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Comment: Comment: calculateTSNE with large dataset
2.9 years ago mikhael.manurung ▴ 280
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848
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Storey's qvalue and interpreting p-value histogram
qvalue
2.9 years ago mikhael.manurung ▴ 280
1
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1
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845
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Input format for `combinations` in `hashedDrops`
DropletUtils
updated 3.0 years ago by ★ 28k • written 3.0 years ago by ▴ 280
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1
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1.3k
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Comment: C: CyTOF Differential Abundance Analysis using DESeq2
4.3 years ago mikhael.manurung ▴ 280
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1
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1.3k
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Comment: C: CyTOF Differential Abundance Analysis using DESeq2
4.3 years ago mikhael.manurung ▴ 280
1
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5
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1.3k
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CyTOF Differential Abundance Analysis using DESeq2
deseq2 mass cytometry CyTOF
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 280
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2.1k
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Comment: C: DESeq2 issue with hierarchical clustering
4.3 years ago mikhael.manurung ▴ 280
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784
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Concatenating different runs from the same pool of barcoded CyTOF samples
batch effect cytof
4.8 years ago mikhael.manurung ▴ 280
2
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1
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921
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Answer: A: RNA-seq analysis with DESeq2
4.9 years ago mikhael.manurung ▴ 280
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1
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2.8k
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Answer: A: limma: comparison of repeat measurements - blocking or within-subject correlatio
4.9 years ago mikhael.manurung ▴ 280
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0
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2.9k
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Comment: C: Pseudotime analysis on bulk RNASeq using monocle
5.0 years ago mikhael.manurung ▴ 280
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1
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1.9k
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Answer: A: WGCNA module Eigengene PC1 and expression correlation
5.1 years ago mikhael.manurung ▴ 280
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0
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1.1k
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Comment: C: Finding Modules with WGCNA - Collapsing Biological Replicates in Expression Data
5.2 years ago mikhael.manurung ▴ 280
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1
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1.1k
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Comment: C: Correlation plot how to improve?
5.2 years ago mikhael.manurung ▴ 280
1
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2.2k
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Comment: C: EdgeR - Complex design - contrasts/coefficients
5.3 years ago mikhael.manurung ▴ 280
0
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1
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961
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Comment: C: different designs for finding DEG by limma
5.4 years ago mikhael.manurung ▴ 280
1
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1.3k
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Comment: C: Design for introducing batch effect in DESeq2
5.4 years ago mikhael.manurung ▴ 280
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0
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1.3k
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Comment: C: Design for introducing batch effect in DESeq2
5.4 years ago mikhael.manurung ▴ 280
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0
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2.7k
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Comment: C: Removing Batch effect on the raw counts or normalised counts
5.4 years ago mikhael.manurung ▴ 280
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1
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2.3k
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Comment: C: Use intercept or not in model matrix for edgeR methylation analysis
5.4 years ago mikhael.manurung ▴ 280
0
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9.7k
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Comment: C: Comparison between two different group's pathway analysis results
5.4 years ago mikhael.manurung ▴ 280
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9.7k
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Comment: C: Comparison between two different group's pathway analysis results
5.4 years ago mikhael.manurung ▴ 280
4
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2
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9.7k
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Answer: A: Comparison between two different group's pathway analysis results
5.4 years ago mikhael.manurung ▴ 280
0
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0
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1.3k
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Comment: C: Help Generating Heat-maps between samples using WGCNA
5.4 years ago mikhael.manurung ▴ 280
1
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1.2k
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Comment: C: Accounting for Gene Set Overlaps in Goana and Kegga Results
5.4 years ago mikhael.manurung ▴ 280
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2
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3.3k
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Comment: C: DESeq2 multiple group comparison (ANOVA) with batch effect
5.4 years ago mikhael.manurung ▴ 280
0
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1
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3.3k
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Comment: C: DESeq2 multiple group comparison (ANOVA) with batch effect
5.4 years ago mikhael.manurung ▴ 280
1
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1
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1.2k
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Answer: A: Accounting for Gene Set Overlaps in Goana and Kegga Results
5.4 years ago mikhael.manurung ▴ 280
1
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2
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1.5k
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Answer: A: DESeq2--compare two log2-transformed fold changes in paired and multi factor sam
5.4 years ago mikhael.manurung ▴ 280
0
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1
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1.3k
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Comment: C: Help Generating Heat-maps between samples using WGCNA
5.4 years ago mikhael.manurung ▴ 280
0
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0
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1.3k
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Comment: C: How to apply a linear mixed model onto an RNA-Seq data?
5.4 years ago mikhael.manurung ▴ 280
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1
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1.3k
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Comment: C: How to apply a linear mixed model onto an RNA-Seq data?
5.4 years ago mikhael.manurung ▴ 280
0
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1
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4.2k
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Comment: C: how to get normalized count data from edgeR using TMM methods
5.4 years ago mikhael.manurung ▴ 280
1
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0
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2.5k
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Comment: C: RNA-seq normalization without filtering
5.4 years ago mikhael.manurung ▴ 280
0
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0
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4.2k
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Comment: C: how to get normalized count data from edgeR using TMM methods
5.4 years ago mikhael.manurung ▴ 280
0
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1
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979
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Comment: C: Most (90%) DE genes of a contrast were upregulated: implication on the assumptio
5.4 years ago mikhael.manurung ▴ 280
0
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3
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979
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Most (90%) DE genes of a contrast were upregulated: implication on the assumptions of TMM-normalisation?
limma edger normalization
updated 5.4 years ago by 52k • written 5.4 years ago by ▴ 280
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0
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1.0k
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Answer: A: use differences in expression as input for co-expression network?
5.5 years ago mikhael.manurung ▴ 280
0
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0
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4.6k
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Answer: A: Heatmap of selected genes
5.5 years ago mikhael.manurung ▴ 280
2
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1
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2.6k
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Answer: A: How to append cluster and UMAP data to a flowSet?
5.5 years ago mikhael.manurung ▴ 280
1
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1
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1.3k
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Comment: C: Testing random effects in limma
5.5 years ago mikhael.manurung ▴ 280
0
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1
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2.3k
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Answer: A: Save ExpressionSet to csv file with columns and rows headers
5.6 years ago mikhael.manurung ▴ 280
1
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0
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1.8k
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Comment: C: Using SVA (surrogate variable analysis) to correct for 'completely' confounded c
5.6 years ago mikhael.manurung ▴ 280
0
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1
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2.1k
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Comment: C: Differential gene expression using edgeR and using a generalised linear model (
5.6 years ago mikhael.manurung ▴ 280
0
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1
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2.1k
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Comment: C: Differential gene expression using edgeR and using a generalised linear model (
5.6 years ago mikhael.manurung ▴ 280
0
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1
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2.7k
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Comment: C: Adjusting for known covariates before coexpression analysis with WGCNA
5.6 years ago mikhael.manurung ▴ 280
5
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3
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2.7k
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Adjusting for known covariates before coexpression analysis with WGCNA
wgcna coexpression sva
updated 5.6 years ago by ★ 3.0k • written 5.6 years ago by ▴ 280
1
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1
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2.1k
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Comment: C: Differential gene expression using edgeR and using a generalised linear model (
5.6 years ago mikhael.manurung ▴ 280
0
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0
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1.9k
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Comment: C: Plot genes with similar expression patterns
5.7 years ago mikhael.manurung ▴ 280
1
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1
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5.6k
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Comment: C: edgeR and batch effect correction for differential analysis
5.7 years ago mikhael.manurung ▴ 280
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