This tutorial & exercise is designed for trainees interested in joining our lab. It reflects our expected computing skills using R, Python, Linux shell commands and bioinformatics workflow languages. Even if you lack the skills for one or more of the languages at the time you start this tutorial, we believe the learning curve for new skills enough to complete the exercises is reasonable given a few hours of effort. Still, please do not hesitate to contact us ([email protected]) if there is a blocker as you go through the material.

An additional note on effort: for student interns and research assistants we expect a minimum of 10hrs/week effort.

In this task you are going to install basic software and packages needed for the analysis, and work with git.

This tutorial (and our research in general) requires R, Python, Script of Scripts (SoS) bioinformatics workflow system and docker. Please follow this setup instruction to complete the installations.

Most of our work will be saved and shared on github in public or private repositories. If you have not used git in the past, please follow the instructions here for a 5 minutes git tutorial.

As the next step please fork this repository, add your name to the file named hello.md, commit it to github and create a pull request so we can see your update and incorporate it to the repository.

This task is an example of a bioinformatics workflow developed at our group. It uses IPython notebook (with JupyterLab IDE as a recommendation), and runs an SoS kernel for bioinformatics workflows.

Please find the example notebook file orientation.ipynb, follow the instructions and complete the Quiz at the end of the notebook.

Please follow the instructions and complete the R exercise orientation.Rmd. Rmd stands for R Markdown. They are text file with R code and narratives that you can open and analyze using software such as Rstudio, or, you can also start a Jupyter Notebook and copy the contents to the notebook to analyze. If you use Jupyter Notebook please separate the markdown text and R codes into different cells.