inst/scripts/dl_reactome_gene_sets.R
In rnabioco/clustifyr: Classifier for Single-cell RNA-seq Using Cell Clusters
library(here)
dl_url <- "http://software.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/msigdb/6.2/c2.cp.reactome.v6.2.symbols.gmt"
proj_dir <- here()
download.file(dl_url,
file.path(proj_dir,
"inst/extdata/c2.cp.reactome.v6.2.symbols.gmt"))
R.utils::gzip(file.path(proj_dir,
"inst/extdata/c2.cp.reactome.v6.2.symbols.gmt"))
# hsPBMC_markers.txt taken from garnett website
dl_url <- "https://cole-trapnell-lab.github.io/garnett/marker_files/hsPBMC_markers.txt"
download.file(dl_url,
file.path(proj_dir,
"inst/extdata/c2.cp.reactome.v6.2.symbols.gmt"))
rnabioco/clustifyr documentation built on Sept. 2, 2024, 11:12 p.m.
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library(here)
dl_url <- "http://software.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/msigdb/6.2/c2.cp.reactome.v6.2.symbols.gmt"
proj_dir <- here()
download.file(dl_url,
file.path(proj_dir,
"inst/extdata/c2.cp.reactome.v6.2.symbols.gmt"))
R.utils::gzip(file.path(proj_dir,
"inst/extdata/c2.cp.reactome.v6.2.symbols.gmt"))
# hsPBMC_markers.txt taken from garnett website
dl_url <- "https://cole-trapnell-lab.github.io/garnett/marker_files/hsPBMC_markers.txt"
download.file(dl_url,
file.path(proj_dir,
"inst/extdata/c2.cp.reactome.v6.2.symbols.gmt"))
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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