gwas→scRNA-seq

CZHanoiOctober 18, 2026

"Come unto me, all ye that labour and are heavy laden,
and I will give you rest."
— Matthew 11:28 (King James Version)

scPagwas

scRNA-seq

①install

ISTBI

mamba create -n scPagwas -c conda-forge -c bioconda \
  r-base=4.3 \
  r-remotes r-devtools \
  r-seurat r-seuratobject \
  r-ggpubr r-data.table r-dplyr r-ggplot2 r-reshape2 \
  r-matrix r-irlba r-glmnet r-rcpp \
  r-bigmemory r-biganalytics r-bigstatsr r-bigreadr \
  r-ggthemes r-ggsci r-ggtext r-gridextra \
  bioconductor-genomicranges bioconductor-iranges bioconductor-rhdf5 \
  git make gcc_linux-64 gxx_linux-64 \
  r-xml r-grimport2 r-haven r-tidyverse r-wgcna \
  bioconductor-impute bioconductor-preprocesscore \
  libxml2 zlib libzlib pkg-config \
  r-irkernel
-y

mamba activate scPagwas

R

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"
)
library(devtools)
install_git("https://github.com/WMU-SuLab/scPagwas.git", ref = "main")
Rscript -e 'IRkernel::installspec(user = TRUE, name = "scpagwas", displayname = "scPagwas-R")'

gsMap

cfff-2604

mamba create -n gsMap python>=3.10
mamba activate gsMap
git clone https://github.com/JianYang-Lab/gsMap
cd gsMap
pip install -e .