BART-spatial is an R package for detecting functional transcription regulators based on spatial transcriptomics/epigenomics data. It integrates spatial variability and pseudo-temporal information with publicly available TF binding profiles, boosting prediction accuracy in the absence of high TF expression. Applied to multiple datasets, BART-spatial outperformed existing methods, identifying stage-specific TFs and revealing regulators undetectable by expression alone. Its compatibility with spatial epigenomics data further strengthens its prediction power and enables cross-validation.
Before installing BART-spatial, please install BARTsc. More details about BARTsc can be seen under https://github.com/hongpan-uva/BARTsc.
# Install BARTsc first
install.packages("devtools")
devtools::install_github("immunogenomics/presto")
devtools::install_github("hongpan-uva/BARTsc")After BARTsc is installed, for the first time the user imports it, BARTsc needs to be initialized with function initialize(). This step will automatically create a python virtual environment and install the BART2 python module and related dependencies. The user can specify the path for storing relevant data library (recommended) and the path for the module.
library("BARTsc")
initialize()# Then install BART-spatial
devtools::install_github("CorazonJW/BARTsp")Please refer to tutorial for details.
This project is licensed under the MIT License - see the LICENSE file for details.