Genomics
CHAPTER I : R basics and exploratory data analysis
CHAPTER II : Basic bioconductor infrastructure
CHAPTER III : Microarray data
CHAPTER IV : High-throughput Sequencing
- Mapping algorithms and softwares
- Tophat2 : Download, build reference genome and align the reads to the reference genome
- Exploratory data analysis for next generation sequencing
- Read counting - NGS
CHAPTER V : Visualizing next geration sequencing data
We will try four ways to look at NGS coverage: using the standalone Java program IGV, using simple plot commands, and using the Gviz and ggbio packages in Bioconductor.
- IGV - Integrative Genomics Viewer
- Visualize NGS data with R and Bioconductor
- ggbio - Visualize genomic data
- Gviz - Visualize genomic data
CHAPTER VII : RNA-sequencing
- Introduction to RNA sequencing
- RNA sequencing data analysis - alignment and reads counting using cufflinks
- RNA sequencing data analysis - Counting, normalization and differential expression
- RNA-Seq differential expression work flow using DESeq2
CHAPTER VIII : Genomic ToolKits
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Categories contained by this category :
Basic Bioconductor infrastructure
Genomic Toolkits
High-throughput Sequencing
Microarray data
R basics and exploratory data analysis
RNA sequencing
Visualizing next geration sequencing data
Articles contained by this category :
fastqcr: An R Package Facilitating Quality Controls of Sequencing Data for Large Numbers of Samples
MIT licence