PASTA documentation

Here we present PASTA (PAthway-oriented Spatial gene impuTAtaion), which is a tool to to imputate pathway expression for a spatial transcriptomic (ST) dataset referring to a single-cell RNA sequencing (scRNA-seq) dataset.

Get started:

• Quick start
  • Set up environment
  • A quick example

Simulation:

• Simulation data
• Basic simulation code for PASTA
• Basic simulation code for Tangram
• Basic simulation code for Seurat (run in R)

Real data application:

• Human Xenium Lung Dataset
  • Imputation
  • Pathway enrichment (run in R)
  • Apply IRIS (run in R)
• Mefish Mouse Brain Dataset
  • Imputation
  • Cluster using the pathway matrix
  • Trajectory analysis (run in R)
• ISS Mouse Primary Visula Cortex Dataset
• CosMx Human frontal cortex dataset
  • Imputation
  • Apply tissue