1. The Bioconductor Project
Hi! Welcome to the course! I'm James, and I'll be your guide as you begin your Bioconductor journey in Chapters 1 and 2. Chapters 3 and 4 will be lead by data scientist and bioinformatician, Paula Martinez.
2. Bioconductor
The Bioconductor project is an open source repository for R packages, datasets, and workflows that are specific for analyzing biological data. The Bioconductor project is a useful extension on CRAN, the R Archive, because it provides us with the software tools to explore, understand, and solve molecular biology questions. Hence, Bioconductor's tagline is "open source software for bioinformatics".
3. What do we measure and why?
Molecular biology questions are usually about either the structure or the function of each of the building blocks of an organism, and very often how they interconnect.
In this course, we will learn commonly used packages for understanding the structure of biological data. We'll find out more about the elements, their regions, their size and order, and how they relate to other data.
DataCamp also provides other courses that cover more advanced bioinformatics topics, such as gene expression and regulation.
4. How to install Bioconductor packages?
The Bioconductor package collection forms its own repository and has its own release schedule. Because Bioconductor has it's own base functions and updates, packages are installed differently. To install Bioconductor packages we need two lines of code.
First, we install BiocManager, which is a package management system through which we can install other Bioconductor packages.
Second, we call BiocManager-colon-colon-install to install any Bioconductor package we desire. Here, we install the popular GenomicRanges package.
Updating packages regularly is important to access new features and improvements.
5. Bioconductor version and package version
Because Bioconductor is under constant development, it's important to check that we are running the latest version. We begin by loading BiocManager, then, we can check the Bioconductor version using the version function.
6. Checking package versions
To load a package, use the library function like with CRAN packages.
It's important for reproducibility to always check the versions of your packages. We can use the sessionInfo() function to find out the version of every package loaded in the session.
7. Package updates
Finally, to find out if any packages can be updated, use the valid() function.
8. Let's practice!
Now it's your turn to begin using Bioconductor.