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Comment: Comment: calculateTSNE with large dataset
2.4 years ago mikhael.manurung ▴ 280
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723
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Storey's qvalue and interpreting p-value histogram
qvalue
2.4 years ago mikhael.manurung ▴ 280
1
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1
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744
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Input format for `combinations` in `hashedDrops`
DropletUtils
updated 2.5 years ago by ★ 28k • written 2.5 years ago by ▴ 280
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1.1k
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Comment: C: CyTOF Differential Abundance Analysis using DESeq2
3.8 years ago mikhael.manurung ▴ 280
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1.1k
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Comment: C: CyTOF Differential Abundance Analysis using DESeq2
3.8 years ago mikhael.manurung ▴ 280
1
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5
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1.1k
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CyTOF Differential Abundance Analysis using DESeq2
deseq2 mass cytometry CyTOF
updated 3.8 years ago by 42k • written 3.8 years ago by ▴ 280
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1.8k
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Comment: C: DESeq2 issue with hierarchical clustering
3.8 years ago mikhael.manurung ▴ 280
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677
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Concatenating different runs from the same pool of barcoded CyTOF samples
batch effect cytof
4.4 years ago mikhael.manurung ▴ 280
2
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1
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778
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Answer: A: RNA-seq analysis with DESeq2
4.4 years ago mikhael.manurung ▴ 280
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2.3k
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Answer: A: limma: comparison of repeat measurements - blocking or within-subject correlatio
4.4 years ago mikhael.manurung ▴ 280
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2.5k
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Comment: C: Pseudotime analysis on bulk RNASeq using monocle
4.5 years ago mikhael.manurung ▴ 280
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1
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1.6k
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Answer: A: WGCNA module Eigengene PC1 and expression correlation
4.7 years ago mikhael.manurung ▴ 280
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912
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Comment: C: Finding Modules with WGCNA - Collapsing Biological Replicates in Expression Data
4.7 years ago mikhael.manurung ▴ 280
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1
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989
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Comment: C: Correlation plot how to improve?
4.8 years ago mikhael.manurung ▴ 280
1
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1.9k
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Comment: C: EdgeR - Complex design - contrasts/coefficients
4.9 years ago mikhael.manurung ▴ 280
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1
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868
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Comment: C: different designs for finding DEG by limma
4.9 years ago mikhael.manurung ▴ 280
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1.1k
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Comment: C: Design for introducing batch effect in DESeq2
4.9 years ago mikhael.manurung ▴ 280
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1.1k
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Comment: C: Design for introducing batch effect in DESeq2
4.9 years ago mikhael.manurung ▴ 280
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2.2k
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Comment: C: Removing Batch effect on the raw counts or normalised counts
4.9 years ago mikhael.manurung ▴ 280
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1
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1.9k
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Comment: C: Use intercept or not in model matrix for edgeR methylation analysis
4.9 years ago mikhael.manurung ▴ 280
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8.3k
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Comment: C: Comparison between two different group's pathway analysis results
4.9 years ago mikhael.manurung ▴ 280
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8.3k
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Comment: C: Comparison between two different group's pathway analysis results
4.9 years ago mikhael.manurung ▴ 280
4
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2
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8.3k
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Answer: A: Comparison between two different group's pathway analysis results
4.9 years ago mikhael.manurung ▴ 280
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0
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1.1k
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Comment: C: Help Generating Heat-maps between samples using WGCNA
4.9 years ago mikhael.manurung ▴ 280
1
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1.1k
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Comment: C: Accounting for Gene Set Overlaps in Goana and Kegga Results
4.9 years ago mikhael.manurung ▴ 280
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2
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2.9k
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Comment: C: DESeq2 multiple group comparison (ANOVA) with batch effect
4.9 years ago mikhael.manurung ▴ 280
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1
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2.9k
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Comment: C: DESeq2 multiple group comparison (ANOVA) with batch effect
4.9 years ago mikhael.manurung ▴ 280
1
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1
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1.1k
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Answer: A: Accounting for Gene Set Overlaps in Goana and Kegga Results
4.9 years ago mikhael.manurung ▴ 280
1
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2
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1.3k
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Answer: A: DESeq2--compare two log2-transformed fold changes in paired and multi factor sam
4.9 years ago mikhael.manurung ▴ 280
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1
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1.1k
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Comment: C: Help Generating Heat-maps between samples using WGCNA
4.9 years ago mikhael.manurung ▴ 280
0
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0
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1.1k
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Comment: C: How to apply a linear mixed model onto an RNA-Seq data?
4.9 years ago mikhael.manurung ▴ 280
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1
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1.1k
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Comment: C: How to apply a linear mixed model onto an RNA-Seq data?
4.9 years ago mikhael.manurung ▴ 280
0
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1
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3.9k
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Comment: C: how to get normalized count data from edgeR using TMM methods
5.0 years ago mikhael.manurung ▴ 280
1
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2.0k
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Comment: C: RNA-seq normalization without filtering
5.0 years ago mikhael.manurung ▴ 280
0
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0
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3.9k
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Comment: C: how to get normalized count data from edgeR using TMM methods
5.0 years ago mikhael.manurung ▴ 280
0
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1
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883
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Comment: C: Most (90%) DE genes of a contrast were upregulated: implication on the assumptio
5.0 years ago mikhael.manurung ▴ 280
0
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3
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883
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Most (90%) DE genes of a contrast were upregulated: implication on the assumptions of TMM-normalisation?
limma edger normalization
updated 5.0 years ago by 51k • written 5.0 years ago by ▴ 280
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936
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Answer: A: use differences in expression as input for co-expression network?
5.0 years ago mikhael.manurung ▴ 280
0
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0
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4.2k
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Answer: A: Heatmap of selected genes
5.0 years ago mikhael.manurung ▴ 280
2
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1
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2.3k
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Answer: A: How to append cluster and UMAP data to a flowSet?
5.0 years ago mikhael.manurung ▴ 280
1
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1
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1.2k
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Comment: C: Testing random effects in limma
5.0 years ago mikhael.manurung ▴ 280
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1
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2.0k
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Answer: A: Save ExpressionSet to csv file with columns and rows headers
5.2 years ago mikhael.manurung ▴ 280
1
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0
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1.5k
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Comment: C: Using SVA (surrogate variable analysis) to correct for 'completely' confounded c
5.2 years ago mikhael.manurung ▴ 280
0
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1
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1.8k
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Comment: C: Differential gene expression using edgeR and using a generalised linear model (
5.2 years ago mikhael.manurung ▴ 280
0
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1
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1.8k
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Comment: C: Differential gene expression using edgeR and using a generalised linear model (
5.2 years ago mikhael.manurung ▴ 280
0
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1
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2.3k
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Comment: C: Adjusting for known covariates before coexpression analysis with WGCNA
5.2 years ago mikhael.manurung ▴ 280
5
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3
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2.3k
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Adjusting for known covariates before coexpression analysis with WGCNA
wgcna coexpression sva
updated 5.2 years ago by ★ 3.0k • written 5.2 years ago by ▴ 280
1
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1
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1.8k
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Comment: C: Differential gene expression using edgeR and using a generalised linear model (
5.2 years ago mikhael.manurung ▴ 280
0
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0
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1.6k
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Comment: C: Plot genes with similar expression patterns
5.2 years ago mikhael.manurung ▴ 280
1
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1
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5.2k
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Comment: C: edgeR and batch effect correction for differential analysis
5.2 years ago mikhael.manurung ▴ 280
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