Showing : DESEq • reset
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DEseq for sample clustering
Visualization Clustering DESeq Visualization Clustering DESeq
updated 14.1 years ago by ★ 13k • written 14.1 years ago by ★ 13k
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RNAseq expression analysis using DESeq: technical replicates, paired samples
RNASeq DESeq RNASeq DESeq
updated 14.1 years ago by ★ 3.8k • written 14.1 years ago by ▴ 420
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Using DESeq with ChIP-seq data - all or non-redundant reads?
Coverage Kidney DESeq Coverage Kidney DESeq
14.2 years ago Ivan Gregoretti ▴ 310
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Using DESeq with ChIP-seq data - all or non-redundant reads?
DESeq DESeq
updated 14.2 years ago by ▴ 310 • written 14.2 years ago by ▴ 70
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Fwd: Problems with edgeR for differential expression
Normalization limma edgeR DESeq Normalization limma edgeR DESeq
14.2 years ago Nick Schurch ▴ 60
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DESeq counts normalized option fails
DESeq DESeq
updated 14.2 years ago by ★ 3.8k • written 14.2 years ago by ▴ 10
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questions about DESeq package: estimateSizeFactors() function
Normalization DESeq Normalization DESeq
updated 14.3 years ago by ★ 3.8k • written 14.3 years ago by ▴ 10
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FW: DESeq query regarding rerVarA and resVarB columns
DESeq DESeq
14.3 years ago Simon Anders ★ 3.8k
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Analysing RNA-Seq data using DESeq package
DESeq DESeq
updated 14.3 years ago by ★ 13k • written 14.3 years ago by ▴ 20
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[Bioc-devel] DEG data analysis
edgeR DESeq edgeR DESeq
14.3 years ago Simon Anders ★ 3.8k
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1.3k
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DESeq: nbinomTest question
DESeq DESeq
updated 14.3 years ago by ★ 3.8k • written 14.3 years ago by ▴ 440
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Differential expression analysis of DESeq
DESeq DESeq
updated 14.4 years ago by 21k • written 14.4 years ago by ▴ 10
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How to output Normalised count data from DESeq?
DESeq DESeq
updated 14.4 years ago by ▴ 810 • written 14.4 years ago by ▴ 970
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DESeq multifactor GLM Error attributed to zero counts (coded as NA) in dataset?
DESeq DESeq
14.4 years ago Simon Anders ★ 3.8k
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mRNA-seq cross-species analysis, is it possible?
Genetics Normalization Proteome DESeq Genetics Normalization Proteome DESeq
updated 14.4 years ago by ▴ 20 • written 14.4 years ago by ▴ 370
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Nanostring ncounterdata - DESeq
RNASeq Normalization Preprocessing DESeq RNASeq Normalization Preprocessing DESeq
updated 14.4 years ago by ★ 3.8k • written 14.4 years ago by ▴ 20
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relations between differentially expressed genes (using DESeq) and correlation coefficient
DESeq DESeq
updated 14.4 years ago by ★ 3.8k • written 14.4 years ago by ▴ 10
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Using DESeq with ChIP-seq data
DESeq DESeq
updated 14.4 years ago by ★ 3.8k • written 14.4 years ago by ▴ 70
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DESeq: GLMs for RNA-Seq with interaction terms
DESeq DESeq
updated 14.5 years ago by ★ 6.5k • written 14.5 years ago by ▴ 20
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edgeR vs DESeq for comparison without replicate
edgeR DESeq edgeR DESeq
updated 14.5 years ago by ▴ 260 • written 14.5 years ago by ▴ 20
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R package for DGE analysis between multiple RNA-Seq samples
edgeR DESeq edgeR DESeq
updated 14.5 years ago by ▴ 260 • written 14.5 years ago by ▴ 10
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DESeq -padj
DESeq DESeq
updated 14.5 years ago by ★ 3.8k • written 14.5 years ago by ▴ 50
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6.6k
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Filtering out tags with low counts in DESeq and EgdeR?
Normalization edgeR DESeq Normalization edgeR DESeq
14.6 years ago Xiaohui Wu ▴ 280
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5
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2.6k
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DESeq and paired samples - pairing vs pooling
Cancer DESeq Cancer DESeq
updated 14.6 years ago by 53k • written 14.6 years ago by ▴ 20
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Filtering out tags with low counts in DESeq and EgdeR?
