R Tutorial : The Bioconductor Project

Key Takeaways

hi I'm Paula Martinez I'll be your instructor I'm a data scientist and I train people on how to analyze their data more efficiently also I'm a bio fermentation interested in genomic variation that leads to diversity for these kinds of analysis I love using R and bioconductor particularly because of the possibilities to work with different data sets and to collaborate within the community during this introduction you will discover the most commonly bioconductor packages we will start with installation and at the end of this chapter you will be able to retrieve whole genome sequences using bioconductor the bioconductor project is an open source so forth it's a ripper story for our packages datasets and workflows that are specific for analyzing biological data the bioconductor project is a useful extension on cran the our archive because it provides us with the software tools to explore understand and solve simple and complex molecular biology questions hence bioconductor stock line is open source software for bioinformatics Blacula biology questions are usually about either the structure or the function of each of the building blocks on an organism and very often how they interconnect to one another in this course you will learn commonly use packages that will help you understand the structure of biological data that is you will find out more about the elements their regions their size and order and how they relate to other data other bioconductor courses on datacom will teach you more about the functions of the building blocks such as gene expression and regulation and how these affect phenotypes such as health disease evolution and much more the bio conductor package collection forms its own repository and has a release schedule different from the archive because bioconductor has its own base functions and updates packages are installed differently to install bioconductor packages you need two lines of code as shown on the slide first use the function source on the script by c-lite that are from the bioconductor that chord this script will install the pious installer package then use the function by c-lite with the name of the package you want to install once you source the buzzy light you will be informed if any new versions of bioconductor are available and will also show you a prompt to update your evasion if needed updating packages regularly it's important to get the new features in case there are upgrades on packages or dependencies you will be asked to update all some unknown of the packages bioconductor is in constant development you can check the passion of bioconductor using the syntax via C installer : : by C version or if you already loaded the BIOS installer package you can call the function by a C version directly to load a package use the function library like with grant packages it's important for reproducibility to always check the versions of your packages you can use the function session info which gives you a list of all the loaded packages under versions or you can inquire the version of each package using package version and the package name finally if you are interested to know if you have out-of-date packages use the function by C valid now it's your turn to use by ok