Full R Bioconductor Training

by Tertiary Infotech Pte. Ltd

These are the exercise files used for Full R Bioconductor Training course.

The course outline can be found in

https://www.tertiarycourses.com.sg/full-r-bioconductor-training.html

https://www.tertiarycourses.com.my/full-r-bioconductor-training-malaysia.html

Day 1

Module 1 : Introduction to bioinformatics

• What is bioinformatics
• Types of online databases and online tools
• Genomics resources
• 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

Day 2

Module 7: Visualizing Data in BioConductor

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

Module 8: Microarray Analysis

• Expression sets 
• Exploratory data analysis
• Clustering
• Linear Regression

Module 9: NGS Analysis

• Working with shortread data
• Filtering sequences
• Matching and counting
• Visualizing NGS

Module 10: Protein Analysis

• Read Fasta file
• Amino acid count
• Compute isoelectric and Mw
• Hydropathy scores

Module 11: Visualizing Genomes

• ggbio package
• Visualizing karyograms
• Visualizing reference track
• Visualizing ideogram
• gvis package
• genomegraphs package