smartSim: Simulation of splice aware single cell Smart-seq3 data

Prerequisites

In order to use this package: you need folowing software:

• conda (https://www.anaconda.com/)

We provide a conda environment containing all required dependencies, which can be created and activated with:

conda env create -f smartSim_env.yml
conda activate smartSim

Note: smartSim is currently only available for Linux (linux-64). This limitation is due to its dependency on the HTSeq package, which is not compatible with Windows or macOS. To ensure full functionality for users on Windows or macOS, we recommend running smartSim within a Linux-based virtual machine, such as an Ubuntu VM (e.g. WSL2 or multipass).

Installation

Make sure the smartSim conda environment is active. Next, smartSim can be installed directly from GitHub using:

library(devtools)
install_github("MarchalLab/smartSim", dependencies = TRUE, repos = BiocManager::repositories())

Alternatively, it can be installed from source using:

install.packages("path/to/smartSim, repos = NULL, type="source")

Required input

• reference gtf file
• reference fasta file
• aligned and barcoded Smart-seq3 data similar to the data you want to simulate (alternatively you can use the provided example dataset as described in the tutorial)

Usage

We provide a tutorial to simulate reads using provided example data here.

Test environment

The R package was developed and tested using:

• R version : 4.4.1 (platform: x86_64-conda-linux-gnu)
• all dependencies are provided in the corresponding conda environment: smartSim_env.yml.
• test environment: All tests were run on a system with:
  • Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz
  • 256 GB RAM
  • Ubuntu 22.04.4 LTS
• session info can be found at: docs/sessionInfo.txt