packages.R

install.packages(c(
"arrow",
"BiocManager",
"deldir",
"devtools",
"doMC",
"doRNG",
"DT",
"GGally",
"ggrepel",
"hdf5r",
"kableExtra",
"knitr",
"maps",
"Matrix.utils",
"metap",
"mixtools",
"NMF",
"openxlsx",
"parallel",
"patchwork",
"pdftools",
"pheatmap",
"plotly",
"PoiClaClu",
"R2HTML",
"RColorBrewer",
"RcppArmadillo",
"rsvd",
"Rtsne",
"S4Vectors",
"sctransform",
"Seurat",
"Signac",
"stringr",
"tidyverse",
"viridis",
"zoo"),
 repos = "http://cran.rstudio.com/",
 dependencies = TRUE)

BiocManager::install(c(
"airpart",
"airway",
"AnnotationHub",
"AUCell",
"batchelor",
"BiocGenerics",
"biomaRt",
"BSgenome",
"BSgenome.Hsapiens.UCSC.hg19",
"clusterProfiler",
"ComplexHeatmap",
"DelayedArray",
"DelayedMatrixStats",
"DESeq2",
"DOSE",
"ensembldb",
"GENIE3",
"GenomicFeatures",
"GenomeInfoDb",
"glmGamPoi",
"enrichplot",
"JASPAR2018",
"limma",
"MAST",
"multtest",
"RcisTarget",
"rhdf5",
"scater",
"SingleCellExperiment",
"SummarizedExperiment",
"TFBSTools",
"vsn"))

devtools::install_github("immunogenomics/harmony")
devtools::install_github("aertslab/SCopeLoomR")
devtools::install_github("aertslab/SCENIC")
devtools::install_github("cole-trapnell-lab/leidenbase")
devtools::install_github("cole-trapnell-lab/monocle3")
devtools::install_github("mojaveazure/loomR")
devtools::install_github("mojaveazure/seurat-disk")
devtools::install_github("satijalab/seurat-data")
devtools::install_github("xzhoulab/iDEA")
devtools::install_github("lucylgao/clusterpval")