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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
2.6 years ago Nik Tuzov ▴ 90
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Comment: Comment: stat value is throwed out after lfcShrink in DESeq2
4.0 years ago Nik Tuzov ▴ 90
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1.2k
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Comment: Comment: DeSEQ2 factor effect without interaction effect
4.0 years ago Nik Tuzov ▴ 90
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594
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Comment: C: The basis for the full rank design matrix requirement in DESeq2
4.9 years ago Nik Tuzov ▴ 90
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3
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594
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The basis for the full rank design matrix requirement in DESeq2
deseq2
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 90
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1.0k
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Comment: C: Error when providing contrast coefficients to lfcShrink() of DESeq2 package
5.1 years ago Nik Tuzov ▴ 90
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4
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1.0k
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Error when providing contrast coefficients to lfcShrink() of DESeq2 package
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 90
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1.6k
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Comment: C: FCSTransTransform() implementation in flowCore
5.6 years ago Nik Tuzov ▴ 90
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4
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1.6k
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FCSTransTransform() implementation in flowCore
flowCore FCSTrans flow cytometry
updated 5.6 years ago by ▴ 310 • written 5.6 years ago by ▴ 90
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2.1k
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Comment: C: Estimation of non-trivial contrasts in MAST
5.7 years ago Nik Tuzov ▴ 90
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1
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2.1k
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Comment: C: Estimation of non-trivial contrasts in MAST
5.8 years ago Nik Tuzov ▴ 90
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2.1k
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Comment: C: Estimation of non-trivial contrasts in MAST
5.8 years ago Nik Tuzov ▴ 90
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1.5k
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Comment: C: Logistic regression in MAST - question
5.9 years ago Nik Tuzov ▴ 90
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3
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1.5k
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Logistic regression in MAST - question
mast
updated 5.9 years ago by ▴ 270 • written 5.9 years ago by ▴ 90
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2.1k
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Comment: C: Estimation of non-trivial contrasts in MAST
5.9 years ago Nik Tuzov ▴ 90
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7
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2.1k
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Estimation of non-trivial contrasts in MAST
mast
updated 5.9 years ago by ▴ 270 • written 5.9 years ago by ▴ 90
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5.1k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
7.3 years ago Nik Tuzov ▴ 90
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5.1k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
7.3 years ago Nik Tuzov ▴ 90
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0
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5.1k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
7.3 years ago Nik Tuzov ▴ 90
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14
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5.1k
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Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2
updated 7.3 years ago by 52k • written 7.3 years ago by ▴ 90
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5.1k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
7.3 years ago Nik Tuzov ▴ 90
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0
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5.1k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
7.3 years ago Nik Tuzov ▴ 90
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1
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5.1k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
7.3 years ago Nik Tuzov ▴ 90
0
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1
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2.1k
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Comment: C: Seeking confirmation on manually setting contrasts for a 3-factor design in DESe
7.4 years ago Nik Tuzov ▴ 90
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6.8k
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Comment: C: modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
7.4 years ago Nik Tuzov ▴ 90
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1
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6.8k
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Comment: C: modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
7.4 years ago Nik Tuzov ▴ 90
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1
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2.1k
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Comment: C: Seeking confirmation on manually setting contrasts for a 3-factor design in DESe
7.4 years ago Nik Tuzov ▴ 90
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1
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2.0k
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Comment: C: Interactions in DESeq2
7.4 years ago Nik Tuzov ▴ 90
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1
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3.0k
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Comment: C: Zero inflation in RUV normalization and DE for single cell data
7.4 years ago Nik Tuzov ▴ 90
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1
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3.0k
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Comment: C: Zero inflation in RUV normalization and DE for single cell data
7.4 years ago Nik Tuzov ▴ 90
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2
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3.0k
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Comment: C: Zero inflation in RUV normalization and DE for single cell data
7.4 years ago Nik Tuzov ▴ 90
2
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9
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3.0k
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Zero inflation in RUV normalization and DE for single cell data
ruv ruvseq ruvnormalize single-cell zero-inflated
updated 7.4 years ago by ▴ 980 • written 7.4 years ago by ▴ 90
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Comment: C: Does it make sense to consider RUVr normalization for single cell RNA analysis?
7.5 years ago Nik Tuzov ▴ 90
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1
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2.7k
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Comment: C: Does it make sense to consider RUVr normalization for single cell RNA analysis?
7.5 years ago Nik Tuzov ▴ 90
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3
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2.7k
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Does it make sense to consider RUVr normalization for single cell RNA analysis?
RUV ruvseq ruvr ruvnormalize single cell
7.5 years ago Nik Tuzov ▴ 90
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7.0k
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Comment: C: Limma-voom vs limma-trend
8.0 years ago Nik Tuzov ▴ 90
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1
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7.0k
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Comment: C: Limma-voom vs limma-trend
8.0 years ago Nik Tuzov ▴ 90
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1
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7.0k
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Comment: C: Limma-voom vs limma-trend
8.0 years ago Nik Tuzov ▴ 90
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0
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7.0k
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Comment: C: Limma-voom vs limma-trend
8.1 years ago Nik Tuzov ▴ 90
3
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9
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7.0k
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Limma-voom vs limma-trend
limma limma voom limma-trend
updated 8.1 years ago by 52k • written 8.1 years ago by ▴ 90
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0
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2.1k
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Comment: C: Overriding of shrinkage in DESeq2
8.7 years ago Nik Tuzov ▴ 90
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2
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2.1k
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Comment: C: Overriding of shrinkage in DESeq2
8.7 years ago Nik Tuzov ▴ 90
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1
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2.1k
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Comment: C: Overriding of shrinkage in DESeq2
8.8 years ago Nik Tuzov ▴ 90
10
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9
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2.1k
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Overriding of shrinkage in DESeq2
deseq2
updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 90
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1
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4.2k
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Comment: C: Low-count filtering with uneven sequencing depth between samples?
9.1 years ago Nik Tuzov ▴ 90
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2
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4.2k
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Comment: C: Low-count filtering with uneven sequencing depth between samples?
9.1 years ago Nik Tuzov ▴ 90
0
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1
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4.2k
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Comment: C: Low-count filtering with uneven sequencing depth between samples?
9.1 years ago Nik Tuzov ▴ 90
0
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0
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3.1k
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Comment: C: (how) can I make heatmaps/PCA in DESeq2 using normalized counts from cummeRbund?
9.2 years ago Nik Tuzov ▴ 90
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1
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8.4k
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Comment: C: Normalization methodology in DESeq/DESeq2 vs edgeR
9.2 years ago Nik Tuzov ▴ 90
0
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1
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3.1k
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Comment: C: (how) can I make heatmaps/PCA in DESeq2 using normalized counts from cummeRbund?
9.2 years ago Nik Tuzov ▴ 90
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