Installation Guide

Hardware Requirements

Hardware Requirements

Statescope can operate on a variety of systems depending on the data size:

• Small-scale data: Suitable for Binder (1 CPU, 2GB RAM on Google Cloud).
• Large-scale data: Performance improves significantly with higher computational power. Our recommendation for optimal performance is:
  • CPU: 40 threads (Xeon 2.60GHz or equivalent)
  • Memory: 128 GB RAM

Statescope’s Empirical Bayes procedure includes independent optimization steps that can be parallelized to leverage multiple CPUs for faster execution.

Note: For faster performance, the Statescope deconvolution module has GPU support, which can make computations 3-4 times faster.

OS Requirements

BLADE is primarily tested on Linux-based operating systems. We recommend:

• Linux distributions: CentOS 7 or Ubuntu 16.04.

Note: While BLADE might work on other OS platforms (macOS, Windows with WSL), these setups may require additional configurations.

Installation Steps

Installation Tutorials

Python Installation

Python Installation

To install Statescope using pip, run the following command:

pip install Statescope

To manage dependencies, use Conda and the environment.yml file for a consistent environment setup:

1. Download the environment.yml file: Download environment.yml

   • Place the file in your working directory.

2. Create the Conda environment:

   conda env create -f environment.yml -n blade_env

3. Activate the environment:

   conda activate blade_env

4. Update the environment if necessary:

   conda env update -f environment.yml

R Installation

R Installation

To install BLADE from Bioconductor, use the following commands:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BLADE")

Setting up an R Environment (Placeholder Steps)

1. Install R and RStudio from CRAN or RStudio.

2. Use the following commands to set up a project environment in RStudio:

   install.packages("renv")
   renv::init()

3. Ensure all dependencies are installed by running:

   renv::restore()

4. Verify the installation:

   library(BLADE)

GitHub Repository

GitHub Installation

To clone the GitHub repository, execute the following commands:

git clone https://github.com/aryamaanbose/BLADE_tasks.git
cd BLADE_tasks

Setting up the Repository (Placeholder Steps)

1. Ensure git is installed:

   git --version

2. Create a Conda environment and install dependencies:

   conda env create -f environment.yml -n blade_repo_env
   conda activate blade_repo_env

3. Pull updates regularly:

   git pull origin main

4. Start using the repository for your tasks.

#####Make it bigger Demo You can find the demo for Statescope in the GitHub repository. It is provided as a Jupyter notebook and can be accessed here.

Additional Information

Step 1: Installing Conda

If you don’t already have Conda installed, you can download and install Miniconda by following these steps:

1. Go to the Miniconda download page.
2. Download the appropriate installer for your OS.
3. Follow the installation instructions for your operating system to set up Conda.

After installation, you can verify Conda by running:

conda --version

Step 2: Updating the Environment

To keep your environment up-to-date, pull the latest changes from the repository and update the environment:

git pull origin main
conda env update -f environment.yml