The MSTExplorer package is an extension of the EWCE package. It is designed to run expression weighted celltype enrichment (EWCE) on multiple gene lists in parallel. The results are then stored both as separate .rds files, one for each individual EWCE analysis, as well as a in a single dataframe containing all the results. This package is useful in cases where you have a large number of related, but separate, gene lists.
Within R:
if(!require("remotes")) install.packages("remotes")
remotes::install_github("neurogenomics/MSTExplorer")
library(MSTExplorer)If you use MSTExplorer, please cite:
Kitty B. Murphy, Robert Gordon-Smith, Jai Chapman, Momoko Otani, Brian M. Schilder, Nathan G. Skene (2023) Identification of cell type-specific gene targets underlying thousands of rare diseases and subtraits. medRxiv, https://doi.org/10.1101/2023.02.13.23285820
UK Dementia Research Institute
Department of Brain Sciences
Faculty of Medicine
Imperial College London
GitHub
utils::sessionInfo()## R version 4.4.2 (2024-10-31)
## Platform: aarch64-apple-darwin20
## Running under: macOS Sequoia 15.2
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## BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
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## time zone: Europe/London
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## attached base packages:
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## [1] gtable_0.3.6 jsonlite_1.8.9 renv_1.0.11
## [4] dplyr_1.1.4 compiler_4.4.2 BiocManager_1.30.25
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## [13] ggplot2_3.5.1 R6_2.5.1 generics_0.1.3
## [16] knitr_1.49 yulab.utils_0.1.8 tibble_3.2.1
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## [25] rlang_1.1.4 utf8_1.2.4 badger_0.2.4
## [28] xfun_0.49 fs_1.6.5 cli_3.6.3
## [31] magrittr_2.0.3 rworkflows_1.0.3 digest_0.6.37
## [34] grid_4.4.2 rstudioapi_0.17.1 lifecycle_1.0.4
## [37] vctrs_0.6.5 evaluate_1.0.1 glue_1.8.0
## [40] data.table_1.16.2 fansi_1.0.6 colorspace_2.1-1
## [43] rmarkdown_2.29 tools_4.4.2 pkgconfig_2.0.3
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