RNAseq analysis with R
1
NGS data exploration
1.1
Required packages for these exercises
1.2
Reading from a fasta file
1.3
Parsing FastQ files
2
RNAseq data analysis
2.1
Data pre-processing
2.2
Mapping
2.2.1
Examining the mapped reads
2.3
Quantification
2.4
Exploratory analysis
2.5
Understanding the dataset
2.6
Prefiltering
2.7
Normalisation
2.7.1
Defining the model matrix
2.7.2
MA-plots
2.8
Using visualisation to verify (sanity checks)
2.8.1
Principal Component Analysis (PCA)
2.9
Differential expression analysis
2.9.1
Fitting the model
2.9.2
Comparisons
2.9.3
Extract top DE features
2.10
Verification using visualisation
2.10.1
Hierachical clustering
2.11
Gene Annotation
2.12
Gene set enrichment
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Differentially expressed gene analysis of RNA-seq data using R
Chapter 2
RNAseq data analysis