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SkillsFuture Course - R Bioconductor Training for Bioinformatics

Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology. Bioconductor is based primarily on the statistical R programming language,

This course will cover:

  1. Sequencing Using Bioconductor
  2. Extract Data from NCBI
  3. Databases in Bioconductor
  4. DNS Microarray

Outline

Module 1 : Introduction to bioinformatics

  1. What is bioinformatics
  2. Types of online databases and online tools
  3. Genomics resources
  4. Protenomics resources

Module 2 : Introduction to bioConductor

  • BioConductor Website
  • installing BioConductor in R
  • Bioconductor packages, vignettes, tutorials
  • Bioconductor datasets(biocViews)

Module 3 : Databases in BioConductor

  • Annotation Hub
  • biomarts (online biomarts)
  • Genomic (full genomes)
  • GEOquery (NCBI Gene expression Omnibus) & ArrayExpress
  • KEGG (Kyto Encyclopedia for Genes and Genomes)
  • Gene libraries

Module 4 : Data files in BioConductor

  • Data containers
  • Importing data types
  • Downloading DNA
  • Manipulating DNA

Module 5: DNA Blast

  • NCBI blast 
  • Gene sequence blast
  • Protein blast

Module 6 : Ranges into BioConductor

  • Iranges
  • Granges
  • Granges plotting
  • Granges w genes

Module 7: Visualizing Data in BioConductor

  • Visualizing genomic features
  • Visualizing DNA content
  • Visualizing gene expression

Speaker/s

Dwight Nuwan Fonseka have a degree in Biotechnology (from NUS) ,Advanced diploma in Pharamceutical management (from MDIS) and Masters in Education (from NTU). He have 8 years experience of teaching biology at O and A levels/ IB level in international schools in Singapore and overseas.
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