KGExplorer

Authors: Brian Schilder, Hiranyamaya Dash

README updated: Dec-19-2024

KGExplorer: Biomedical Knowledge Network Construction and Analysis

Query, construct, and analyse large-scale biomedical knowledge graphs and ontologies.

If you use KGExplorer, 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

Installation

if(!require("BiocManager")) install.packages("BiocManager")

BiocManager::install("neurogenomics/KGExplorer")
library(KGExplorer)

Documentation

Website

Getting started

---

Session Info

utils::sessionInfo()

## R Under development (unstable) (2024-12-15 r87442)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] rmarkdown_2.29
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6        jsonlite_1.8.9      renv_1.0.11        
##  [4] dplyr_1.1.4         compiler_4.5.0      BiocManager_1.30.25
##  [7] tidyselect_1.2.1    rvcheck_0.2.1       scales_1.3.0       
## [10] yaml_2.3.10         fastmap_1.2.0       here_1.0.1         
## [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       
## [19] desc_1.4.3          dlstats_0.1.7       munsell_0.5.1      
## [22] rprojroot_2.0.4     pillar_1.10.0       RColorBrewer_1.1-3 
## [25] rlang_1.1.4         badger_0.2.4        xfun_0.49          
## [28] fs_1.6.5            cli_3.6.3           magrittr_2.0.3     
## [31] rworkflows_1.0.3    digest_0.6.37       grid_4.5.0         
## [34] lifecycle_1.0.4     vctrs_0.6.5         evaluate_1.0.1     
## [37] glue_1.8.0          data.table_1.16.4   colorspace_2.1-1   
## [40] tools_4.5.0         pkgconfig_2.0.3     htmltools_0.5.8.1