Showing : DESEQ2 • reset
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DESeq2/apeglm s-values: Why average FSR (or FSOS) instead of maximum?
DESeq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
1
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1
reply
645
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Differential expression where only certain samples are paired
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 10
4
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4
replies
4.8k
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Why does DEseq2 take a long time to run on large dataset ?
DEseq2 large dataset
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 10
4
votes
7
replies
3.1k
views
Question: Pair-wise DESeq Analysis with 3 Factor Levels - RNA-Seq
deseq2 design model rnaseq multiple factor levels
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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1
reply
815
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DESeq2 multiple treatments
deseq2
7.0 years ago preetomregon • 0
0
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2
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1.2k
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Deseq2 paired analysis
deseq2 paired samples interaction terms
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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1
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685
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DESeq2 with 3 treatment +3 genotype
deseq2
7.0 years ago hussienfotoh • 0
0
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7
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1.1k
views
Differential Expression - DESeq2 identifies to many differentially expressed genes (~20,000)
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 10
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6
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1.0k
views
[DESeq2] Pre-filtering counts got different results after running results
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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2
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1.3k
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[Deseq2] Estimating size factors using samples which have been excluded for QC
deseq2 estimatesizefactors
updated 7.0 years ago by ★ 7.9k • written 7.0 years ago by • 0
0
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5
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1.4k
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DESeq2 for a 3-way interaction analysis?
deseq2
updated 7.0 years ago by 43k • written 7.1 years ago by • 0
0
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1
reply
802
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DESeq2 Batch effects
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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3
replies
1.3k
views
DeSeq2 extract internal expression values
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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7
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2.4k
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DESeq2 with several biological replicates
rnaseq deseq2 differential gene expression
7.0 years ago bharata1803 ▴ 60
1
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6
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3.1k
views
DESeq2: two genotypes, one treatment
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 20
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1
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1.5k
views
RNAseq gene expression analysis in Personalized genomics
TCGA deseq2 edger limma
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
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1
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1.4k
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
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5
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2.6k
views
salmon output file for differential expression analysis
salmon rna seq deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
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3
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1.3k
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p-values smaller than machine epsilon in DESeq2
deseq2 pvalue
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
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2
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1.3k
views
Question re "Group-specific condition effects, individuals nested within groups"
deseq2 linear model
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
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1
reply
1.7k
views
Use DiffBind to find differential peaks among multiple cell types
diffbind atac-seq differential analysis deseq2
updated 7.1 years ago by ★ 5.2k • written 7.1 years ago by • 0
0
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4
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1.1k
views
DESeq2 Multi-Sample Test
deseq2
updated 7.1 years ago by ★ 1.4k • written 7.1 years ago by • 0
0
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4
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1.5k
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DESeq2 MA plot normalisation Issue
deseq2 normalization maplot rnaseq
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
1
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2
replies
861
views
Any way to get a p-value for multiple comparisons in DESeq2?
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 20
2
votes
3
replies
1.8k
views
Multi-factor with interaction model in EdgeR and DESeq2
edger deseq2 rnaseq differential gene expression
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
4
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7
replies
4.6k
views
Handling biological replicates across batches in DESeq2
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 40
0
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1
reply
1.8k
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Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 2.5 years ago by • 0 • written 7.1 years ago by • 0
3
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6
replies
1.9k
views
nbinomLRT function all cores usage
deseq2 nbinomLRT sample size biocparallel
updated 7.1 years ago by ▴ 980 • written 7.1 years ago by • 0
4
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4
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2.7k
views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm deseq2 rna-seq
updated 7.1 years ago by 43k • written 7.1 years ago by ★ 5.0k
0
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3
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1.5k
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DEseqDataSetFromMatrix not working
deseq2
updated 7.1 years ago by • 0 • written 7.1 years ago by • 0
1
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8
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1.4k
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plot of normalized counts for a single gene
deseq2
7.1 years ago lkianmehr • 0
0
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3
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2.5k
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Transcript counts in DESeq2
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
1
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1
reply
956
views
How does my DESeq2 code handle more than two conditions?
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
2
votes
14
replies
3.0k
views
Differentiating between batch and treatment effects in edgeR, DESeq2
rnaseq batch effect deseq2 edger
updated 7.1 years ago by ★ 29k • written 7.1 years ago by ▴ 30
1
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14
replies
2.3k
views
Diff. Expression with DESeq2 (Two conditions)
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
1
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1
reply
860
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Differential gene expression between 2 samples
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
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1
reply
1.1k
views
Multiple factor design for differential expression with DESeq2
deseq2 differential gene expression multiple factor design
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
2
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2
replies
1.8k
views
How to use TPM in plotMA in DESeq2
TPM deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
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1
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1.7k
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Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2 gsea tpm rnaseq salmon rna seq
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
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4
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1.3k
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DESeq2 memory allocation question
deseq2 memory problem
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 60
7
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9
replies
4.5k
views
Dispersion fit and p-value distributions
deseq2 rnaseq fdrtool
updated 7.1 years ago by ★ 7.9k • written 7.1 years ago by ▴ 140
1
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10
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8.3k
views
SVAseq and DESeq2 workflow
sva deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
0
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15
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3.6k
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DESeq2 Time Series and "control" condition
deseq2 time course
7.1 years ago sum732 • 0
1
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2
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1.4k
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DESEQ2 Finding Unchanged Genes
deseq2 differential gene expression
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 20
5
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6
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2.2k
views
How to set up appropriate analysis using sample type and condition for DESeq2
deseq2 differential gene expression design
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
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4
replies
2.8k
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PCA plot of variance stabilized transformation of normalized counts in limma
limma-voom deseq2 EdgeR
updated 7.1 years ago by ★ 13k • written 7.1 years ago by ▴ 20
0
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3
replies
27k
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plotMA in deseq2
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 40
1
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6
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1.7k
views
Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
deseq2 rna-seq
7.1 years ago hffqyd • 0
1
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9
replies
1.7k
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DESeq2 for large de novo transcripts assembly
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
3
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2
replies
1.5k
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Using deseq2 with batch effects and classification as downstream analysis
deseq2 batch effect classification
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
4,839 results • Page 58 of 97
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Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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