Home

👋   Welcome to my personal GitHub wiki! Here you will find tutorials and information that - if you are a student working wtih me - will likely make things easier.

I work mostly in the single-cell and CRISPR fields. My PhD work focuses on developing new methods for such analyses as well as applying novel approaches to patient tumor single-cell datasets. I primarily use the Google Cloud Platform (GCP), using an ubuntu-lts 20.04 distribution of linux. I also code primarily in python though use R when needed.

Google Cloud:

• Tutorial: Get started with a new Google VM
• Resource: Resize a persistent disk on the fly

Linux:

• Tutorial: Add shortcut access to Jupyter Notebooks
• Tutorial: Permanently authenticate a GitHub repo
• Tutorial: Prepare an R kernel for Jupyter Notebooks

Python

Eventually, I would like to add more information and tutorials for single-cell oriented tools as well as more details for bioinformatics programming in python. In the meantime, here are some resources I have found useful:

Code in Jupyter Notebooks using nb_black

Install via:

pip install nb_black

To use, in the first cell of a jupyter notebook, enter:

%load_ext nb_black

Display all rows / columns of a pandas DataFrame in Jupyter Notebooks

pd.set_option('display.max_columns', None)
pd.set_option('display.max_rows', None)

Alternatively:

pd.options.display.max_columns = None
pd.options.display.max_rows = None

source