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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
3.6 years ago Nik Tuzov ▴ 90
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Comment: Comment: stat value is throwed out after lfcShrink in DESeq2
5.0 years ago Nik Tuzov ▴ 90
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1.6k
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Comment: Comment: DeSEQ2 factor effect without interaction effect
5.0 years ago Nik Tuzov ▴ 90
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749
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Comment: C: The basis for the full rank design matrix requirement in DESeq2
5.9 years ago Nik Tuzov ▴ 90
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3
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749
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The basis for the full rank design matrix requirement in DESeq2
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 90
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1.3k
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Comment: C: Error when providing contrast coefficients to lfcShrink() of DESeq2 package
6.1 years ago Nik Tuzov ▴ 90
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4
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1.3k
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Error when providing contrast coefficients to lfcShrink() of DESeq2 package
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 90
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2.0k
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Comment: C: FCSTransTransform() implementation in flowCore
6.6 years ago Nik Tuzov ▴ 90
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4
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2.0k
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FCSTransTransform() implementation in flowCore
flowCore FCSTrans flow cytometry
updated 6.6 years ago by ▴ 310 • written 6.6 years ago by ▴ 90
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Comment: C: Estimation of non-trivial contrasts in MAST
6.7 years ago Nik Tuzov ▴ 90
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2.6k
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Comment: C: Estimation of non-trivial contrasts in MAST
6.8 years ago Nik Tuzov ▴ 90
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2.6k
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Comment: C: Estimation of non-trivial contrasts in MAST
6.8 years ago Nik Tuzov ▴ 90
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1
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1.9k
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Comment: C: Logistic regression in MAST - question
6.8 years ago Nik Tuzov ▴ 90
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1.9k
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Logistic regression in MAST - question
mast
updated 6.8 years ago by ▴ 280 • written 6.8 years ago by ▴ 90
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2.6k
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Comment: C: Estimation of non-trivial contrasts in MAST
6.8 years ago Nik Tuzov ▴ 90
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7
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2.6k
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Estimation of non-trivial contrasts in MAST
mast
updated 6.8 years ago by ▴ 280 • written 6.9 years ago by ▴ 90
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6.0k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
8.3 years ago Nik Tuzov ▴ 90
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6.0k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
8.3 years ago Nik Tuzov ▴ 90
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0
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6.0k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
8.3 years ago Nik Tuzov ▴ 90
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14
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6.0k
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Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2
updated 8.3 years ago by 53k • written 8.3 years ago by ▴ 90
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6.0k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
8.3 years ago Nik Tuzov ▴ 90
0
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0
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6.0k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
8.3 years ago Nik Tuzov ▴ 90
0
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1
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6.0k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
8.3 years ago Nik Tuzov ▴ 90
0
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1
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2.5k
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Comment: C: Seeking confirmation on manually setting contrasts for a 3-factor design in DESe
8.4 years ago Nik Tuzov ▴ 90
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8.0k
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Comment: C: modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
8.4 years ago Nik Tuzov ▴ 90
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1
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8.0k
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Comment: C: modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
8.4 years ago Nik Tuzov ▴ 90
0
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1
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2.5k
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Comment: C: Seeking confirmation on manually setting contrasts for a 3-factor design in DESe
8.4 years ago Nik Tuzov ▴ 90
0
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1
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2.4k
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Comment: C: Interactions in DESeq2
8.4 years ago Nik Tuzov ▴ 90
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1
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3.6k
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Comment: C: Zero inflation in RUV normalization and DE for single cell data
8.4 years ago Nik Tuzov ▴ 90
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1
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3.6k
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Comment: C: Zero inflation in RUV normalization and DE for single cell data
8.4 years ago Nik Tuzov ▴ 90
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2
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3.6k
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Comment: C: Zero inflation in RUV normalization and DE for single cell data
8.4 years ago Nik Tuzov ▴ 90
2
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9
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3.6k
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Zero inflation in RUV normalization and DE for single cell data
ruv ruvseq ruvnormalize single-cell zero-inflated
updated 8.4 years ago by ▴ 980 • written 8.4 years ago by ▴ 90
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3.3k
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Comment: C: Does it make sense to consider RUVr normalization for single cell RNA analysis?
8.4 years ago Nik Tuzov ▴ 90
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3.3k
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Comment: C: Does it make sense to consider RUVr normalization for single cell RNA analysis?
8.4 years ago Nik Tuzov ▴ 90
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3
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3.3k
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Does it make sense to consider RUVr normalization for single cell RNA analysis?
RUV ruvseq ruvr ruvnormalize single cell
8.5 years ago • updated 8.4 years ago Nik Tuzov ▴ 90
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8.2k
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Comment: C: Limma-voom vs limma-trend
9.0 years ago Nik Tuzov ▴ 90
0
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1
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8.2k
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Comment: C: Limma-voom vs limma-trend
9.0 years ago Nik Tuzov ▴ 90
0
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1
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8.2k
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Comment: C: Limma-voom vs limma-trend
9.0 years ago Nik Tuzov ▴ 90
0
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0
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8.2k
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Comment: C: Limma-voom vs limma-trend
9.1 years ago Nik Tuzov ▴ 90
3
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9
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8.2k
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Limma-voom vs limma-trend
limma limma voom limma-trend
updated 9.1 years ago by 53k • written 9.1 years ago by ▴ 90
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2.7k
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Comment: C: Overriding of shrinkage in DESeq2
9.6 years ago Nik Tuzov ▴ 90
0
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2
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2.7k
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Comment: C: Overriding of shrinkage in DESeq2
9.6 years ago Nik Tuzov ▴ 90
0
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1
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2.7k
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Comment: C: Overriding of shrinkage in DESeq2
9.8 years ago Nik Tuzov ▴ 90
10
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9
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2.7k
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Overriding of shrinkage in DESeq2
deseq2
updated 9.8 years ago by 43k • written 9.8 years ago by ▴ 90
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1
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4.9k
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Comment: C: Low-count filtering with uneven sequencing depth between samples?
10.1 years ago Nik Tuzov ▴ 90
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2
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4.9k
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Comment: C: Low-count filtering with uneven sequencing depth between samples?
10.1 years ago Nik Tuzov ▴ 90
0
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1
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4.9k
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Comment: C: Low-count filtering with uneven sequencing depth between samples?
10.1 years ago Nik Tuzov ▴ 90
0
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0
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3.5k
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Comment: C: (how) can I make heatmaps/PCA in DESeq2 using normalized counts from cummeRbund?
10.2 years ago Nik Tuzov ▴ 90
0
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1
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9.3k
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Comment: C: Normalization methodology in DESeq/DESeq2 vs edgeR
10.2 years ago Nik Tuzov ▴ 90
0
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1
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3.5k
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Comment: C: (how) can I make heatmaps/PCA in DESeq2 using normalized counts from cummeRbund?
10.2 years ago Nik Tuzov ▴ 90
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