Installation

You can install STREAM via below commands:

# First, check and install the dependency packages using cran
cran_packages <- c("data.table", "dplyr", "ggplot2", "igraph", "Matrix", 
                   "pbapply", "qgraph", "RColorBrewer", "RCurl", "Ryacas",
                   "easypackages", "enrichR", "pbmcapply", "qualV",
                   "scales", "stats", "utils"
                   )

to_install_cran <- cran_packages[!sapply(cran_packages, requireNamespace, quietly = TRUE)]
if (length(to_install_cran) > 0) {
    install.packages(to_install_cran)
}


# Second, check and install BiocManager has been installed
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")


# Third, check and install the dependency packages by BiocManager
bioc_packages <- c("AnnotationDbi", "BSgenome", "BSgenome.Hsapiens.UCSC.hg19", "BSgenome.Hsapiens.UCSC.hg38", 
                   "BSgenome.Mmusculus.UCSC.mm10", "EnsDb.Mmusculus.v79", "EnsDb.Hsapiens.v75", 
                   "EnsDb.Hsapiens.v86", "biomaRt", "ensembldb", "GenomeInfoDb", "GenomicAlignments", 
                   "GenomicRanges", "JASPAR2022", "motifmatchr", "Repitools", "regioneR", 
                   "rTRM", "SingleCellExperiment", "STRINGdb", "SummarizedExperiment", 
                   "IRISFGM", "simpIntLists", "TFBSTools"
                   )

to_install_bioc <- bioc_packages[!sapply(bioc_packages, requireNamespace, quietly = TRUE)]
if (length(to_install_bioc) > 0) {
    BiocManager::install(to_install_bioc)
}


# Fourth, check and install devtools
if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")


# Fifth, check and install the dependency packages by devtools
github_packages <- c( 
                     "mskilab-org/gUtils",  
                     "cole-trapnell-lab/monocle3", 
                     "satijalab/Seurat", 
                     "satijalab/Signac"
                     )

# Extracting package names from GitHub paths
package_names_github <- sapply(strsplit(github_packages, "/"), `[`, 2)

to_install_github <- github_packages[!sapply(package_names_github, requireNamespace, quietly = TRUE)]
if (length(to_install_github) > 0) {
    devtools::install_github(to_install_github)
}


# Sixth, install STREAM
devtools::install_github("OSU-BMBL/STREAM")

## Skipping installation of 'stream2' and its dependencies from a github remote

# Check session information
sessionInfo()

## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Red Hat Enterprise Linux
## 
## Matrix products: default
## BLAS/LAPACK: /opt/intel/2021.3/mkl/2021.3.0/lib/intel64/libmkl_gf_lp64.so.1
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.33     R6_2.5.1          jsonlite_1.8.7    evaluate_0.21    
##  [5] cachem_1.0.8      rlang_1.1.1       cli_3.6.1         rstudioapi_0.15.0
##  [9] jquerylib_0.1.4   bslib_0.5.1       rmarkdown_2.23    tools_4.2.1      
## [13] xfun_0.40         yaml_2.3.7        fastmap_1.1.1     compiler_4.2.1   
## [17] htmltools_0.5.6   knitr_1.43        sass_0.4.7