
vst transformation and zero counts
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by ▴ 740
1
vote
12
replies
2.6k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
20 months ago paria.alipour • 0
0
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3
replies
1.3k
views
utf-8 codec can't decode byte 0xd5
importr DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
0
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1
reply
475
views
Problems with filtering DESeq Results (log2fold change)
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
0
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3
replies
1.2k
views
DESeq2: Adjust for treatment effect patient vs control
DESeq2
updated 20 months ago by 43k • written 21 months ago by • 0
0
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1
reply
1.8k
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 18 months ago by 43k • written 21 months ago by • 0
0
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2
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834
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help checking the design matrix and contrast in DESeq2 "not full rank" scenario
DESeq2
21 months ago • updated 20 months ago ccshao ▴ 70
0
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1
reply
654
views
Double batch effect (Individuals nested within blocks in DESeq2)
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
1
vote
2
replies
933
views
DESeq2 issue: can't create DESeq2 object
DESeq2 RBioinf
21 months ago Magdalena • 0
0
votes
1
reply
446
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
replies
754
views
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
replies
1.1k
views
DESEQ2 Repeated Measures-like design error help
DESeq2
updated 20 months ago by 43k • written 21 months ago by ▴ 10
0
votes
3
replies
1.0k
views
DESeq2 interaction terms RIPseq analysis
DESeq2 RIPSeq
updated 21 months ago by 43k • written 21 months ago by • 0
2
votes
2
replies
1.7k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
21 months ago jackafiore • 0
4
votes
2
replies
2.6k
views
How to do DESeq2 on Kallisto Data
DESeq2 Kallisto
updated 21 months ago by ▴ 40 • written 21 months ago by • 0
1
vote
2
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2.4k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.5 years ago by • 0
0
votes
2
replies
722
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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857
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DESeq2 nomalize value
DESeq2
21 months ago 史哲 • 0
0
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4
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1.9k
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink DESeq2
written 22 months ago by • 0
2
votes
1
reply
738
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by ▴ 20
0
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3
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1.1k
views
LOG2FC DESEQ2
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
4,836 results • Page 7 of 97
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Comment: Save the Date: BioC2026 by eja.gsssssswwse.r.m • 0
Que notícia incrivel sobre o BioC2026 Para quem gosta de aproveitar o conteudo online, também e possvel Baixar [snaptube versão antiga][1] …
Comment: Ensembl 115 has been released! by eja.gsssssswwse.r.m • 0
Keeping up with Ensembls latest release ensures access to cutting-edge genomic information. For those balancing research and leisure, a mob…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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