QSBSC

Quantitative Systems Biology of Single Cells class repository

We will add more here as the course proceeds.

Installing R packages for Dr. Irish's lectures

If you have already cloned this repository onto your local computer, in R (or RStudio), you can type: source('<complete_path_to>/R_code/Irish_R_packages.r') where <complete_path_to> is the file path to this repository on your own computer.

Alternatively, you can execute the code in R by accessing the file directly from GitHub using: source('https://github.com/darrentyson/QSBSS/raw/master/R_code/Irish_R_packages.r')

First homework assignment

Using your choice of how to interact with GitHub (Sourcetree, command line interface (CLI), GitHub Desktop, etc.), you should clone this repository onto your local computer and perform the steps described in the commented lines at the bottom of ./R_code/Tyson/TestCodeForDataLoadingAndGit.r

Tip for keeping Git repo clutter-free

If you are using SourceTree you should go to Preferences and Edit File the Global Ignore list (a hidden file named .gitignore_global usually saved in your user directory that you could also edit manually.)

You should add things like this into the file:

*~
.DS_Store
.Rhistory
.Rapp.history
Iconr
*.pyc

So files matching these criteria do not get uploaded to GitHub when you commit (they will not be tracked).

2019-02-18: Added new flow cytometry data into `Data` directory

Please see the README file on GitHub https://github.com/darrentyson/QSBSC/tree/master/Data/CytobankData/experiment_46259_files

A warning about using Excel to open data files containing gene names

For those of you still considering using Excel on occasion to inspect data files, please read this paper and understand the risks involved: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1044-7

Homework for 2019-02-25

Please read both papers: https://doi.org/10.7554/eLife.27041.001 and http://science.sciencemag.org/content/360/6392/981 The Wagner et al. (Allon Klein's eLife) paper will be presented by Cody Heiser and Corey Hayford will walk through the code to reproduce Fig1B from the paper (see R_code/Klein_paper). You may copy the file R_code/Klein_paper/make_figure.Rmd into your own directory and modify/execute as you like. We will have an open discussion about the eLife paper the second half of class.

darrentyson/QSBSC