boost R Package

Authors: Xi Jiang, Danni Luo, Esteban F. Morales, Jie Yang, Huimin Li, Yuanchun Zhan, Bo Yao, Suhana Bedi, Qiwei Li, Guanghua Xiao and Xiaowei Zhan

The R package boost (Bayesian Modeling of Spatial Transcriptomics Data) provides a collection of functions to detect spatially variable (SV) genes in spatial transcriptomics (ST) data. This package provides two novel Bayesian methods, as well as other standard procedures, for facilitating studies in Spatial Transcriptomics Arena (STAr) .

Contents:

• Installation
• Load Data
• Data Pre-processing
  • Data Filtration
  • Size Factor Estimation
  • Expression Counts Normalization
• SV Gene Detection
  • BOOST-GP
  • BOOST-Ising
  • BinSpect
  • SPARK
  • Plot SV Gene
• Simulation Study - Example
  • Load Data
  • Data Preparation
  • Run SV Gene Detection Methods
  • Rank Aggregation
  • Compute Performace Metrics