Bayesian limma edgeR DESeq Bayesian limma edgeR DESeq
14.6 years ago Xiaohui Wu ▴ 280
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1.4k
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RNA-Seq with multiple factors [was Informations about DESeq package]
RNASeq edgeR baySeq DESeq RNASeq edgeR baySeq DESeq
14.7 years ago Gordon Smyth 53k
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770
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Questions about package DESeq
RNASeq DESeq RNASeq DESeq
14.7 years ago Mr.B ▴ 10
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809
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Informations about DESeq package
RNASeq DESeq RNASeq DESeq
14.7 years ago Bruno Roman ▴ 10
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1.3k
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DESeq - non-differential expression
Sequencing miRNA Genetics DESeq Sequencing miRNA Genetics DESeq
updated 14.7 years ago by ▴ 180 • written 14.7 years ago by ▴ 10
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deseq for multiple groups with no replicate
DESeq DESeq
updated 14.7 years ago by ★ 13k • written 14.7 years ago by ▴ 120
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Using DESeq or EdgeR for Exon Differential Expression Analysis
affy edgeR DESeq affy edgeR DESeq
14.7 years ago Davis McCarthy ▴ 260
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4
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1.9k
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Using DESeq or EdgeR for Exon Differential Expression Analysis
Normalization edgeR DESeq Normalization edgeR DESeq
updated 14.7 years ago by ▴ 30 • written 14.7 years ago by ★ 6.0k
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DESeq variance stabilisation and clustering
Genetics Clustering PROcess DESeq Genetics Clustering PROcess DESeq
updated 14.8 years ago by ▴ 30 • written 14.8 years ago by ▴ 20
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832
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GLMs in DESeq (convergence problems)
edgeR DESeq edgeR DESeq
14.8 years ago Seanna McTaggart ▴ 20
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1.0k
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GLMs in DESeq (convergence problems)
edgeR DESeq edgeR DESeq
14.8 years ago Gordon Smyth 53k
0
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1
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785
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GLMs in DESeq
DESeq DESeq
updated 14.8 years ago by ★ 3.8k • written 14.8 years ago by ▴ 20
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RNASeq, differential expression between group, and large variance within groups
RNASeq qPCR edgeR DESeq RNASeq qPCR edgeR DESeq
updated 14.8 years ago by ★ 6.0k • written 14.8 years ago by 53k
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working with two factors in DESeq to analyze RNA-seq
DESeq ASSIGN DESeq ASSIGN
updated 14.9 years ago by 53k • written 14.9 years ago by ▴ 150
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2.3k
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DESeq: residuals instead of read counts
RNASeq DESeq RNASeq DESeq
updated 14.9 years ago by ★ 3.8k • written 15.0 years ago by ▴ 10
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question about DeSeq
DESeq DESeq
updated 15.0 years ago by ★ 3.8k • written 15.0 years ago by ▴ 80
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1
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2.4k
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DESeq with no replicates
Sequencing miRNA SmallRNA DESeq Sequencing miRNA SmallRNA DESeq
updated 15.0 years ago by ★ 13k • written 15.0 years ago by ▴ 350
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2.0k
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a few questions on DESeq
DESeq DESeq
updated 15.1 years ago by ★ 3.8k • written 15.1 years ago by ▴ 50
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3
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3.1k
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Outlier detection in DEseq
Genetics DESeq Genetics DESeq
updated 15.2 years ago by ★ 3.8k • written 15.2 years ago by ▴ 20
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1.9k
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to know about the reason in results obtained using DESeq and cufflinks
DESeq DESeq
updated 15.3 years ago by ★ 3.8k • written 15.3 years ago by ▴ 40
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Advise on analyzing NGS of many genes or intergenic peaks in many conditions
GO edgeR DESeq GO edgeR DESeq
15.3 years ago Xiaohui Wu ▴ 280
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817
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Differential expresson in more than 2 samples using NGS?
edgeR DESeq edgeR DESeq
15.3 years ago Gordon Smyth 53k
0
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7
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2.2k
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Differential expresson in more than 2 samples using NGS?
edgeR DESeq edgeR DESeq
15.3 years ago Xiaohui Wu ▴ 280
0
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0
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1.5k
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Normalization of polyA RNA-seq?
Normalization edgeR DESeq Normalization edgeR DESeq
15.4 years ago Xiaohui Wu ▴ 280
0
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2
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1.5k
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get full variance per gene from DESeq
DESeq DESeq
updated 15.4 years ago by ▴ 20 • written 15.4 years ago by ★ 13k
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988
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DESeq question correlation
DESeq DESeq
15.4 years ago Wolfgang Huber ★ 13k
512 results • Page 10 of 11
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Answer: Limma-voom sample weights and impact on DEG numbers by Gordon Smyth 53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
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Limma-voom sample weights and impact on DEG numbers
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
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Popular Question to Gordon Smyth 53k
Popular Question to Hervé Pagès 16k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Istvan Albert ▴ 50
Popular Question to Dario Strbenac ★ 1.6k
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