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Created An Answer That Has Been Accepted
Awarded 5091 times (see all awards). Earned by the
following contributors:
7 years, 10 months ago
The city by the bay
A: Time-course group difference analysis with repeated individuals using limma-voom
7 years, 10 months ago
The city by the bay
A: DEG with Limma without replicates and best plots to represent results
7 years, 11 months ago
The city by the bay
A: Creating design and contrast matrices for DEG with Limma for 2 factors?
7 years, 11 months ago
The city by the bay
A: limma decideTests global method with multiple groups
7 years, 11 months ago
The city by the bay
A: adding a description column to glmTreat output
7 years, 11 months ago
The city by the bay
A: Error in `rownames<-`(`*tmp*`, value = list(genes
7 years, 11 months ago
The city by the bay
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
8 years ago
The city by the bay
A: csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
8 years ago
The city by the bay
A: Why edgeR::aveLogCPM() is simlar to log2(rowMeans(cpm)) instead of rowMeans(cpm(
8 years ago
The city by the bay
A: csaw: how does unequal sample size affect filtering filterWindows step
8 years, 1 month ago
The city by the bay
A: Common dispersion value using edgeR for DEGs analysis
8 years, 1 month ago
The city by the bay
A: Advice regarding RNAseq data with no replicates, best approach to accomplish fol
8 years, 1 month ago
The city by the bay
A: Testing for DE genes between samples of isolated cells, accounting for expressio
8 years, 1 month ago
The city by the bay
A: Estimating cell size factors for single cell RNA-seq data
8 years, 2 months ago
The city by the bay
A: Normalizing vs RNA content in scRNAseq data
8 years, 2 months ago
The city by the bay
A: Modeling input data in ChIP-seq experiments with EdgeR, DESeq(2) or Limma
8 years, 2 months ago
The city by the bay
A: using edgeR or limma for 5C data normalization
8 years, 2 months ago
The city by the bay
EdgeR -ANOVA-like test vs testing individual contrasts
8 years, 2 months ago
The city by the bay
Saving output from glmTreat to a csv file?
8 years, 2 months ago
The city by the bay
DEG with Limma without replicates and best plots to represent results
8 years, 2 months ago
The city by the bay
Limma PlotMDS: what values should be used?
8 years, 2 months ago
The city by the bay
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
8 years, 2 months ago
The city by the bay
Time-course group difference analysis with repeated individuals using limma-voom
8 years, 2 months ago
The city by the bay
Unbalanced experiment with multiple samples from each patient.
8 years, 2 months ago
The city by the bay
edgeR long vectors support when normalizing abundance matrix
8 years, 2 months ago
The city by the bay
Advice regarding RNAseq data with no replicates, best approach to accomplish fold-change
8 years, 2 months ago
The city by the bay
Testing for DE genes between samples of isolated cells, accounting for expression in whole tissue
8 years, 2 months ago
The city by the bay
Common dispersion value using edgeR for DEGs analysis
8 years, 2 months ago
The city by the bay
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
8 years, 2 months ago
The city by the bay
goana limma- extract list of DE genes and genes in the enriched GO terms?
8 years, 2 months ago
The city by the bay
Experiment design contrasts any time edgeR
8 years, 2 months ago
The city by the bay
csaw: how does unequal sample size affect filtering filterWindows step
8 years, 2 months ago
The city by the bay
Finding genes respond differently to treatment between many genotype comparison
8 years, 2 months ago
The city by the bay
Using duplicateCorrelation to handle replicate samples
8 years, 2 months ago
The city by the bay
Help with design matrix for two cell types, multiple treatments
8 years, 2 months ago
The city by the bay
Sparse matrices in Bioconductor objects for single-cell analyses
8 years, 2 months ago
The city by the bay
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
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