deskPlink is a Shiny Graphical User Interface
(GUI) that enables users to input a VCF-formatted file (genetic information) and
a table as comma separated values (CSV), with quantitative and/ or categorical
variables as columns and rows matching each of the samples. Names in VCF and CSV
must match 1:1.
PLINK is a variant association analysis toolset, designed to perform a range
of basic, large-scale analyses in a computationally efficient manner. For more
information please refer to upstream
documentation.
# install.packages("remotes")
library(remotes)
install_github("adRn-s/deskPlink")
library(deskPlink)
run()
conda create -n deskPlink r-remotes plink=1.90 r-DT r-shiny r-shinyFiles r-fs
conda activate deskPlink
R_LIBS_USER="$CONDA_PREFIX/lib/R/library"
RSTUDIO_WHICH_R="$CONDA_PREFIX/bin/R"
nohup /usr/bin/rstudio # PATH depends on your OS.
By defining R_LIBS_USER and RSTUDIO_WHICH_R shell environmental variables RStudio will spawn the correct R session inside a Bioconda environment with managed dependencies. Proceed to Installation and Usage steps described above.
PRs are welcome! If you'd like to contribute please use the provided
reproducible environment: $ conda env create --name deskPlink --file env.yaml