Installation

Version Selection

Please choose the appropriate version of scATS based on your R environment:

v0.5.6 (Recommended): For users with R >= 4.4.
v0.5.5 (Legacy): For users with R < 4.4.

Requirements

System Dependencies

Before installing scATS, please ensure that samtools is installed and available in your system’s PATH.

conda install -c bioconda samtools

R Dependencies

The following R packages are required for all versions of scATS. You can install them using the following command:

install.packages(c(
    'R.utils', 
    'TTR', 
    'VGAM',
    'prettyunits',
    'httr2',
    'mclust',
    'mixtools'))

Note: 💡 For v0.5.5, you must manually install the smoother package from the CRAN archive before installing scATS:

install.packages('https://cran.r-project.org/src/contrib/Archive/smoother/smoother_1.3.tar.gz', repos = NULL, type = 'source')

Installation

To install scATS, you have two options: either install directly from GitHub or use the compressed source file.

Via GitHub (only for v0.5.6):

if (!require("devtools")) install.packages("devtools")
devtools::install_github("LuChenLab/r-scATS", force = TRUE)

# or
if (!require("remotes")) install.packages("remotes")
remotes::install_github("LuChenLab/r-scATS")

Via Source File (for v0.5.6 and v0.5.5):

Alternatively, you can install scATS using the source file downloaded from the repository :

# Install scATS from a downloaded source file
R CMD INSTALL scATS_0.5.6.tar.gz

# or
install.packages("scATS_0.5.6.tar.gz", repos=NULL)

Installation Logs

To ensure reproducibility, we provide comprehensive installation logs for three different installation methods across multiple R versions:

Docker Guide

We provide a pre-configured Docker container to eliminate system-specific dependency conflicts.

Step 1: Install Docker

If you do not have Docker installed, please follow the official Docker installation guide.

Step 2: Run the scATS Container

Pull the pre-built image from the GitHub Container Registry and start an interactive session:

# Pull the image
docker pull ghcr.io/kayla-xu/scats-evi:r451

# Run the container
docker run -it ghcr.io/kayla-xu/scats-evi:r451

Step 3: Build Docker Locally (Optional)

If you prefer to build the image locally, use the provided Dockerfiles. Building logs are also provided for your reference.

# Build the base environment
docker build --no-cache \
  -t scATS/base:r451 \
  -f Dockerfile_base_r451 . \
  2>&1 | tee Dockerfile_base_r451.log

# Build the final scATS image
docker build --no-cache \
  -t scATS/evi:r451 \
  -f Dockerfile_scats_r451 . \
  2>&1 | tee Dockerfile_scats_r451.log