README.md

Multiplexed imaging of patients with post-acute COVID-19

⬅️ read the preprint here

This repository contains source code used to analyze the data in the above manuscript.

Organization

• The metadata directory contains metadata relevant to annotate the samples
• This CSV file is the master record of all analyzed samples
• The src directory contains source code used to analyze the data
• Raw data (i.e. MCD files) will be under the data directory.
• Processing of the data will create files under the processed directory.
• Outputs from the analysis will be present in a results directory, with subfolders pertaining to each part of the analysis as described below.

Reproducibility

Requirements

• Python 3.10+
• Python packages as specified in the requirements file - install with make requirements or pip install -r requirements.txt.

Running

To see all available steps type:

$ make

Steps used for the initiall processing of raw data are marked with the [dev] label.

Makefile for the covid-pasc-imc project/package.
Available commands:
help                Display help and quit
requirements        Install Python requirements
download_data       Download processed data from Zenodo (for reproducibility)
analysis            Run the actual analysis

To reproduce analysis using the pre-preocessed data, one would so:

$ make help
$ make requirements   # install python requirements using pip
$ make download_data  # download processed from Zenodo
$ make analysis       # run the analysis scripts