PROST: A quantitative pattern recognition framework for spatial transcriptomics

PROST is a flexible framework to quantify gene spatial expression patterns and detect spatial tissue domains using spatially resolved transcriptomics with various resolutions. PROST consists of two independent workflows: PROST Index (PI) and PROST Neural Network (PNN).

Using PROST you can do:

• Quantitative identification of spatial patterns of gene expression changes by the proposed PROST Index (PI).

• Unsupervised identification of spatial tissue domains using a PROST Neural Network (PNN).

Contents:

• Installation
• Quick Start
• How to use PROST
• Tutorial 1: Application on 10x Visium human dorsolateral prefrontal cortex (DLPFC) dataset.
• Tutorial 2: Application on Stereo-seq mouse olfactory bulb dataset.
• Tutorial 3: Application on SeqFISH mouse embryo dataset.
• Tutorial 4: Application on osmFISH Somatosensory Cortex dataset.
• Tutorial 5: Application on simulated osmFISH Somatosensory Cortex dataset.
• Tutorial 6: Application on Slide-seq mouse Cerebellum dataset.
• Tutorial 7: Tutorial of PROST index.
• API

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