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install_regular_packages.R
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83 lines (63 loc) · 2.88 KB
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list_of_packages <- c("ggplot2", "dplyr", "gridGraphics", "gridExtra",
"ggrepel", "DBI", "svglite", "htmltools", "org.Mm.eg.db",
"igraph", "psych", "org.Dr.eg.db", "clusterProfiler",
"edgeR", "UpSetR", "plyr", "DESeq2", "readxl", "plotly",
"data.table", "installr", "knitr", "gtools", "vsn",
"Rsamtools", "GenomicAlignments",
"SummarizedExperiment", "sva", "BiocParallel", "biomaRt",
"curl", "stats", "rvcheck", "tidyverse", "grid", "brew",
"VennDiagram", "RColorBrewer", "ComplexHeatmap",
"colorspace", "circlize", "tidyr", "matrixStats", "rlang",
"sodium", "devtools", "shinymanager", "DT", "fontawesome",
"shinydashboard", "shinycssloaders", "rmarkdown",
"markdown", "visNetwork", "heatmaply", "wesanderson",
"shinyauthr", "Seurat", "shinythemes","ggVennDiagram",
"caret", "tidymodels", "BiocManager", "languageserver",
"patchwork", "ggbiplot", "DiffBind", "GenomicFeatures",
"ChIPseeker", "rstatix", "ggpubr", "viridis",
"ReactomePA", "Cardinal", "MetaboAnnotation", "IRkernel",
"RforMassSpectrometry/RforMassSpectrometry", "openxlsx",
'ggdendro', 'shinyhelper', "Matrix", "glue", "hdf5r",
"reticulate", "R.utils", "readr", "future", "shiny",
"magrittr", "msigdb", "GSEABase", "limma", "EBImage", "paletteer", "shiny.semantic")
new_packages <- list_of_packages[!(list_of_packages %in% installed.packages()[,"Package"])]
new_packages <- unique(new_packages)
new_packages
if(length(new_packages)) install.packages(new_packages, Ncpus=8)
new_packages <- list_of_packages[!(list_of_packages %in% installed.packages()[,"Package"])]
new_packages <- unique(new_packages)
new_packages
BiocManager::install(new_packages)
devtools::install_github("neurorestore/Libra")
# for shinycell2
# run these in bash
# Install dependencies for trackplot (on command line)
# git clone https://github.com/CRG-Barcelona/libbeato.git
# cd ./libbeato
# git checkout 0c30432
# ./configure
# make
# make install
# cd ..
# git clone https://github.com/CRG-Barcelona/bwtool.git
# cd ./bwtool
# ./configure
# make
# make check
# make install
# OR directly through R
# system("git clone https://github.com/CRG-Barcelona/libbeato.git")
# setwd("./libbeato")
# system("git checkout 0c30432")
# system("./configure")
# system("make")
# system("make install")
# setwd("..")
# system("git clone https://github.com/CRG-Barcelona/bwtool.git")
# setwd("./bwtool")
# system("./configure")
# system("make")
# system("make check")
# system("make install")
# setwd("..")
devtools::install_github("the-ouyang-lab/ShinyCell2")