GBM-Perturb

This repository contains analysis in Python and R for the output of in vivo perturb-seq experiments as described in Liu et al, bioRxiv 2023.

Getting set up

Installing dependencies

First, you'll want to install dependencies. Python and R dependencies are managed separately.

R

Dependencies are managed as an R project through renv. Activate the project by installing renv and running:

renv::init()
renv::restore()

in the top-level project directory. This will install dependencies as specified in renv.lock.

Python

This repository uses Poetry for Python dependency management. Install poetry, navigate to the project directory, and run poetry install. This will install all packages according to the versions specified in poetry.lock.

Directories

Next, you'll want to create a top-level output directory and a top-level data directory. The code in this repository assumes that these directories (and sometimes subdirectories) exist. output generally contains output plots and data, while data contains input metadata and raw data. We have chosen to leave most of our existing directory structure following these data and output directories intact as examples; there's user flexibility on where things go.

Navigating the repository

Here is the directory structure as used by us as developers:

.
├── R
│   ├── malignant
│   ├── microenvironment
│   ├── revisions
│   └── utils
├── README.md
├── data
├── genome-biology-methods.Rproj
├── output
├── poetry.lock
├── pyproject.toml
├── python
│   ├── chromatin_analysis.ipynb
│   ├── doubles_coefficient_analysis.ipynb
│   └── gl261_cinemaot.ipynb
├── renv.lock
├── shared_data
│   └── deseq_output
└── shell

• R contains R code
• python contains Python code
• shell contains shell scripts for CUT&TAG analysis
• shared_data/deseq_output contains comprehensive DESeq2 outputs for our perturb-seq data relative to non-targeting same treatment condition controls. This data was generated using the R DElegate package.

Maintenance

Authored by Christopher Zou, Ashir Borah, and John Liu. Feel free to fork/ping us through issues for questions.