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Created An Answer With At Least 3 Up-Votes
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following contributors:
8 years, 2 months ago
The city by the bay
Difficulty in finding DEG using TCGA data from FireBrowse
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
How to use limma to do regularization for Ballgown
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
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
8 years, 2 months ago
The city by the bay
edgeR: Tagwise dispersion when using offset matrix
8 years, 2 months ago
The city by the bay
differential expression analysis of htseq data with edgeR/voom
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
Discrepancy in the output of decideTests (total not equal to sum of up/down genes)
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
Common dispersion value using edgeR for DEGs analysis
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
csaw - workflow to incorporate input/control 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
Paired Test - Design Matrix and Contrast Matrix Voom and Limma
8 years, 2 months ago
The city by the bay
Can featurecounts count number of mapped reads rapidly in arbitrary regions?
8 years, 2 months ago
The city by the bay
design matrix - control for biological replicates
8 years, 2 months ago
The city by the bay
Combining newer/older RNAseq data, batch correcting
8 years, 2 months ago
The city by the bay
Using edgeR or DESeq2 to analyze allele-specific expression?
8 years, 2 months ago
The city by the bay
edgeR - how to convert DGELRT and other classes to .csv files
8 years, 2 months ago
The city by the bay
Design matrix and contrast for RNA knockdown experiment
8 years, 2 months ago
The city by the bay
Building contrasts for combined treatment groups to compare to a control
8 years, 2 months ago
The city by the bay
LogFC: how do you determine the cutoff for differentially expressed genes?
8 years, 2 months ago
The city by the bay
DE for genes with very low counts using limma.
8 years, 2 months ago
The city by the bay
Dealing with (blood) contamination in RNA-seq data
8 years, 3 months ago
The city by the bay
A: Sparse matrices in Bioconductor objects for single-cell analyses
8 years, 3 months ago
The city by the bay
A: differential expression analysis of htseq data with edgeR/voom
8 years, 4 months ago
The city by the bay
A: Experiment design contrasts any time edgeR
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