SPsimSeq version v2.0.0

The current version includes implementation of the Gaussian-copulas for a realistic simulation by retaining the gene to gene dependence structure in the source real gene expression data. New documentation, informative error messages, and flexibility are also part of the new release.

SPsimSeq version 1.0.0

The first release of the package SPsimSeq, which is only available on Github. Included are both .tar.gz and .zip installation files. Before you install the package, please make sure all dependencies are installed as well.

# Install bioconductor if necessary
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()
# Install dependencies from Bioconductor
BiocManager::install(c("SingleCellExperiment", "edgeR"))
# Install dependencies from CRAN
install.packages(c("MASS", "Hmisc", "fitdistrplus"))

For Windows

• download the file SPsimSeq_1.0.0.zip
• From R, use the following code for installation:

install.packages("path/to/SPsimSeq_1.0.0.zip", type = "binary", repos = NULL)

For Linux/Mac

• download the file SPsimSeq_1.0.0.tar.gz
• From R, use the following code for installation

install.packages("path/to/SPsimSeq_1.0.0.tar.gz", type = "source", repos = NULL)