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Comment:
Comment: calculateTSNE with large dataset
2.2 years ago
mikhael.manurung
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Comment:
C: CyTOF Differential Abundance Analysis using DESeq2
3.6 years ago
mikhael.manurung
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Comment:
C: CyTOF Differential Abundance Analysis using DESeq2
3.6 years ago
mikhael.manurung
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C: DESeq2 issue with hierarchical clustering
3.6 years ago
mikhael.manurung
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Comment:
C: Pseudotime analysis on bulk RNASeq using monocle
4.3 years ago
mikhael.manurung
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Comment:
C: Finding Modules with WGCNA - Collapsing Biological Replicates in Expression Data
4.5 years ago
mikhael.manurung
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909
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Comment:
C: Correlation plot how to improve?
4.5 years ago
mikhael.manurung
▴ 270
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Comment:
C: EdgeR - Complex design - contrasts/coefficients
4.6 years ago
mikhael.manurung
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812
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Comment:
C: different designs for finding DEG by limma
4.7 years ago
mikhael.manurung
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Comment:
C: Design for introducing batch effect in DESeq2
4.7 years ago
mikhael.manurung
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Comment:
C: Design for introducing batch effect in DESeq2
4.7 years ago
mikhael.manurung
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C: Removing Batch effect on the raw counts or normalised counts
4.7 years ago
mikhael.manurung
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Comment:
C: Use intercept or not in model matrix for edgeR methylation analysis
4.7 years ago
mikhael.manurung
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Comment:
C: Comparison between two different group's pathway analysis results
4.7 years ago
mikhael.manurung
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C: Comparison between two different group's pathway analysis results
4.7 years ago
mikhael.manurung
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Comment:
C: Help Generating Heat-maps between samples using WGCNA
4.7 years ago
mikhael.manurung
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Comment:
C: Accounting for Gene Set Overlaps in Goana and Kegga Results
4.7 years ago
mikhael.manurung
▴ 270
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Comment:
C: DESeq2 multiple group comparison (ANOVA) with batch effect
4.7 years ago
mikhael.manurung
▴ 270
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2.7k
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Comment:
C: DESeq2 multiple group comparison (ANOVA) with batch effect
4.7 years ago
mikhael.manurung
▴ 270
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993
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Comment:
C: Help Generating Heat-maps between samples using WGCNA
4.7 years ago
mikhael.manurung
▴ 270
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996
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Comment:
C: How to apply a linear mixed model onto an RNA-Seq data?
4.7 years ago
mikhael.manurung
▴ 270
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996
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Comment:
C: How to apply a linear mixed model onto an RNA-Seq data?
4.7 years ago
mikhael.manurung
▴ 270
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1
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3.8k
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Comment:
C: how to get normalized count data from edgeR using TMM methods
4.7 years ago
mikhael.manurung
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1.8k
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Comment:
C: RNA-seq normalization without filtering
4.7 years ago
mikhael.manurung
▴ 270
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3.8k
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Comment:
C: how to get normalized count data from edgeR using TMM methods
4.7 years ago
mikhael.manurung
▴ 270
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828
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Comment:
C: Most (90%) DE genes of a contrast were upregulated: implication on the assumptio
4.7 years ago
mikhael.manurung
▴ 270
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1.1k
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Comment:
C: Testing random effects in limma
4.8 years ago
mikhael.manurung
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1.4k
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Comment:
C: Using SVA (surrogate variable analysis) to correct for 'completely' confounded c
4.9 years ago
mikhael.manurung
▴ 270
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1
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1.6k
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Comment:
C: Differential gene expression using edgeR and using a generalised linear model (
4.9 years ago
mikhael.manurung
▴ 270
0
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1
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1.6k
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Comment:
C: Differential gene expression using edgeR and using a generalised linear model (
4.9 years ago
mikhael.manurung
▴ 270
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1
reply
2.1k
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Comment:
C: Adjusting for known covariates before coexpression analysis with WGCNA
5.0 years ago
mikhael.manurung
▴ 270
1
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1
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1.6k
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Comment:
C: Differential gene expression using edgeR and using a generalised linear model (
5.0 years ago
mikhael.manurung
▴ 270
0
votes
0
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1.4k
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Comment:
C: Plot genes with similar expression patterns
5.0 years ago
mikhael.manurung
▴ 270
1
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1
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4.9k
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Comment:
C: edgeR and batch effect correction for differential analysis
5.0 years ago
mikhael.manurung
▴ 270
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3.1k
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Comment:
C: limma random effects and multi level experiments
5.0 years ago
mikhael.manurung
▴ 270
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0
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1.2k
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Comment:
C: How to regress phenotype ~ gene + covars in limma?
5.0 years ago
mikhael.manurung
▴ 270
1
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1.1k
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Comment:
C: LIMMA how to model unidentified source of covariate
5.1 years ago
mikhael.manurung
▴ 270
1
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1
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1.7k
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Comment:
C: Flow cytometry optimization of transformation parameters
5.1 years ago
mikhael.manurung
▴ 270
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0
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2.5k
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Comment:
C: Useful of Normal Enrichment Score (NES) in GSEA
5.2 years ago
mikhael.manurung
▴ 270
0
votes
1
reply
1.7k
views
Comment:
C: Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
5.2 years ago
mikhael.manurung
▴ 270
0
votes
0
replies
917
views
Comment:
C: Cydar's countCells tolerance parameter for arcsinh-transformed data
5.2 years ago
mikhael.manurung
▴ 270
0
votes
1
reply
917
views
Comment:
C: Cydar's countCells tolerance parameter for arcsinh-transformed data
5.2 years ago
mikhael.manurung
▴ 270
1
vote
0
replies
26k
views
Comment:
C: DESeq2 log2FC shrink before GSEA or not?
5.2 years ago
mikhael.manurung
▴ 270
0
votes
1
reply
1.3k
views
Comment:
C: variancePartition - testing for individuals
5.2 years ago
mikhael.manurung
▴ 270
0
votes
1
reply
1.3k
views
Comment:
C: variancePartition - testing for individuals
5.2 years ago
mikhael.manurung
▴ 270
0
votes
0
replies
691
views
Comment:
C: Comparing groups with paired samples by using limma
5.2 years ago
mikhael.manurung
▴ 270
0
votes
0
replies
1.3k
views
Comment:
C: Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
5.3 years ago
mikhael.manurung
▴ 270
0
votes
1
reply
830
views
Comment:
C: Limma time course experiments
5.3 years ago
mikhael.manurung
▴ 270
0
votes
0
replies
2.2k
views
Comment:
C: Controlling numerical covariates: differential gene expression with limma voom
5.4 years ago
mikhael.manurung
▴ 270
0
votes
1
reply
2.3k
views
Comment:
C: Count filter for differential expression
5.4 years ago
mikhael.manurung
▴ 270
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