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Rasilab-Spelman Comp Bio internship 2023

  • Katharine Chen
  • Grace Quarterman
  • Christine Bynum
  • Rasi Subramaniam's lab at Fred Hutch Cancer Center

Documentation

https://github.com/kychen37/rasilab_spelman_2023/blob/main/notes/gq_and_cb_methodology.md

Project Workflow

Useful resources

Markdown

  • "What is markdown" and "Why use markdown" sections of this guide
  • Markdown is typically used in text editors (like VSCode)
  • Note that this document is written in markdown, which automatically renders into the denoted formatting when pushed/opened on github

Command line & terminal

Github

  • Make an account on github and verify your email address
  • Install git to your laptops by following this site
  • Clone our group's remote repository to your local computer by opening the terminal and executing the following: git clone https://github.com/kychen37/rasilab_spelman_2023.git
    • Since this repo was made in my account (kychen37), I needed to added gquarter and christinebynum users to the repo on github under Settings before they had permission to push/pull
  • Each user needs to then generate a personal access token:
    • Go to your user settings -> Developer settings -> Personal access tokens -> Tokens (classic) -> Generate new token (classic)
    • Under Note, name the token something descriptive and check 'repo'
    • Press Generate token, copy the entire token to a different location like a notepad
  • Follow the top comment on https://stackoverflow.com/questions/46645843/where-to-store-my-git-personal-access-token for saving the personal access token to the git credential helper so you don't have to keep copy/pasting it each time you push
    • git config --global user.name "Katharine Chen"
    • git config --global user.email [email protected]
    • git config --global credential.helper manager-core
  • The default behavior of git is to rebase, but if you don't set it explicitly it will give you an error each time you try to pull, so run:
    • git config --global pull.rebase true
  • Now you can run the usual git workflow:
    • git add filename of the file you editted
    • git commit -m "descriptive message about what was editted
    • git push origin main
  • You should also do git pull origin main to get any changes to the remote repo that other users may have pushed

R programming

Installing R

Programming in python

Installing miniconda:

  • What is miniconda?
  • Mac: https://docs.conda.io/projects/conda/en/latest/user-guide/install/macos.html
    • Follow the link "Miniconda installer for macOS."
    • Click on the link "Miniconda3 macOS Intel x86 64-bit bash", which will download the installation to your Downloads folder
    • Open terminal and navigate to your Downloads folder (hint cd)
    • Run: sh Miniconda3-latest-MacOSX-x86_64.sh and follow prompts in terminal (say 'yes' to 'conda init' question)
    • After installation is done, close and reopen terminal
    • Run: conda list, which should show a list of packages if the installation was successful (will probably say something like conda not found if it was unsuccessful)
  • Windows: https://docs.conda.io/projects/conda/en/latest/user-guide/install/windows.html
    • Open the executable and follow instructions
  • After you've finished installing miniconda, install pandas by typing: conda install pandas on the command line
  • If you need any more packages down the road, you would run: conda install packagename on the command line
    • e.g. numpy and matplotlib are common python packages, to install them you would run: conda install numpy, conda install matplotlib

VSCode

  • A very useful text editing and coding application
  • Various extensions make coding/writing in VSCode much easier

Setting up Jupyter kernels in VSCode

  • In VSCode, find the Extensions panel
  • Search for the extension called Jupyter and download it
  • Open a python interactive notebook (called a Jupyter notebook)
    • For Mac: press CMD+SHIFT+P to open the drop-down menu -> click Create Jupyter notebook
  • In top right corner: select "Select Kernel" -> "Python environments" -> choose the "base (miniconda3/bin/python)"
  • Start coding!
    • The first time you run a code chunk, VSCode may ask you to download some needed additional extensions, download those

Link to Notes/ Checklist