STAAR

"The ancient Oracle said that I was the wisest of all the Greeks.
It is because I alone, of all the Greeks, know that I know nothing."
— Plato, Apology 21a–23b (paraphrase of Socrates)

环境安装

mamba create -n STAAR -c conda-forge -c bioconda -c r r-base r-remotes r-devtools r-biocmanager bioconductor-genesis bioconductor-rtracklayer bioconductor-seqarray bioconductor-seqvartools git make pkg-config cxx-compiler fortran-compiler zlib libzlib zstd libdeflate -y

mamba activate STAAR
R

进入R安装：

library(devtools)

proxy <- "http://127.0.0.1:17897"

Sys.setenv(
  http_proxy  = proxy,
  https_proxy = proxy,
  HTTP_PROXY  = proxy,
  HTTPS_PROXY = proxy,
  all_proxy   = proxy,
  ALL_PROXY   = proxy,
  no_proxy    = "localhost,127.0.0.1,::1",
  NO_PROXY    = "localhost,127.0.0.1,::1",
  GITHUB_PAT  = "贴出github_token"
)

Sys.getenv("GITHUB_PAT")

devtools::install_github("xihaoli/STAAR", auth_token = Sys.getenv("GITHUB_PAT"))
remotes::install_github(
  "edvanburen/cellSTAAR",
  auth_token = Sys.getenv("GITHUB_PAT")
)

library(devtools)
devtools::install_github("li-lab-genetics/MetaSTAARlite",ref="main", auth_token = Sys.getenv("GITHUB_PAT"))