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Created An Answer With At Least 3 Up-Votes
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following contributors:
9 years, 7 months ago
The city by the bay
A: Bounded Regression with Limma for RRBS?
9 years, 7 months ago
The city by the bay
A: Very low EdgeR Pvalues with very small sample size
9 years, 7 months ago
The city by the bay
A: Getting normalized read counts from region counts
9 years, 7 months ago
The city by the bay
A: how duplicates reads would affect Differential expression analysis results
9 years, 7 months ago
The city by the bay
A: design matrix - control for biological replicates
9 years, 7 months ago
The city by the bay
A: Plot normalized expression or count values for a specific gene in limma
9 years, 8 months ago
The city by the bay
A: Differential expression analysis: comparison of DESeq2 and edgeR robust results
9 years, 8 months ago
The city by the bay
A: Extremely Big Number of Differences from Multi-level Design in RNA-seq Analysis
9 years, 8 months ago
The city by the bay
A: Detection of methylated regions from MeDIP data using csaw
9 years, 8 months ago
The city by the bay
A: csaw - workflow to incorporate input/control samples?
9 years, 8 months ago
The city by the bay
deseq2, edger different number of replicates and extraction kit
9 years, 8 months ago
The city by the bay
limma Time Course Experiment with many time points
9 years, 8 months ago
The city by the bay
How to do contrasts in CAMERA/ROMER/ROAST/etc in Limma?
9 years, 8 months ago
The city by the bay
Mutation effect on expression (RNA-Seq) using limma
9 years, 8 months ago
The city by the bay
ROAST after edgeR glmTreat and average RPKM filter
9 years, 8 months ago
The city by the bay
Is it valid to use only genes of interest before eBayes step in limma?
9 years, 8 months ago
The city by the bay
Error when calculating DE using the classical approach in edgeR
9 years, 8 months ago
The city by the bay
Differential expression analysis: comparison of DESeq2 and edgeR robust results
9 years, 8 months ago
The city by the bay
RNA-seq analysis using EdgeR- I need to make sure that the codes that I use to analyze the data are correct
9 years, 8 months ago
The city by the bay
Csaw : filter windows based on matched negative control
9 years, 8 months ago
The city by the bay
Discrepancy in the output of decideTests (total not equal to sum of up/down genes)
9 years, 8 months ago
The city by the bay
csaw - workflow to incorporate input/control samples?
9 years, 8 months ago
The city by the bay
Can featurecounts count number of mapped reads rapidly in arbitrary regions?
9 years, 8 months ago
The city by the bay
design matrix - control for biological replicates
9 years, 8 months ago
The city by the bay
Combining newer/older RNAseq data, batch correcting
9 years, 8 months ago
The city by the bay
Using edgeR or DESeq2 to analyze allele-specific expression?
9 years, 8 months ago
The city by the bay
edgeR - how to convert DGELRT and other classes to .csv files
9 years, 8 months ago
The city by the bay
Design matrix and contrast for RNA knockdown experiment
9 years, 8 months ago
The city by the bay
Design and contrast question limma (additive or nested or duplicateCorrelation())??
9 years, 8 months ago
The city by the bay
DE for genes with very low counts using limma.
9 years, 8 months ago
The city by the bay
Differential expression analysis - additive genetic model (how to implement it)
9 years, 8 months ago
The city by the bay
One replicate (one-color OR two-color) is enough to use Limma?
9 years, 8 months ago
The city by the bay
duplicateCorrelation and Pearson Correlation
9 years, 8 months ago
The city by the bay
Rsubread featureCounts with strand information
9 years, 8 months ago
The city by the bay
Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
9 years, 8 months ago
The city by the bay
EdgeR: is more than one control per batch an issue?
9 years, 8 months ago
The city by the bay
how to use edgeR analysis RNA-seq data with a obvious deviation sample
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