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May 3, 2024 09:16
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Install these packages after creating a new R installation
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renv::install("BiocManager", prompt = FALSE) | |
renv::install("languageserver", prompt = FALSE) | |
renv::install("tidyverse", prompt = FALSE) | |
renv::install("xaringan", prompt = FALSE) | |
renv::install("targets", prompt = FALSE) | |
renv::install("visNetwork", prompt = FALSE) | |
renv::install("httpgd", prompt = FALSE) | |
renv::install("patchwork", prompt = FALSE) | |
renv::install("devtools", prompt = FALSE) | |
renv::install("roxygen2", prompt = FALSE) | |
renv::install("ggrepel", prompt = FALSE) | |
renv::install("plotly", prompt = FALSE) | |
renv::install("flexdashboard", prompt = FALSE) | |
renv::install("DT", prompt = FALSE) | |
renv::install("knitr", prompt = FALSE) | |
renv::install("tidylog", prompt = FALSE) | |
renv::install("tidytext", prompt = FALSE) | |
# GitHub | |
options(repos = BiocManager::repositories()) | |
renv::install("paulklemm/rvisidata", prompt = FALSE) | |
renv::install("paulklemm/rmyknife", prompt = FALSE) | |
renv::install("paulklemm/mygo", prompt = FALSE) | |
renv::install("paulklemm/dereportr", prompt = FALSE) | |
renv::install("paulklemm/trapdiff", prompt = FALSE) | |
renv::install("krassowski/complex-upset", prompt = FALSE) | |
# Lukas | |
renv::install("shiny", prompt = FALSE) | |
renv::install("shinydashboard", prompt = FALSE) | |
renv::install("shinyWidgets", prompt = FALSE) | |
renv::install("shinyhelper", prompt = FALSE) | |
renv::install("shinyFiles", prompt = FALSE) | |
renv::install("shinybusy", prompt = FALSE) | |
renv::install("mojaveazure/seurat-disk", prompt = FALSE) | |
renv::install("proxyC", prompt = FALSE) | |
# mapscvi has problems because of LFS. | |
renv::install("/beegfs/scratch/bruening_scratch/pklemm/rpackages/mapscvi", prompt = FALSE) | |
# With Pat | |
enterprise_github_host <- "github.sf.mpg.de/api/v3" | |
# devtools::install_github("lsteuernagel/mapscvi", host = enterprise_github_host) | |
devtools::install_github(repo = "bruening-lab/corinna.trap.datasets", host = enterprise_github_host) | |
devtools::install_github(repo = "lsteuernagel/scUtils", host = enterprise_github_host) | |
devtools::install_github(repo = "lsteuernagel/fibeR", host = enterprise_github_host) |
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