Usage

Installation

Create a new conda environment

  $ conda create -n unagi python=3.9
  $ conda activate unagi

UNAGI installation

Option 1: Install from pip

  $ pip install scUNAGI

Option 2: Install from Github

Installing UNAGI directly from GitHub ensures you have the latest version.

  $ git clone https://github.com/mcgilldinglab/UNAGI.git
  $ cd UNAGI
  $ pip install .

Prerequisites

  • Python >=3.9 (Python3.9 is recommanded)

  • pyro-ppl>=1.8.6

  • scanpy>=1.9.5

  • anndata==0.8.0

  • torch >= 2.0.0

  • matplotlib>=3.7.1

  • iDREM (Mandatory)

iDREM installation:

git clone https://github.com/phoenixding/idrem.git

iDREM prerequisites:

  • Java To use iDREM, a version of Java 1.7 or later must be installed. If Java 1.7 or later is not currently installed, please refer to http://www.java.com for installation instructions.

  • JavaScript To enable the interactive visualization powered by Javascript, please make sure that you have Internet connection. (The users are still able to run the software off-line, but Internet access is needed to view the result interactively.)

Example data

To use the example dataset, run the tutorials or reproduce the manuscript results.

  • clone the github repo.

  $ git clone https://github.com/mcgilldinglab/UNAGI.git

  • Download required files.

Required files

Preprocessed CMAP database: One Drive.

  • Mandatory data to run UNAGI.

Preprocessed IPF snRNA-seq dataset: One Drive.

  • UNAGI outcomes to reproduce the figures and tables generated for the manuscript.

Example dataset: Link.

  • The dataset for UNAGI walktrhough demonstration.