Documentation Overview

The current documentation include the following sections:

Home:

• Documentation Overview: Provides a summary of the contents and structure of NEDA.

Installation:

• Installing NEDA: Guidelines on installing NEDA and its dependent software tools.
• Example Datasets: Information on accessing three provided example datasets.

Pixel-level Analysis:

• Introduction: Introduction to Pixel-level Analysis in NEDA.
• Preparing Input Data: Overview of required input files.
• Preparing Job Configuration: Preparing the input configuration file.
• Preprocessing: Initialize computing environment and creating minibatches.
• LDA Factorization: Application of Latent Dirichlet Allocation (LDA) for spatial factor identification.
• Seurat Clustering: Multi-dimensional clustering with Seurat to identify cell types.
• Transform: Converting to a factor space using the provided model via FICTURE.
• Pixel-level Decoding: Decoding of pixel-level factors or clusters using FICTURE.

Cell Segmentation-based Analysis:

• Introduction: An Overview of the prelimary single-cell analysis.
• Preparing Input Data: Details of required input files.
• Create Cell-indexed SGE: Computing environment setup and preparation of a cell-indexed spatial digital gene expression (SGE) matrix.
• Seurat Clustering: Application of multi-dimensional clustering with Seurat for cell type factor inference.