SmartQC

Installation

1. First, install the required dependencies:

# Install devtools if not already installed
if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
#if installation becomes a problem, particularly in HPC environments, you can use remotes below (less dependencies)

# Install Bioconductor dependencies
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install(c("preprocessCore", "BiocGenerics", "DelayedArray", "DelayedMatrixStats",
                       "limma", "lme4", "S4Vectors", "SingleCellExperiment",
                       "SummarizedExperiment", "batchelor", "HDF5Array",
                       "terra", "ggrastr", "densvis", "biomaRt", "glmGamPoi"))

# Install GitHub dependencies
devtools::install_github("chris-mcginnis-ucsf/DoubletFinder@1b1d4e2")
devtools::install_github('satijalab/seurat-wrappers@community-vignette')
devtools::install_github("arc85/singleseqgset")
devtools::install_github('cole-trapnell-lab/monocle3')

#A note on this branch: this will be the Seurat 4 version of the workflow. 
#The dependencies have changed to the point keeping the same scripts or libraries is not sustainable
#To prevent leftover SeuratObject v5 properties from causing conflicts, you should run
if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
options(repos = c("https://satijalab.r-universe.dev", getOption("repos")))
remotes::install_version("SeuratObject", "4.1.4")
remotes::install_version("Seurat", "4.4.0", upgrade = FALSE)

#and restart your R session so that the change is registered

# Install SmartQC
devtools::install_github('jarcoshodar/smartqc')

2. After installation, add the SmartQC executable to your PATH:

# Run this in R to get the installation path
smartqc_path <- system.file("bin", package = "smartqc")
cat(paste0("\nAdd the following line to your ~/.bashrc or ~/.bash_profile file:\n\n",
           "export PATH=\"$PATH:", smartqc_path, "\"\n\n",
           "Then, run 'source ~/.bashrc' or 'source ~/.bash_profile' in your terminal.\n"))

3. Copy the output line and add it to your ~/.bashrc or ~/.bash_profile file.

4. Reload your shell configuration:

source ~/.bashrc  # or source ~/.bash_profile

Usage

After installation and adding SmartQC to your PATH, you can use it from the command line:

smartqc -r /path/to/root -s StudyName -g MOUSE

or

smartqc -i /path/to/input -o /path/to/output.rds -g HUMAN

For more options, run:

smartqc --help

Troubleshooting

If you encounter any issues with the installation or usage of SmartQC, please check the following:

1. Ensure all dependencies are correctly installed.
2. Verify that the SmartQC bin directory is in your PATH.
3. If you're using RStudio or a specific R environment, make sure it's aware of the updated PATH.

For further assistance, please open an issue on the GitHub repository.