R Bioconductor Training for Bioinformatics
Details
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:
- Sequencing Using Bioconductor
- Extract Data from NCBI
- Databases in Bioconductor
- DNS Microarray
Outline
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
Module 7: Visualizing Data in BioConductor
- Visualizing genomic features
- Visualizing DNA content
- Visualizing gene expression
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